Adding metadata

author: root <root@alpha.trunkmasters.com> 2026-06-04 05:35:26 -0500
committer: root <root@alpha.trunkmasters.com> 2026-06-04 05:35:26 -0500
commit: f716a9fe6455d39eef01e718aae68dae61c19704 (patch)
tree: 0c52bbae1c242fbc296bd650fcd1167685f81492 /sci-chemistry
parent: 3f9cf298e89cd5037b982abba06091224ee76daf (diff)
download: baldeagleos-repo-f716a9fe6455d39eef01e718aae68dae61c19704.tar.gz
baldeagleos-repo-f716a9fe6455d39eef01e718aae68dae61c19704.tar.xz
baldeagleos-repo-f716a9fe6455d39eef01e718aae68dae61c19704.zip
233 files changed, 0 insertions, 11730 deletions
diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.9.1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.9.1.ebuild
deleted file mode 100644
index 1c45696cc20a..000000000000
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.9.1.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-DISTUTILS_USE_PEP517=setuptools
-
-if [[ ${PV} = *9999* ]]; then
-	scm_eclass=git-r3
-	EGIT_REPO_URI="https://github.com/Becksteinlab/${PN}.git"
-	EGIT_BRANCH="develop"
-else
-	scm_eclass=vcs-snapshot
-	SRC_URI="https://github.com/Becksteinlab/${PN}/archive/release-${PV}.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
-
-inherit distutils-r1 ${scm_eclass}
-
-DESCRIPTION="Python framework for Gromacs"
-HOMEPAGE="https://gromacswrapper.readthedocs.io"
-
-LICENSE="GPL-3 LGPL-3"
-SLOT="0"
-
-RDEPEND="
-	dev-python/six[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	sci-libs/numkit[${PYTHON_USEDEP}]
-"
-BDEPEND="
-	${RDEPEND}
-	test? ( >=dev-python/pandas-0.17[${PYTHON_USEDEP}] )
-"
-
-distutils_enable_tests pytest
diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest
deleted file mode 100644
index 847d1b70cc94..000000000000
--- a/sci-chemistry/GromacsWrapper/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST GromacsWrapper-0.9.1.tar.gz 1942919 BLAKE2B 295df8896aa3d92b5e1832c3b5a3a8eb2f3a9ae7e7d5a90a62fb449f0f76cf0235ba0cfdce2476c67903514579da399765f5e236c11cd781b959388f2273fa84 SHA512 f9c326dc669605f61a2b9adce64120a88f14369294e8692a078d489b18d8135fd9285c8947860d640c48ad1910f53f4e3d646f26c12dae55996f6462543be9b0
diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml
deleted file mode 100644
index 0096486f68a8..000000000000
--- a/sci-chemistry/GromacsWrapper/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="person">
-    <email>alexxy@gentoo.org</email>
-    <name>Alexey Shvetsov</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">Becksteinlab/GromacsWrapper</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/MDAnalysis/MDAnalysis-2.9.0.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-2.9.0.ebuild
deleted file mode 100644
index 835835ec8e90..000000000000
--- a/sci-chemistry/MDAnalysis/MDAnalysis-2.9.0.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_USE_PEP517=setuptools
-PYPI_NO_NORMALIZE=1
-
-inherit distutils-r1
-
-DESCRIPTION="A python library to analyze and manipulate molecular dynamics trajectories"
-HOMEPAGE="https://www.mdanalysis.org"
-SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/package-${PV}.tar.gz -> ${P}.gh.tar.gz"
-S="${WORKDIR}/mdanalysis-package-${PV}/package"
-
-LICENSE="GPL-2"
-
-SLOT="0"
-
-KEYWORDS="~amd64"
-
-# TODO: fix this
-# ImportError: MDAnalysis not installed properly. This can happen if your C extensions have not been built.
-RESTRICT="test"
-
-RDEPEND="
-	>=dev-python/numpy-1.16.0[${PYTHON_USEDEP}]
-	>=dev-python/scipy-1.0.0[${PYTHON_USEDEP}]
-	>=sci-biology/biopython-1.71[${PYTHON_USEDEP}]
-	>=dev-python/networkx-1.0[${PYTHON_USEDEP}]
-	>=dev-python/griddataformats-0.4.0[${PYTHON_USEDEP}]
-	>=dev-python/joblib-0.12[${PYTHON_USEDEP}]
-	>=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}]
-	>=dev-python/mmtf-python-1.0.0[${PYTHON_USEDEP}]
-	>=dev-python/tqdm-4.43.0[${PYTHON_USEDEP}]
-	>=dev-python/gsd-1.9.3[${PYTHON_USEDEP}]
-	dev-python/threadpoolctl[${PYTHON_USEDEP}]
-"
-BDEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
-
-src_prepare() {
-	# fix deprecated NPY API
-	sed \
-		-e "s:NPY_IN_ARRAY:NPY_ARRAY_IN_ARRAY:g" \
-		-e "s:NPY_ALIGNED:NPY_ARRAY_ALIGNED:g" \
-		-e "s:NPY_ENSURECOPY:NPY_ARRAY_ENSURECOPY:g" \
-		-i MDAnalysis/lib/src/transformations/transformations.c || die
-	distutils-r1_src_prepare
-}
diff --git a/sci-chemistry/MDAnalysis/Manifest b/sci-chemistry/MDAnalysis/Manifest
deleted file mode 100644
index a3cbff31c9f3..000000000000
--- a/sci-chemistry/MDAnalysis/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST MDAnalysis-2.9.0.gh.tar.gz 62932576 BLAKE2B 785c1919c383d646222943375e5ce7fa886c32d3db51ce3973da516cf629ce6081f2d16fe548cd32aaf9e5435374532266046fd54e8ad63870e7e3e17ef18c27 SHA512 fa13da003ede823a4a9ffb6e396f80a8b7e5a858431e9c0a78ded734d9872fa4f7ebf28e5e1a0bb45add5a2a9c05206be571371607879df0d5ff0eda750d1885
diff --git a/sci-chemistry/MDAnalysis/metadata.xml b/sci-chemistry/MDAnalysis/metadata.xml
deleted file mode 100644
index 31c543b5ba11..000000000000
--- a/sci-chemistry/MDAnalysis/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="pypi">MDAnalysis</remote-id>
-		<remote-id type="github">MDAnalysis/MDAnalysis</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/ParmEd/Manifest b/sci-chemistry/ParmEd/Manifest
deleted file mode 100644
index ec26f250d1a6..000000000000
--- a/sci-chemistry/ParmEd/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ParmEd-4.3.0.tar.gz 70101920 BLAKE2B 66da35ece5f6c244b8205f3889bee3c86471b3d54814ba3dd6096ab5f057b1276d74b1fe4f37523a629ecb18412aafddc0ed13e68d24abe10dda40247d0b30e4 SHA512 44abe47e1a8c904d74c91fe5f1c30d52e8683f0bddc3abaaee51fa38075c1d6be7b5977bb72cb4f0d266aa157e39f6028e94d0240b8c63fa66f1a7ccd7c4b569
diff --git a/sci-chemistry/ParmEd/ParmEd-4.3.0.ebuild b/sci-chemistry/ParmEd/ParmEd-4.3.0.ebuild
deleted file mode 100644
index 2490d4db32f7..000000000000
--- a/sci-chemistry/ParmEd/ParmEd-4.3.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 2022-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Parameter and topology file editor and molecular mechanical simulator engine"
-HOMEPAGE="https://parmed.github.io/ParmEd/html/index.html"
-SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="LGPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-PATCHES=( "${FILESDIR}/${P}-tests.patch" )
-
-DEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-python_test() {
-	# disable online tests
-	local -x CI=true
-	epytest
-}
diff --git a/sci-chemistry/ParmEd/files/ParmEd-4.3.0-tests.patch b/sci-chemistry/ParmEd/files/ParmEd-4.3.0-tests.patch
deleted file mode 100644
index cfe7c86ce6a1..000000000000
--- a/sci-chemistry/ParmEd/files/ParmEd-4.3.0-tests.patch
+++ /dev/null
@@ -1,191 +0,0 @@
-diff '--color=auto' -urN ParmEd-4.3.0.orig/test/test_parmed_amber.py ParmEd-4.3.0/test/test_parmed_amber.py
---- a/test/test_parmed_amber.py	2025-04-03 19:06:17.286507346 +0300
-+++ b/test/test_parmed_amber.py	2025-04-03 19:06:21.645553864 +0300
-@@ -82,9 +82,9 @@
-         with self.assertRaises(AmberError):
-             parm.add_flag('NEW_FLAG2', '10i6')
- 
--    def test_optimized_reader(self):
--        """ Check that the optimized reader imports correctly """
--        from parmed.amber import _rdparm
-+    #def test_optimized_reader(self):
-+    #    """ Check that the optimized reader imports correctly """
-+    #    from parmed.amber import _rdparm
- 
-     def test_nbfix_from_structure(self):
-         """ Tests AmberParm.from_structure with NBFIXes """
-diff '--color=auto' -urN ParmEd-4.3.0.orig/test/test_parmedtools_actions.py ParmEd-4.3.0/test/test_parmedtools_actions.py
---- a/test/test_parmedtools_actions.py	2025-04-03 19:06:17.306507441 +0300
-+++ b/test/test_parmedtools_actions.py	2025-04-03 19:07:47.378464084 +0300
-@@ -1298,36 +1298,36 @@
-         act = PT.printLJMatrix(gasparm, gasparm[0].nb_idx)
-         self.assertEqual(str(act), saved.PRINT_LJMATRIX)
- 
--    def test_delete_bond(self):
--        """ Test deleteBond on AmberParm """
--        parm = copy(gasparm)
--        # Pick the bond we plan to delete, pick out every angle and dihedral
--        # that contains that bond, and then delete it. Then make sure none of
--        # the valence terms that contained that bond remain afterwards. We
--        # already have a test to make sure that the __contains__ method works
--        # for atoms and bonds.
--        for bond in parm.atoms[0].bonds:
--            if parm.atoms[4] in bond: break
--        deleted_angles = list()
--        deleted_dihedrals = list()
--        for angle in parm.angles:
--            if bond in angle: deleted_angles.append(angle)
--        for dihedral in parm.dihedrals:
--            if bond in dihedral: deleted_dihedrals.append(dihedral)
--        act = PT.deleteBond(parm, '@1', '@5', 'verbose')
--        str(act)
--        act.execute()
--        self.assertTrue(bond not in parm.bonds)
--        for angle in deleted_angles:
--            self.assertTrue(angle not in parm.angles)
--        for dihedral in deleted_dihedrals:
--            self.assertTrue(dihedral not in parm.dihedrals)
--        # Nothing to do, make sure it doesn't fail, and does nothing
--        act = PT.deleteBond(parm, '@1', '@20')
--        nbnd = len(parm.bonds)
--        str(act)
--        act.execute()
--        self.assertEqual(nbnd, len(parm.bonds))
-+#    def test_delete_bond(self):
-+#        """ Test deleteBond on AmberParm """
-+#        parm = copy(gasparm)
-+#        # Pick the bond we plan to delete, pick out every angle and dihedral
-+#        # that contains that bond, and then delete it. Then make sure none of
-+#        # the valence terms that contained that bond remain afterwards. We
-+#        # already have a test to make sure that the __contains__ method works
-+#        # for atoms and bonds.
-+#        for bond in parm.atoms[0].bonds:
-+#            if parm.atoms[4] in bond: break
-+#        deleted_angles = list()
-+#        deleted_dihedrals = list()
-+#        for angle in parm.angles:
-+#            if bond in angle: deleted_angles.append(angle)
-+#        for dihedral in parm.dihedrals:
-+#            if bond in dihedral: deleted_dihedrals.append(dihedral)
-+#        act = PT.deleteBond(parm, '@1', '@5', 'verbose')
-+#        str(act)
-+#        act.execute()
-+#        self.assertTrue(bond not in parm.bonds)
-+#        for angle in deleted_angles:
-+#            self.assertTrue(angle not in parm.angles)
-+#        for dihedral in deleted_dihedrals:
-+#            self.assertTrue(dihedral not in parm.dihedrals)
-+#        # Nothing to do, make sure it doesn't fail, and does nothing
-+#        act = PT.deleteBond(parm, '@1', '@20')
-+#        nbnd = len(parm.bonds)
-+#        str(act)
-+#        act.execute()
-+#        self.assertEqual(nbnd, len(parm.bonds))
- 
-     def test_summary(self):
-         """ Test summary action on AmberParm """
-@@ -3340,45 +3340,45 @@
-         self.assertRaises(exc.ParmError, lambda:
-                 PT.printLJMatrix(amoebaparm, '@1'))
- 
--    def test_delete_bond(self):
--        """ Test deleteBond for AmoebaParm """
--        parm = copy(amoebaparm)
--        for bond in parm.atoms[0].bonds:
--            if parm.atoms[1] in bond: break
--        TrackedList = type(parm.bond_types)
--        objs_with_bond = []
--        for attribute in dir(parm):
--            # skip descriptors
--            if attribute in ('topology', 'positions', 'box_vectors',
--                             'velocities', 'coordinates', 'coords', 'vels'):
--                continue
--            attr = getattr(parm, attribute)
--            if not isinstance(attr, TrackedList): continue
--            for obj in attr:
--                try:
--                    if bond in obj:
--                        objs_with_bond.append(attr)
--                        break
--                except TypeError:
--                    break
--        self.assertTrue(len(objs_with_bond) > 0)
--        act = PT.deleteBond(parm, '@1', '@2', 'verbose')
--        str(act)
--        act.execute()
--        self.assertTrue(bond not in parm.bonds)
--        for attr in objs_with_bond:
--            for obj in attr:
--                self.assertNotIn(bond, attr)
--
--    @pytest.mark.xfail
--    def test_summary(self):
--        """ Test summary action for AmoebaParm """
--        parm = copy(amoebaparm)
--        act = PT.summary(parm)
--        self.assertEqual(str(act), saved.SUMMARYA1)
--        PT.loadRestrt(parm, self.get_fn('nma.rst7')).execute()
--        act = PT.summary(parm)
--        self.assertEqual(str(act), saved.SUMMARYA2)
-+    #def test_delete_bond(self):
-+    #    """ Test deleteBond for AmoebaParm """
-+    #    parm = copy(amoebaparm)
-+    #    for bond in parm.atoms[0].bonds:
-+    #        if parm.atoms[1] in bond: break
-+    #    TrackedList = type(parm.bond_types)
-+    #    objs_with_bond = []
-+    #    for attribute in dir(parm):
-+    #        # skip descriptors
-+    #        if attribute in ('topology', 'positions', 'box_vectors',
-+    #                         'velocities', 'coordinates', 'coords', 'vels'):
-+    #            continue
-+    #        attr = getattr(parm, attribute)
-+    #        if not isinstance(attr, TrackedList): continue
-+    #        for obj in attr:
-+    #            try:
-+    #                if bond in obj:
-+    #                    objs_with_bond.append(attr)
-+    #                    break
-+    #            except TypeError:
-+    #                break
-+    #    self.assertTrue(len(objs_with_bond) > 0)
-+    #    act = PT.deleteBond(parm, '@1', '@2', 'verbose')
-+    #    str(act)
-+    #    act.execute()
-+    #    self.assertTrue(bond not in parm.bonds)
-+    #    for attr in objs_with_bond:
-+    #        for obj in attr:
-+    #            self.assertNotIn(bond, attr)
-+
-+    #@pytest.mark.xfail
-+    #def test_summary(self):
-+    #    """ Test summary action for AmoebaParm """
-+    #    parm = copy(amoebaparm)
-+    #    act = PT.summary(parm)
-+    #    self.assertEqual(str(act), saved.SUMMARYA1)
-+    #    PT.loadRestrt(parm, self.get_fn('nma.rst7')).execute()
-+    #    act = PT.summary(parm)
-+    #    self.assertEqual(str(act), saved.SUMMARYA2)
- 
-     def test_scale(self):
-         """ Test scale action for AmoebaParm """
-@@ -3668,11 +3668,11 @@
-         with self.assertRaises(exc.HMassRepartitionError):
-             PT.HMassRepartition(struct, 100).execute()
- 
--    def test_delete_bond(self):
--        """ Tests deleteBond on arbitrary Structure instances """
--        from parmed import periodic_table
--        struct = create_random_structure(parametrized=True)
--        act = PT.deleteBond(struct, '@%d' % (struct.bonds[0].atom1.idx+1),
--                '@%d' % (struct.bonds[0].atom2.idx+1))
--        str(act)
--        act.execute()
-+    #def test_delete_bond(self):
-+    #    """ Tests deleteBond on arbitrary Structure instances """
-+    #    from parmed import periodic_table
-+    #    struct = create_random_structure(parametrized=True)
-+    #    act = PT.deleteBond(struct, '@%d' % (struct.bonds[0].atom1.idx+1),
-+    #            '@%d' % (struct.bonds[0].atom2.idx+1))
-+    #    str(act)
-+    #    act.execute()
diff --git a/sci-chemistry/ParmEd/metadata.xml b/sci-chemistry/ParmEd/metadata.xml
deleted file mode 100644
index 84eaa2e2cd49..000000000000
--- a/sci-chemistry/ParmEd/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">ParmEd/ParmEd</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/autodock/Manifest b/sci-chemistry/autodock/Manifest
deleted file mode 100644
index 8b5de32f0db1..000000000000
--- a/sci-chemistry/autodock/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST autodock-4.2.6-drop-register-keyword.patch 36676 BLAKE2B d91969d9d84b8940ddabf34dc017174deb1dafe0867f9ff5d2e528c4f3b4086b285f299220caa9406139146d460c2fba529e8b85c4aee927cabbdf34e91d3541 SHA512 39358c1d70f80c0a54066eb9ef600980c993dffaf1f7b7d558d29a4404c00a4d02ba0e871ae538474e452425f79795aad38eb0fca38a2663ccf6a64f57a40933
-DIST autodocksuite-4.2.6-src.tar.gz 35438010 BLAKE2B 88e036ecc0492fb83f31b90fd0983ec57d889a61d17249f672a3e30e942f6c329dc2494088a8fc7c5bc39a5bdbb38fb1514f1750c7145374f202a928d477faa9 SHA512 75b8878f948c4f6bc28adb442997192dad0c36bbede2fd698623903cb27b06b4df3ba038bfc70fc13b4bdee864fd2344f0f7208be2020da4e01a00b842b46bbb
diff --git a/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild b/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild
deleted file mode 100644
index cd79276f14cd..000000000000
--- a/sci-chemistry/autodock/autodock-4.2.6-r1.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools readme.gentoo-r1
-
-MY_PN="autodocksuite"
-MY_P="${MY_PN}-${PV}"
-
-DESCRIPTION="A suite of automated docking tools"
-HOMEPAGE="https://autodock.scripps.edu/"
-SRC_URI="
-	https://autodock.scripps.edu/downloads/autodock-registration/tars/dist$(ver_rs 1- '')/${MY_P}-src.tar.gz
-	https://dev.gentoo.org/~nowa/${PN}-4.2.6-drop-register-keyword.patch
-"
-S="${WORKDIR}/src"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples openmp"
-# Tests require python2
-RESTRICT="test"
-
-# False positives caused by nested configure scripts
-QA_CONFIGURE_OPTIONS=".*"
-
-DISABLE_AUTOFORMATTING="yes"
-DOC_CONTENTS="
-The AutoDock development team requests all users to fill out the
-registration form at:
-
-http://autodock.scripps.edu/downloads/autodock-registration
-
-The number of unique users of AutoDock is used by Prof. Arthur J.
-Olson and the Scripps Research Institude to support grant
-applications.
-"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-buildsystem.patch
-	"${DISTDIR}"/${PN}-4.2.6-drop-register-keyword.patch
-)
-
-src_prepare() {
-	default
-
-	local i
-
-	sed \
-		-e "s/\tcsh/\tsh/" \
-		-i auto{dock,grid}/Makefile.am || die
-	for i in autodock autogrid; do
-		pushd $i &>/dev/null
-		eautoreconf
-		popd &>/dev/null
-	done
-}
-
-src_configure() {
-	local i
-	for i in autodock autogrid; do
-		pushd $i &>/dev/null
-		econf $(use_enable openmp)
-		popd &>/dev/null
-	done
-}
-
-src_compile() {
-	emake -C autodock
-	emake -C autogrid
-}
-
-# Refer: https://github.com/gentoo/gentoo/pull/31489/files#r1321120609
-#src_test() {
-#	elog "Testing autodock"
-#	cd "${S}/autodock/Tests" || die
-#	cp ../*.dat . || die
-#	${EPYTHON} test_autodock4.py || die "AutoDock tests failed."
-#	einfo "Testing autogrid"
-#	cd "${S}/autogrid/Tests" || die
-#	${EPYTHON} test_autogrid4.py || die "AutoGrid tests failed."
-#}
-
-src_install() {
-	if use openmp; then
-		newbin autodock/autodock4.omp ${PN}4
-		dobin autogrid/autogrid4
-	else
-		dobin autodock/autodock4 autogrid/autogrid4
-	fi
-
-	insinto /usr/share/${PN}
-	doins -r \
-		autodock/{AD4_parameters.dat,AD4_PARM99.dat} \
-		$(usex examples "autodock/EXAMPLES" "")
-
-	DOCS=(
-		RELEASENOTES
-		autodock/{AUTHORS,README}
-		autodock/USERGUIDES/AutoDock4.{0,1,2}_UserGuide.doc
-		autodock/USERGUIDES/AutoDock4.2_UserGuide.pdf
-	)
-	einstalldocs
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch b/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch
deleted file mode 100644
index 443dfcd868ce..000000000000
--- a/sci-chemistry/autodock/files/autodock-4.2.6-buildsystem.patch
+++ /dev/null
@@ -1,44 +0,0 @@
- a/autodock/Makefile.am | 6 +++---
- b/autogrid/Makefile.am | 4 ++--
- 2 files changed, 5 insertions(+), 5 deletions(-)
-
-diff --git a/src/autodock/Makefile.am b/src/autodock/Makefile.am
-index 799a3c4..911897b 100644
---- a/autodock/Makefile.am
-+++ b/autodock/Makefile.am
-@@ -459,7 +459,8 @@ endif
- 
- BUILT_SOURCES = $(autodock4_SOURCES) default_parameters.h
- 
--AM_CXXFLAGS = -O3 # Agressive optimization
-+AM_CXXFLAGS =
-+#AM_CXXFLAGS = -O3 # Agressive optimization
- #AM_CXXFLAGS = -g # debug
- 
-     # if gnu c++ compiler
-@@ -488,8 +489,7 @@ endif
- AM_CPPFLAGS = -DNOSQRT \
- 	      -DUSE_DOUBLE \
-               -DUSE_8A_NBCUTOFF \
--	      -DUSE_INT_AS_FOURBYTELONG \
--	      -O3
-+	      -DUSE_INT_AS_FOURBYTELONG
- # AM_LDFLAGS = -g # -g is MP debug
- 
- 
-diff --git a/src/autogrid/Makefile.am b/src/autogrid/Makefile.am
-index b531099..b78b380 100644
---- a/autogrid/Makefile.am
-+++ b/autogrid/Makefile.am
-@@ -94,9 +94,9 @@ autogrid4_SOURCES = main.cpp \
- BUILT_SOURCES = default_parameters.h
- 
- 
--AM_CFLAGS = -Wall -O3 # All warnings, Agressive optimization
-+AM_CFLAGS = -Wall # All warnings, Agressive optimization
- 
--AM_CPPFLAGS = -Wall -O3 -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization
-+AM_CPPFLAGS = -Wall -I $(srcdir) -I$(srcdir)/../autodock # All warnings, Agressive optimization
- AM_CPPFLAGS += -Wno-write-strings # increase compatibility with pre 4.x compilers for string handling
- #  M Pique - add USE_8A_NBCUTOFF
- AM_CPPFLAGS += -DUSE_8A_NBCUTOFF
diff --git a/sci-chemistry/autodock/metadata.xml b/sci-chemistry/autodock/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/autodock/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
deleted file mode 100644
index 5fd6ce73bd36..000000000000
--- a/sci-chemistry/autodock_vina/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST autodock_vina-1.2.7.tar.gz 46488149 BLAKE2B 15ac50af12c6ac47b8ac6d8db6869a445b7535d72022934ec2658cbde2bb508fa36bfb932b2550fdef59342b98e2e604a4cf2a03a46e680781cefb47f2bb7b95 SHA512 b96d2f14bf26b63b3f132750e7b056632d8e48649ce24e267972e698d60b834c9dcd93907b22bd27413843a34112d6db32acef1793b8b2a5a14e813c66548633
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.2.7.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.2.7.ebuild
deleted file mode 100644
index 999c5bd46aca..000000000000
--- a/sci-chemistry/autodock_vina/autodock_vina-1.2.7.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-MY_PN=AutoDock-Vina
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Program for drug discovery, molecular docking and virtual screening"
-HOMEPAGE="http://vina.scripps.edu/"
-SRC_URI="https://github.com/ccsb-scripps/AutoDock-Vina/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${MY_PN}-${PV}/build/linux/release"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="debug"
-
-RDEPEND="dev-libs/boost:="
-DEPEND="${RDEPEND}"
-
-PATCHES=( "${FILESDIR}"/${P}-gentoo.patch )
-
-src_prepare() {
-	pushd "${WORKDIR}/${MY_PN}-${PV}"  > /dev/null || die
-	sed -e "s:VERSION:\"${PV}\":g" \
-		-i src/main/main.cpp \
-		-i src/split/split.cpp || die
-	default
-	popd > /dev/null || die
-}
-
-src_configure() {
-	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -DBOOST_TIMER_ENABLE_DEPRECATED -std=c++14
-}
-
-src_compile() {
-	emake \
-		BASE="${EPREFIX}"/usr/ \
-		GPP="$(tc-getCXX)" \
-		C_OPTIONS=$(usex debug '' -DNDEBUG)
-}
-
-src_install() {
-	dobin vina{,_split}
-}
diff --git a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.7-gentoo.patch b/sci-chemistry/autodock_vina/files/autodock_vina-1.2.7-gentoo.patch
deleted file mode 100644
index 86016aeb201d..000000000000
--- a/sci-chemistry/autodock_vina/files/autodock_vina-1.2.7-gentoo.patch
+++ /dev/null
@@ -1,64 +0,0 @@
-diff -urN a/build/linux/debug/Makefile b/build/linux/debug/Makefile
---- a/build/linux/debug/Makefile
-+++ b/build/linux/debug/Makefile
-@@ -1,7 +1,7 @@
- BASE=/usr
- BOOST_VERSION=
- BOOST_INCLUDE = $(BASE)/include
--C_PLATFORM=-static -pthread
-+C_PLATFORM=-pthread
- GPP=g++
- C_OPTIONS= -g -std=gnu++11
- BOOST_LIB_VERSION=
-diff -urN a/build/linux/release/Makefile b/build/linux/release/Makefile
---- a/build/linux/release/Makefile
-+++ b/build/linux/release/Makefile
-@@ -1,7 +1,7 @@
- BASE=/usr/local
- BOOST_VERSION=
- BOOST_INCLUDE = $(BASE)/include
--C_PLATFORM=-static -pthread
-+C_PLATFORM=-pthread
- GPP=g++
- C_OPTIONS= -O3 -DNDEBUG -std=c++11
- BOOST_LIB_VERSION=
-diff -urN a/build/makefile_common b/build/makefile_common
---- a/build/makefile_common
-+++ b/build/makefile_common
-@@ -14,7 +14,7 @@
- #CC = ${GPP} ${C_PLATFORM} -ansi -pedantic -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
- CC = ${GPP} ${C_PLATFORM} -ansi -Wno-long-long ${C_OPTIONS} $(INCFLAGS)
- 
--LDFLAGS = -L$(BASE)/lib -L.
-+LDFLAGS = -L.
- 
- # test if boost_thread-mt exists, this is
- # necessary as some versions of boost only
-@@ -32,22 +32,22 @@
- ifeq ($(BOOST_STATIC), y)
- LIBS = ${BASE}/lib/libboost_system${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_thread${threadmt}${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_serialization${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_filesystem${BOOST_LIB_VERSION}.a ${BASE}/lib/libboost_program_options${BOOST_LIB_VERSION}.a
- else
--LIBS = -l boost_system${BOOST_LIB_VERSION} -l boost_thread${threadmt}${BOOST_LIB_VERSION} -l boost_serialization${BOOST_LIB_VERSION} -l boost_filesystem${BOOST_LIB_VERSION} -l boost_program_options${BOOST_LIB_VERSION}#-l pthread
-+LIBS = -l boost_thread -l boost_serialization -l boost_filesystem -l boost_program_options -l pthread
- endif
- 
- .SUFFIXES: .cpp .o
- 
- %.o : ../../../src/lib/%.cpp 
--	$(CC) $(CFLAGS) -o $@ -c $< 
-+	$(CC) $(CXXFLAGS) -o $@ -c $< 
- 
- %.o : ../../../src/design/%.cpp 
--	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
-+	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
- 	
- %.o : ../../../src/main/%.cpp 
--	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
-+	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
- 
- %.o : ../../../src/split/%.cpp 
--	$(CC) $(CFLAGS) -I ../../../src/lib -o $@ -c $< 
-+	$(CC) $(CXXFLAGS) -I ../../../src/lib -o $@ -c $< 
- 
- all: vina vina_split
- 
diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml
deleted file mode 100644
index ec0a09453889..000000000000
--- a/sci-chemistry/autodock_vina/metadata.xml
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-		AutoDock Vina is a new open-source program for drug discovery, molecular
-		docking and virtual screening, offering multi-core capability, high
-		performance and enhanced accuracy and ease of use. [1]
-		AutoDock Vina has been designed and implemented by Dr. Oleg Trott
-		in the Molecular Graphics Lab at The Scripps Research Institute.
-		If you used AutoDock Vina in your work, please cite:
-		O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy
-		of docking with a new scoring function, efficient optimization and
-		multithreading
-		Journal of Computational Chemistry 31 (2010) 455-461
-	</longdescription>
-	<upstream>
-		<remote-id type="github">ccsb-scripps/AutoDock-Vina</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/avogadro2/Manifest b/sci-chemistry/avogadro2/Manifest
deleted file mode 100644
index 33f673a07e4f..000000000000
--- a/sci-chemistry/avogadro2/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST avogadro2-1.103.0-i18n.tar.gz 1496239 BLAKE2B 722e43c43854640a85a80fcd7e2cbf9d4d5929cb7e431eb7d7739014f878701106677343887f34fbb7d8e0c21e948d5efe26447bfd7a6c97f95552dfe8b0efd7 SHA512 8c767a9415be04cb19691ae533f13c210fdf1cbfe0cdf914271d024bfa90960b3edbc2d5a9230c0504c3004b6eea7a4f5b0cd40fe83b53dda1c5cc9d079221f6
-DIST avogadro2-1.103.0.tar.gz 3848364 BLAKE2B c17b9ef43c4b3980b0083c91d9b60995d801c20033ab55d25a0bcc579b59106aa74423818fdf04921ea55a3fd3acfdfd849c4851b0b922615ebf50408ad59f44 SHA512 1298e929a0cd415ecb325250c94b9e70e5142fb029f7ee9314194ef4a086fbbfc190945d19139086629bd55c0c00aca8b04680a82389e573fcb0d0055e62c171
-DIST avogadro2-2.0.0-i18n.tar.gz 1572705 BLAKE2B ab9bdbc6e8095f9866754decf254db75d9018ea9217a42967562162fc409695b91896708ebd51bb4969ccce2e92d58c4732d4642b0c5d92695a347970b536ee2 SHA512 34793f87f81462d648c4acc4f61ec7a4ce48b626c8699f72a3720e845c235bd8d02ab7670bb68bc6ce728fd469ef0c924eb5b4fa4f54aa2d23dba5e1a4445339
-DIST avogadro2-2.0.0.tar.gz 3878161 BLAKE2B b6679d9ca07ff1d13eaa70170bed4df6c1968104556c60a2aa94c6848b87e4fe1267ff52afd5b39be6e900e4bbe0398f21ec620b08f7ba74b7541071ae762294 SHA512 235f9b1f4f0d5366b219c21c4e8938b4c21e6020f130ebfcaa281cc0c6e131ba42d87108b2ac74ff27d539a16515975a1b5fad3fbef4ea73a1f738372c9e6826
diff --git a/sci-chemistry/avogadro2/avogadro2-1.103.0.ebuild b/sci-chemistry/avogadro2/avogadro2-1.103.0.ebuild
deleted file mode 100644
index 8169605e2f8e..000000000000
--- a/sci-chemistry/avogadro2/avogadro2-1.103.0.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-MY_PN=avogadroapp
-inherit cmake optfeature xdg
-
-DESCRIPTION="Advanced molecule editor and visualizer 2"
-HOMEPAGE="https://www.openchemistry.org/ https://two.avogadro.cc/"
-SRC_URI="
-	https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/OpenChemistry/avogadro-i18n/archive/${PV}.tar.gz -> ${P}-i18n.tar.gz
-"
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-LICENSE="BSD GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc rpc"
-
-RDEPEND="
-	dev-cpp/eigen:=
-	dev-qt/qtbase:6[concurrent,gui,network,opengl,ssl,widgets]
-	~sci-libs/avogadrolibs-${PV}[archive,qt6]
-"
-DEPEND="
-	${RDEPEND}
-"
-BDEPEND="doc? ( app-text/doxygen )"
-
-src_unpack() {
-	default
-	mv "${WORKDIR}"/avogadro-i18n-${PV} "${WORKDIR}"/avogadro-i18n || die
-}
-
-src_prepare() {
-	if use doc; then
-		doxygen -u docs/doxyfile.in 2>/dev/null || die
-	fi
-
-	# disable automatic update dialog
-	sed -e '\@  checkUpdate()@s:^:  //:' \
-		-i avogadro/mainwindow.cpp || die
-
-	cmake_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_SKIP_RPATH=ON
-		-DBUILD_DOCUMENTATION=$(usex doc)
-		-DAvogadro_ENABLE_RPC=$(usex rpc)
-		# test requires qttesting/paraview
-		-DENABLE_TESTING=OFF
-		-DQT_VERSION=6
-		# skip detection of jkqtplotter
-		# avogadrolibs handles it without the need for rebuilding avogadro2
-		-DUSE_PLOTTER=OFF
-	)
-
-	# Need this to prevent overwriting the documentation OUTDIR
-	use doc && mycmakeargs+=(
-			-DChemData_SOURCE_DIR="${S}"
-			-DChemData_BINARY_DIR="${BUILD_DIR}"
-	)
-
-	cmake_src_configure
-}
-
-src_compile() {
-	cmake_src_compile
-
-	use doc && cmake_build documentation
-}
-
-src_install() {
-	use doc && local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
-
-	cmake_src_install
-
-	# remove CONTRIBUTING, LICENSE and duplicate README
-	rm -r "${ED}"/usr/share/doc/${PF}/avogadro2 || die
-}
-
-pkg_postinst() {
-	optfeature "environments of downloaded plugins" dev-util/pixi
-	optfeature "charts and spectra" sci-libs/avogadrolibs[jkqtplotter]
-
-	xdg_pkg_postinst
-}
diff --git a/sci-chemistry/avogadro2/avogadro2-2.0.0.ebuild b/sci-chemistry/avogadro2/avogadro2-2.0.0.ebuild
deleted file mode 100644
index 8169605e2f8e..000000000000
--- a/sci-chemistry/avogadro2/avogadro2-2.0.0.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-MY_PN=avogadroapp
-inherit cmake optfeature xdg
-
-DESCRIPTION="Advanced molecule editor and visualizer 2"
-HOMEPAGE="https://www.openchemistry.org/ https://two.avogadro.cc/"
-SRC_URI="
-	https://github.com/OpenChemistry/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz
-	https://github.com/OpenChemistry/avogadro-i18n/archive/${PV}.tar.gz -> ${P}-i18n.tar.gz
-"
-S="${WORKDIR}/${MY_PN}-${PV}"
-
-LICENSE="BSD GPL-2+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc rpc"
-
-RDEPEND="
-	dev-cpp/eigen:=
-	dev-qt/qtbase:6[concurrent,gui,network,opengl,ssl,widgets]
-	~sci-libs/avogadrolibs-${PV}[archive,qt6]
-"
-DEPEND="
-	${RDEPEND}
-"
-BDEPEND="doc? ( app-text/doxygen )"
-
-src_unpack() {
-	default
-	mv "${WORKDIR}"/avogadro-i18n-${PV} "${WORKDIR}"/avogadro-i18n || die
-}
-
-src_prepare() {
-	if use doc; then
-		doxygen -u docs/doxyfile.in 2>/dev/null || die
-	fi
-
-	# disable automatic update dialog
-	sed -e '\@  checkUpdate()@s:^:  //:' \
-		-i avogadro/mainwindow.cpp || die
-
-	cmake_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_SKIP_RPATH=ON
-		-DBUILD_DOCUMENTATION=$(usex doc)
-		-DAvogadro_ENABLE_RPC=$(usex rpc)
-		# test requires qttesting/paraview
-		-DENABLE_TESTING=OFF
-		-DQT_VERSION=6
-		# skip detection of jkqtplotter
-		# avogadrolibs handles it without the need for rebuilding avogadro2
-		-DUSE_PLOTTER=OFF
-	)
-
-	# Need this to prevent overwriting the documentation OUTDIR
-	use doc && mycmakeargs+=(
-			-DChemData_SOURCE_DIR="${S}"
-			-DChemData_BINARY_DIR="${BUILD_DIR}"
-	)
-
-	cmake_src_configure
-}
-
-src_compile() {
-	cmake_src_compile
-
-	use doc && cmake_build documentation
-}
-
-src_install() {
-	use doc && local HTML_DOCS=( "${BUILD_DIR}"/docs/html/. )
-
-	cmake_src_install
-
-	# remove CONTRIBUTING, LICENSE and duplicate README
-	rm -r "${ED}"/usr/share/doc/${PF}/avogadro2 || die
-}
-
-pkg_postinst() {
-	optfeature "environments of downloaded plugins" dev-util/pixi
-	optfeature "charts and spectra" sci-libs/avogadrolibs[jkqtplotter]
-
-	xdg_pkg_postinst
-}
diff --git a/sci-chemistry/avogadro2/metadata.xml b/sci-chemistry/avogadro2/metadata.xml
deleted file mode 100644
index 5362eca4d59d..000000000000
--- a/sci-chemistry/avogadro2/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="rpc">Enable communication between programs using the RPC protocol and standard JSON messages</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">OpenChemistry/avogadroapp</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/bodr/Manifest b/sci-chemistry/bodr/Manifest
deleted file mode 100644
index c8f6a5dd665a..000000000000
--- a/sci-chemistry/bodr/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST bodr-10.tar.bz2 225671 BLAKE2B cda3d66da530cb28898389080807c4ed8602bb8871ee9e9ff75ba4a7a40ee676308539adb26d61b3361b53f37c099fa784438def9b768828a941c3693c7315a2 SHA512 a3e0e7195914938d8824127aa4777c4054c302ef7811d82d1e012d9be5d7a13d7f2225d4216f4a30ae7dbf70eb3b0b38571c3ee0dbe1d97af15f04171dd51bec
diff --git a/sci-chemistry/bodr/bodr-10.ebuild b/sci-chemistry/bodr/bodr-10.ebuild
deleted file mode 100644
index f7c246ff2281..000000000000
--- a/sci-chemistry/bodr/bodr-10.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="The Blue Obelisk Data Repository listing element and isotope properties"
-HOMEPAGE="https://sourceforge.net/projects/bodr"
-SRC_URI="https://downloads.sourceforge.net/${PN}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-BDEPEND="dev-libs/libxslt"
-
-src_prepare() {
-	default
-	sed -i -e "s/COPYING//g" Makefile.* || die
-}
diff --git a/sci-chemistry/bodr/metadata.xml b/sci-chemistry/bodr/metadata.xml
deleted file mode 100644
index 05ed327d6fa9..000000000000
--- a/sci-chemistry/bodr/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-		Blue Obelisk Data Repository (BODR) is a shared data repository. It lists
-		many important chemoinformatics data such as elemental properties, atomic
-		radii, etc. including references to original literature. Software developers
-		can use this repository on online webpages or in chemistry software for
-		free.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">bodr</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/cara-bin/Manifest b/sci-chemistry/cara-bin/Manifest
deleted file mode 100644
index 32f447168028..000000000000
--- a/sci-chemistry/cara-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST Start1.2.cara.xz 43124 BLAKE2B 5c045662e156eda4c1a2075c52f1d35ad073a1bdef2655297f1df91dd3cd21a3eec5ff389bdd8765a1df2e9016cc09a1547db676de39c6233fd1eac82286cdda SHA512 26874d634491558dc593a0ec32e83d5cfceedc69bbf901f4d25d6b9515b84aebffbf495d1ac34b3664b8b5822954edf62c5b88dcca6bcfcb152715caa88f5f03
-DIST cara_1.8.4_linux.gz 6677463 BLAKE2B 3f67df10698b3f2851de1b221eeab94b497fb8a041fc6875755e18e06ae2e8c9c3cd670d99e21bf8034d5e3ac0a5d2ab46e101ba65813004809e1a1975e3b29e SHA512 e264cfbef640f267132dfd48b940203a319c8f34de71c5b786c6bfc2ab561bdf3fbd79516d619ca52b2aca64a2887f770fabfabedb76433c5f78aa02c65f898f
diff --git a/sci-chemistry/cara-bin/cara-bin-1.8.4-r2.ebuild b/sci-chemistry/cara-bin/cara-bin-1.8.4-r2.ebuild
deleted file mode 100644
index 1d96423e269c..000000000000
--- a/sci-chemistry/cara-bin/cara-bin-1.8.4-r2.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-MY_PN="${PN%%-bin}"
-MY_P="${MY_PN}_${PV}"
-
-DESCRIPTION="Analysis of NMR spectra and Computer Aided Resonance Assignment"
-SRC_URI="
-	http://www.cara.nmr-software.org/downloads/${MY_P}_linux.gz
-	https://dev.gentoo.org/~jlec/distfiles//Start1.2.cara.xz"
-HOMEPAGE="http://www.nmr.ch"
-
-LICENSE="CARA"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-	!prefix? (
-		>=media-libs/fontconfig-2.10.92[abi_x86_32(-)]
-		>=media-libs/freetype-2.5.0.1[abi_x86_32(-)]
-		>=x11-libs/libICE-1.0.8-r1[abi_x86_32(-)]
-		>=x11-libs/libSM-1.2.1-r1[abi_x86_32(-)]
-		>=x11-libs/libX11-1.6.2[abi_x86_32(-)]
-		>=x11-libs/libXcursor-1.1.14[abi_x86_32(-)]
-		>=x11-libs/libXext-1.3.2[abi_x86_32(-)]
-		>=x11-libs/libXi-1.7.2[abi_x86_32(-)]
-		>=x11-libs/libXrandr-1.4.2[abi_x86_32(-)]
-		>=x11-libs/libXrender-0.9.8[abi_x86_32(-)]
-	)
-	sys-libs/glibc
-	sys-libs/libstdc++-v3:5"
-DEPEND=""
-
-RESTRICT="bindist mirror"
-
-QA_PREBUILT="opt/cara/*"
-
-S="${WORKDIR}"
-
-src_install() {
-	exeinto /opt/cara
-	doexe ${MY_P}_linux
-	dosym ../cara/${MY_P}_linux /opt/bin/cara
-	dodoc Start1.2.cara
-}
diff --git a/sci-chemistry/cara-bin/metadata.xml b/sci-chemistry/cara-bin/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/cara-bin/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest
deleted file mode 100644
index 6c773b88604d..000000000000
--- a/sci-chemistry/chemex/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST chemex-2026.4.0.tar.gz 139333 BLAKE2B 7519aa31d34bef57abd928df751803222c92521b672451341daf0aefb0e28c55195ca640e7187c6cd4f66381eb7dda944a381b1efb6344a8fad7e852d0371dc9 SHA512 c9fa9d86128999823de3e9abb2dc0e518e7fceec0b30c361b96f7752dfcb7c8b18d8147ebf06e965c565faba384e07a9e92cb450120a7fa33689150233c3fc39
-DIST chemex-2026.5.0.tar.gz 139373 BLAKE2B 226e3e6119b7c81567ef949672371190b76e69d0551c75137cf95d0b16875f2dba83c3dd1be29def6fb9002d779422ef1f683603ef2eb1e398eb419edf508493 SHA512 831978bf149d841660e5ea98eab18a2d21b7969fbfc7f36cfcf74cada5d2fa19fdfc585d4aaffc85b3b0c1cb8124d327716ae23ffa63bf3ac485187fad5934ae
diff --git a/sci-chemistry/chemex/chemex-2026.4.0.ebuild b/sci-chemistry/chemex/chemex-2026.4.0.ebuild
deleted file mode 100644
index ad9ff99811c4..000000000000
--- a/sci-chemistry/chemex/chemex-2026.4.0.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_SINGLE_IMPL="yes"
-DISTUTILS_USE_PEP517=uv-build
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit distutils-r1 pypi
-
-DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data"
-HOMEPAGE="https://github.com/gbouvignies/chemex https://pypi.org/project/chemex/"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-#RESTRICT="!test? ( test )"
-# FIXME: Restrict until tests are readded https://github.com/gbouvignies/ChemEx/issues/51
-RESTRICT="test"
-
-RDEPEND="
-	$(python_gen_cond_dep '
-		>=dev-python/annotated-types-0.7.0[${PYTHON_USEDEP}]
-		>=dev-python/cachetools-5.5.1[${PYTHON_USEDEP}]
-		>=dev-python/emcee-3.1.6[${PYTHON_USEDEP}]
-		>=dev-python/lmfit-1.3.2[${PYTHON_USEDEP}]
-		>=dev-python/matplotlib-3.10.0[${PYTHON_USEDEP}]
-		>=dev-python/numpy-2.2.3[${PYTHON_USEDEP}]
-		>=dev-python/pydantic-2.10.6[${PYTHON_USEDEP}]
-		>=dev-python/rapidfuzz-3.12.1[${PYTHON_USEDEP}]
-		>=dev-python/rich-13.9.4[${PYTHON_USEDEP}]
-		>=dev-python/scipy-1.15.2[${PYTHON_USEDEP}]
-	')
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
diff --git a/sci-chemistry/chemex/chemex-2026.5.0.ebuild b/sci-chemistry/chemex/chemex-2026.5.0.ebuild
deleted file mode 100644
index ad9ff99811c4..000000000000
--- a/sci-chemistry/chemex/chemex-2026.5.0.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DISTUTILS_SINGLE_IMPL="yes"
-DISTUTILS_USE_PEP517=uv-build
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit distutils-r1 pypi
-
-DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data"
-HOMEPAGE="https://github.com/gbouvignies/chemex https://pypi.org/project/chemex/"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE="test"
-
-#RESTRICT="!test? ( test )"
-# FIXME: Restrict until tests are readded https://github.com/gbouvignies/ChemEx/issues/51
-RESTRICT="test"
-
-RDEPEND="
-	$(python_gen_cond_dep '
-		>=dev-python/annotated-types-0.7.0[${PYTHON_USEDEP}]
-		>=dev-python/cachetools-5.5.1[${PYTHON_USEDEP}]
-		>=dev-python/emcee-3.1.6[${PYTHON_USEDEP}]
-		>=dev-python/lmfit-1.3.2[${PYTHON_USEDEP}]
-		>=dev-python/matplotlib-3.10.0[${PYTHON_USEDEP}]
-		>=dev-python/numpy-2.2.3[${PYTHON_USEDEP}]
-		>=dev-python/pydantic-2.10.6[${PYTHON_USEDEP}]
-		>=dev-python/rapidfuzz-3.12.1[${PYTHON_USEDEP}]
-		>=dev-python/rich-13.9.4[${PYTHON_USEDEP}]
-		>=dev-python/scipy-1.15.2[${PYTHON_USEDEP}]
-	')
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests pytest
diff --git a/sci-chemistry/chemex/metadata.xml b/sci-chemistry/chemex/metadata.xml
deleted file mode 100644
index c930e5101991..000000000000
--- a/sci-chemistry/chemex/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>pacho@gentoo.org</email>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">gbouvignies/chemex</remote-id>
-		<remote-id type="pypi">chemex</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/chemical-mime-data/Manifest b/sci-chemistry/chemical-mime-data/Manifest
deleted file mode 100644
index db84314bdfd1..000000000000
--- a/sci-chemistry/chemical-mime-data/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST chemical-mime-data-0.1.95_pre20171122.tar.gz 84515 BLAKE2B 42f76b44408c04e5a254c17502ea2c297727bb58fa3e86b8bca7f0c4c056ae7400b31f06b7d0c64b0712e97ab8a1f82549f44a3677720cd37a301ba99adb3d7a SHA512 a031e7a5bc31a74adcd8e5d827de71b6e0eafdceba16cf6f7407aa0266a9a082b0011963b315d2369f39abf45c4b41cedafccddbc2171673bf96ccbea51a4790
diff --git a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild b/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild
deleted file mode 100644
index b6291c211fa1..000000000000
--- a/sci-chemistry/chemical-mime-data/chemical-mime-data-0.1.95_pre20171122.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit autotools xdg
-
-DESCRIPTION="A collection of data files to add support for chemical MIME types"
-HOMEPAGE="https://github.com/dleidert/chemical-mime"
-COMMIT="4fd66e3b3b7d922555d1e25587908b036805c45b"
-SRC_URI="https://github.com/dleidert/chemical-mime/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN/-data/}-${COMMIT}"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="amd64 arm arm64 x86"
-
-RDEPEND="x11-misc/shared-mime-info"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-util/intltool
-	dev-util/desktop-file-utils
-	dev-libs/libxslt
-	virtual/pkgconfig
-"
-
-PATCHES=(
-	# https://github.com/dleidert/chemical-mime/issues/5
-	"${FILESDIR}"/${PN}-0.1.95-turbomole.patch
-)
-
-src_prepare() {
-	default
-	# https://github.com/dleidert/chemical-mime/issues/4
-	sed -i -e \
-		'/<_comment/a\\t\t<generic-icon name="image-x-generic"/>' \
-		src/chemical-mime-database.xml.in || die
-	sed -i -e \
-		's:acronym|alias|comment|:acronym|alias|comment|generic-icon|:' \
-		xsl/cmd_freedesktop_org.xsl || die
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--disable-update-database \
-		--without-gnome-mime \
-		--without-kde-mime \
-		--without-kde-magic
-}
diff --git a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.95-turbomole.patch b/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.95-turbomole.patch
deleted file mode 100644
index adef4ee04869..000000000000
--- a/sci-chemistry/chemical-mime-data/files/chemical-mime-data-0.1.95-turbomole.patch
+++ /dev/null
@@ -1,47 +0,0 @@
---- a/src/chemical-mime-database.xml.in.old	2023-03-20 16:22:36.841959114 +0100
-+++ b/src/chemical-mime-database.xml.in	2023-03-20 16:26:38.315772298 +0100
-@@ -1418,7 +1418,7 @@
- 		<cm:specification url="http://www.ebi.ac.uk/help/formats.html"/>
- 	</mime-type>
- 
--	<mime-type type="chemical/x-turbomole-basis" cm:support="no">
-+	<mime-type type="chemical/x-turbomole-basis" cm:support="yes">
- 		<_comment>Turbomole basis set</_comment>
- 		<glob pattern="basis"/>
- 		<sub-class-of type="text/plain"/>
-@@ -1432,7 +1432,7 @@
- 		<cm:specification url="http://www.cosmologic.de/data/DOK_HTML/"/>
- 	</mime-type>
- 
--	<mime-type type="chemical/x-turbomole-control" cm:support="no">
-+	<mime-type type="chemical/x-turbomole-control" cm:support="yes">
- 		<_comment>Turbomole control file</_comment>
- 		<glob pattern="control"/>
- 		<sub-class-of type="text/plain"/>
-@@ -1448,7 +1448,7 @@
- 		<cm:specification url="http://www.cosmologic.de/data/DOK_HTML/node230.html"/>
- 	</mime-type>
- 
--	<mime-type type="chemical/x-turbomole-coord" cm:support="no">
-+	<mime-type type="chemical/x-turbomole-coord" cm:support="yes">
- 		<_comment>Turbomole coordinate file</_comment>
- 		<glob pattern="coord"/>
- 		<glob pattern="*.tmol"/>
-@@ -1463,7 +1463,7 @@
- 		<cm:specification url="http://www.cosmologic.de/data/DOK_HTML/"/>
- 	</mime-type>
- 
--	<mime-type type="chemical/x-turbomole-grad" cm:support="no">
-+	<mime-type type="chemical/x-turbomole-grad" cm:support="yes">
- 		<_comment>Turbomole gradient file</_comment>
- 		<glob pattern="gradient"/>
- 		<sub-class-of type="text/plain"/>
-@@ -1511,7 +1511,7 @@
- 		<cm:specification url="http://www.cosmologic.de/data/DOK_HTML/"/>
- 	</mime-type>
- 
--	<mime-type type="chemical/x-turbomole-scfmo" cm:support="no">
-+	<mime-type type="chemical/x-turbomole-scfmo" cm:support="yes">
- 		<_comment>Turbomole SCF MO file</_comment>
- 		<acronym>MO</acronym>
- 		<expanded-acronym>Molecular Orbital</expanded-acronym>
diff --git a/sci-chemistry/chemical-mime-data/metadata.xml b/sci-chemistry/chemical-mime-data/metadata.xml
deleted file mode 100644
index 59742c34e797..000000000000
--- a/sci-chemistry/chemical-mime-data/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<maintainer type="project">
-	<email>sci-chemistry@gentoo.org</email>
-	<name>Gentoo Chemistry Project</name>
-</maintainer>
-<upstream>
-	<remote-id type="sourceforge">chemical-mime</remote-id>
-	<remote-id type="github">dleidert/chemical-mime</remote-id>
-</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/chemtool/Manifest b/sci-chemistry/chemtool/Manifest
deleted file mode 100644
index 60ea9764c148..000000000000
--- a/sci-chemistry/chemtool/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST chemtool-1.6.14.tar.gz 817735 BLAKE2B 065c5069402b5960fc2c9b686a9c0e9954b98c43a1d70385ca56e8407fffbe09fd87023f1f7177140745987c69731766f64a8b8015370ef38593bbcd3f073e64 SHA512 066c83c61aced3134b081767e788143a047889a2fee4b6535c2b0a3166bccc73d75981e1cf35b7bcaa5b8fe2e0227b28693b659decd82f7783cb4082ac6ed2bd
-DIST chemtool.png 1601 BLAKE2B f443547954baf296b15ae8604b84df0a5a23c3bb92df3c0f6f7e8f1d7b7ae67a90a39b9e0a50a4c5105d1f6de2796caf37d67d7a8e872dc026386486109b185b SHA512 3402a3e096dc0f8a40bced0259992478950e5bddd16281cf6b2c8f819f45964d2fd30644f5d6e81c6d72028d5d298c39621369433670f3733d8940be14044a21
diff --git a/sci-chemistry/chemtool/chemtool-1.6.14-r1.ebuild b/sci-chemistry/chemtool/chemtool-1.6.14-r1.ebuild
deleted file mode 100644
index cddf65f0df6c..000000000000
--- a/sci-chemistry/chemtool/chemtool-1.6.14-r1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit autotools desktop
-
-DESCRIPTION="A GTK program for drawing organic molecules"
-HOMEPAGE="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/"
-SRC_URI="http://ruby.chemie.uni-freiburg.de/~martin/chemtool/${P}.tar.gz
-	https://upload.wikimedia.org/wikipedia/commons/5/58/Adamantane_acsv.svg -> chemtool.png"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="emf"
-
-RDEPEND="
-	dev-libs/glib:2
-	>=media-gfx/fig2dev-3.2.9-r1
-	x11-libs/gtk+:2
-	x11-libs/libX11
-	x11-libs/pango
-	emf? ( media-libs/libemf )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-no-underlinking.patch
-	"${FILESDIR}"/${P}-fno-common.patch
-	"${FILESDIR}"/${P}-fix-tests.patch
-)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--enable-undo \
-		--enable-menu \
-		--without-kdedir \
-		$(use_enable emf)
-}
-
-src_install() {
-	default
-
-	insinto /usr/share/chemtool/examples
-	doins -r examples/.
-
-	doicon "${DISTDIR}"/chemtool.png
-	make_desktop_entry chemtool Chemtool chemtool "Education;Science;Chemistry"
-}
diff --git a/sci-chemistry/chemtool/files/chemtool-1.6.14-fix-tests.patch b/sci-chemistry/chemtool/files/chemtool-1.6.14-fix-tests.patch
deleted file mode 100644
index 755ae3f01914..000000000000
--- a/sci-chemistry/chemtool/files/chemtool-1.6.14-fix-tests.patch
+++ /dev/null
@@ -1,6 +0,0 @@
---- /dev/null
-+++ b/src-cht/Makefile.am
-@@ -0,0 +1,3 @@
-+bin_PROGRAMS = cht
-+
-+cht_SOURCES = cht.c
diff --git a/sci-chemistry/chemtool/files/chemtool-1.6.14-fno-common.patch b/sci-chemistry/chemtool/files/chemtool-1.6.14-fno-common.patch
deleted file mode 100644
index d782f8e4a625..000000000000
--- a/sci-chemistry/chemtool/files/chemtool-1.6.14-fno-common.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- a/ct1.h
-+++ b/ct1.h
-@@ -273,12 +273,12 @@
- extern float importfactor;
- extern int importoffset;
- 
--char **intype;
--char **inmode;
--int babelin;
--char **outtype;
--char **outmode;
--int babelout;
-+extern char **intype;
-+extern char **inmode;
-+extern int babelin;
-+extern char **outtype;
-+extern char **outmode;
-+extern int babelout;
- extern char *babel;
- extern GdkGC *mygc[8],*background_gc,*hlgc;
- extern int curpen;
---- a/inout.c
-+++ b/inout.c
-@@ -30,6 +30,13 @@
- extern GdkFont *font[7],*smallfont[7],*symbfont[7],*boldfont[7],*slfont[7];
- #endif
- 
-+char **intype;
-+char **inmode;
-+int babelin;
-+char **outtype;
-+char **outmode;
-+int babelout;
-+
- static char babeloutp[4];
- 
- int
diff --git a/sci-chemistry/chemtool/files/chemtool-1.6.14-no-underlinking.patch b/sci-chemistry/chemtool/files/chemtool-1.6.14-no-underlinking.patch
deleted file mode 100644
index 5d2fe36d6bf1..000000000000
--- a/sci-chemistry/chemtool/files/chemtool-1.6.14-no-underlinking.patch
+++ /dev/null
@@ -1,78 +0,0 @@
- Makefile.am  |    6 ++++--
- configure.ac |   24 ++++--------------------
- 2 files changed, 8 insertions(+), 22 deletions(-)
-
-diff --git a/Makefile.am b/Makefile.am
-index 99dbf8c..931ba16 100644
---- a/Makefile.am
-+++ b/Makefile.am
-@@ -22,10 +22,12 @@ localedir = $(datadir)/locale
- DEFS = -DLOCALEDIR=\"$(localedir)\" @DEFS@
- 
- # Make sure the gettext.h include file is found.
--AM_CPPFLAGS = -I. -I$(srcdir) @GTK_CFLAGS@
-+AM_CPPFLAGS = -I. -I$(srcdir) @GTK_CFLAGS@ @EMFINCL@
- 
- # Link time dependencies.
--LDADD = @LIBINTL@ @GTK_LIBS@ @EMFLIBS@ 
-+LDADD = @LIBINTL@ @GTK_LIBS@ @EMFLIBS@ -lX11
-+
-+AM_CFLAGS = -DGTK2
- 
- # Additional files to be distributed.
- EXTRA_DIST = autogen.sh autoclean.sh
-diff --git a/configure.ac b/configure.ac
-index 6d8c45a..c5fab42 100644
---- a/configure.ac
-+++ b/configure.ac
-@@ -32,32 +32,14 @@ AC_PATH_PROG(PKG_CONFIG, pkg-config, no)
- 
- AC_MSG_CHECKING([for GTK version and compile options ])
- 
--if test x$PKG_CONFIG = xno -o x$enable_gtk1 = xyes ; then
--AM_PATH_GTK(1.0.2, , exit 1)
--else
--if $PKG_CONFIG gtk+-2.0 --cflags ; then
--       GTK_CFLAGS="-DGTK2 `$PKG_CONFIG gtk+-2.0 --cflags` "
--       GTK_LIBS=`$PKG_CONFIG gtk+-2.0 --libs`
--dnl    use_gtk2=yes
--       AC_DEFINE([GTK2], [1], [the GTK2 library])
--       enable_stockgtk=yes
--else
--if $PKG_CONFIG --cflags gtk+ ; then
--	GTK_CFLAGS=`$PKG_CONFIG gtk+ --cflags`       
--	GTK_LIBS=`$PKG_CONFIG gtk+ --libs`
--dnl    use_gtk2=no
--fi
--fi
--fi
--
--dnl AC_MSG_RESULT using GTK2 : $use_gtk2
-+PKG_CHECK_MODULES([GTK],[gtk+-2.0])
- 
- dnl Checks for header files.
- AC_PATH_XTRA
- AC_HEADER_DIRENT
- AC_HEADER_STDC
- 
--LDFLAGS="$X_LIBS"
-+LDFLAGS+="$X_LIBS"
- AC_CHECK_LIB([X11],[XOpenDisplay])
- dnl just an ugly hack to work around the more aggressive header checks
- dnl in recent autoconf. Not sure if we should really rely on include
-@@ -184,6 +166,7 @@ if test x$enable_emf = xyes; then
- 	AC_MSG_RESULT(yes)
- 	AC_DEFINE([EMF], [1], [use optional libEMF instead of fig2dev for EMF output])
- 	EMFLIBS="-lEMF -lstdc++"
-+	EMFINCL="-I${includedir}libEMF"
- else
- 	AC_MSG_RESULT(no)
- 	EMFLIBS=""
-@@ -221,6 +204,7 @@ AC_SUBST(localedir)
- AC_SUBST(kdemimedir)
- AC_SUBST(gnomemimedir)
- AC_SUBST(EMFLIBS)
-+AC_SUBST(EMFINCL)
- AC_SUBST(MYGTKSRCS)
- AC_SUBST(MYGTKOBJS)
- AC_SUBST(GTK_CFLAGS)
diff --git a/sci-chemistry/chemtool/metadata.xml b/sci-chemistry/chemtool/metadata.xml
deleted file mode 100644
index 8847960e68ca..000000000000
--- a/sci-chemistry/chemtool/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <use>
-    <flag name="emf">EMF export support</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-chemistry/clashlist/Manifest b/sci-chemistry/clashlist/Manifest
deleted file mode 100644
index f2d8ddced6f2..000000000000
--- a/sci-chemistry/clashlist/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST molprobity-3.17.tgz 26429898 BLAKE2B f2ed8f71c4f71c19aac6278eed40cba0db53e88dc1be7ccb6e3e831d4202456822efe93ded2cc8ca3226efb9ef10999895b191e8b5d5188d577b78c9fa5a8c66 SHA512 a6e986f285ff7e8d167e2d1c935a55b080446c9809d352c95e2ffa32265892b59cd1611730e75ca88aa28387495d3ebd84226e1a9cdd33f0b27b1a8a1b6a469f
diff --git a/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild b/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild
deleted file mode 100644
index 93a119fb6439..000000000000
--- a/sci-chemistry/clashlist/clashlist-3.17-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Build lists of van der Waals clashes from an input PDB file"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
-SRC_URI="mirror://gentoo/molprobity-${PV}.tgz"
-
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-RDEPEND="
-	>=sci-chemistry/cluster-1.3.081231-r1
-	sci-chemistry/probe"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}"
-
-src_prepare() {
-	default
-	sed \
-		-e 's: cluster : molprobity-cluster :g' \
-		-i molprobity3/bin/clashlist || die
-}
-
-src_install() {
-	dobin molprobity3/bin/clashlist
-}
diff --git a/sci-chemistry/clashlist/metadata.xml b/sci-chemistry/clashlist/metadata.xml
deleted file mode 100644
index 64ef25fc38ad..000000000000
--- a/sci-chemistry/clashlist/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-	Clashlist is a simple UNIX script which uses the awk facility along with
-	the programs Probe and Cluster to build lists of van der Waals clashes
-	from an input PDB-format molecular data file (with H atoms). These lists
-	are organized such that collections of interacting residues are grouped
-	together, sorted by the worst clash. For the purposes of this analysis,
-	a clash is defined as a van der Waals overlap &gt;= 0.4 A.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/cluster/Manifest b/sci-chemistry/cluster/Manifest
deleted file mode 100644
index 65945336c332..000000000000
--- a/sci-chemistry/cluster/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST cluster.1.3.081231.src.tgz 8860 BLAKE2B 4bfc6fe9efa3dbde106ad12df7b23990a748fee5446f16fe4e3cf9232697313bd513366a2283ac732cf0c7306ac65af578155328d0b04e4b5b99536553c9b903 SHA512 af5851ef467458d45ee5f2309c6344ae16145ac371a1b9d0a3d8b5769a18b98877cf7cb65b85f71108d927b0e6c363e06b85a67e7cb2e5e0b41af375cb2db7ac
diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
deleted file mode 100644
index d48243b944d8..000000000000
--- a/sci-chemistry/cluster/cluster-1.3.081231-r1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Build lists of collections of interacting items"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
-SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz"
-S="${WORKDIR}"/${PN}1.3src
-
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-ldflags.patch
-	"${FILESDIR}"/${PV}-includes.patch
-)
-
-src_configure() {
-	tc-export CXX
-	default
-}
-
-src_install() {
-	newbin ${PN} molprobity-${PN}
-	dodoc README.cluster
-}
diff --git a/sci-chemistry/cluster/cluster-1.3.081231-r2.ebuild b/sci-chemistry/cluster/cluster-1.3.081231-r2.ebuild
deleted file mode 100644
index 50bc89dc75f4..000000000000
--- a/sci-chemistry/cluster/cluster-1.3.081231-r2.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Build lists of collections of interacting items"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/index.php"
-SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/${PN}/${PN}.${PV}.src.tgz"
-S="${WORKDIR}"/${PN}1.3src
-
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-ldflags.patch
-	"${FILESDIR}"/${PV}-includes.patch
-	"${FILESDIR}"/${PV}-drop-registers.patch
-)
-
-src_configure() {
-	tc-export CXX
-	default
-}
-
-src_install() {
-	newbin ${PN} molprobity-${PN}
-	dodoc README.cluster
-}
diff --git a/sci-chemistry/cluster/files/1.3.081231-drop-registers.patch b/sci-chemistry/cluster/files/1.3.081231-drop-registers.patch
deleted file mode 100644
index c00922591faa..000000000000
--- a/sci-chemistry/cluster/files/1.3.081231-drop-registers.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Bug: https://bugs.gentoo.org/898132
---- a/utility.cpp
-+++ b/utility.cpp
-@@ -107,8 +107,8 @@ int compArgStr(const char *str, const char *arg, int min) {
- }
- 
- int parseInteger(const char *str, int start, int len) {
--	register int value = 0;
--	register char ch;
-+	int value = 0;
-+	char ch;
- 	int neg = 0, inside = 0;
- 
- 	if (!str || start < 0) { return 0; }
-@@ -136,7 +136,7 @@ int parseInteger(const char *str, int start, int len) {
- double parseReal(const char *str, int start, int len) {
-    double value = 0.0, scale = 1.0, expscale = 1.0, expfact = 10.0;
-    int expval = 0;
--   register char ch;
-+   char ch;
-    int inside = 0, infract = 0, inexp = 0, insn = 0, esn = 0;
- 
-    if (!str || start < 0) { return 0; }
diff --git a/sci-chemistry/cluster/files/1.3.081231-includes.patch b/sci-chemistry/cluster/files/1.3.081231-includes.patch
deleted file mode 100644
index a5586a540a4f..000000000000
--- a/sci-chemistry/cluster/files/1.3.081231-includes.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/cluster.cpp b/cluster.cpp
-index 0a8c3c1..1384949 100644
---- a/cluster.cpp
-+++ b/cluster.cpp
-@@ -24,6 +24,7 @@
- #include <iostream>
- #include <vector>
- #include <string>
-+#include <cstring>
- 
- #include <iostream>
- #include <fstream>
diff --git a/sci-chemistry/cluster/files/1.3.081231-ldflags.patch b/sci-chemistry/cluster/files/1.3.081231-ldflags.patch
deleted file mode 100644
index 1b99f6d662f2..000000000000
--- a/sci-chemistry/cluster/files/1.3.081231-ldflags.patch
+++ /dev/null
@@ -1,41 +0,0 @@
- Makefile |   12 ++++++------
- 1 files changed, 6 insertions(+), 6 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 7892054..929564b 100644
---- a/Makefile
-+++ b/Makefile
-@@ -3,27 +3,27 @@ PROG_FLGS   = -D BOOLPREDEFINED
- 
- SRCS = cluster.cpp DisjointSets.cpp utility.cpp
- 
--CFLAGS = $(OPT) $(DEBUG) $(PROG_FLGS)
-+CXXFLAGS += $(OPT) $(DEBUG) $(PROG_FLGS)
- 
- LFLAGS = 
- 
- OBJLIST = cluster.o DisjointSets.o utility.o
- 
--CXX		= g++
-+CXX		?= g++
- 
- .cpp.o:
--	$(CXX) -c $*.cpp $(CFLAGS)
-+	$(CXX) $(CXXFLAGS) -c $*.cpp
- 
--OPT             = -O3
-+OPT             = 
- DEBUG           = $(CXXDEBUGFLAGS)
- 
- all:    cluster
- 
- cluster:    $(OBJLIST)
--	$(CXX) -o $@ $(OBJLIST) $(LFLAGS)
-+	$(CXX) $(LDFLAGS) -o $@ $(OBJLIST)
- 
- depend:
--	makedepend -- $(CFLAGS) -- $(SRCS)
-+	makedepend -- $(CXXFLAGS) -- $(SRCS)
- 
- clean:
- 	@rm -rf *.o *.ckp ii_files
diff --git a/sci-chemistry/cluster/metadata.xml b/sci-chemistry/cluster/metadata.xml
deleted file mode 100644
index 818c6312ce9e..000000000000
--- a/sci-chemistry/cluster/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-  Cluster is a simple UNIX C++ program to build lists of collections
-  of interacting items from records containing interacting pairs
-  and larger fragments.
-
-  It reads in lines consisting of two or more names and output
-  connected clusters of names. Each line of output is
-  prefixed with a cluster number, the size of the cluster
-  and an optional name string.
-  </longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
deleted file mode 100644
index 86e5cc65df76..000000000000
--- a/sci-chemistry/dssp/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811
-DIST dssp-4.5.6.tar.gz 223229 BLAKE2B a5f60e1ea8d8ff8c9e63b9e68464ba81a705bbe2d87ebeaab7f13c9c2c05557b5d5aacf832f0f5f85e66ef653751cb9d53a07d6667fcbd8a7e6aae21a2d753f7 SHA512 06e1d74f5a39673560bd174032523018f063c8c6f2aaad21c4800334d39f81e5b8f68c78a184a14ff33897d9e6bde9810d7efd5f4c769a85705302bc480afdf4
-DIST dssp-4.5.8.tar.gz 225240 BLAKE2B 57602edf8981646716a2f882eff027f67a0e25128d50f5c2c4df53ef37682937879b0e42f41fcc5ea0741e203ccbe91d68e7f9c7022a2672f38f5f50101c5400 SHA512 981ac33060284a548d259fd854bcfb9a8ad10b5867379946ed4288e018ab3f7ea28ef8f3270d1a3db3e43c76d761ca920df6b7bf40e10fe40de37917b3d9e174
-DIST dssp-4.6.1.tar.gz 247855 BLAKE2B a35500bddfb91156e1cc29f95365ad327581f982310d923862f3e32b60af15f71bfca0cf278cd75c111b03d2ae06f7ecb27b33eee4091eeb2725fc77f0cb3a28 SHA512 3152e40ad7086ced6a9b27ad7459ae5c18dc2092aab7fdda12fd06ea6823437f1aa0e211218f85b6a3b2f81cd2614aab0d940b806ab4c2fe907a18352b6b2c30
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
deleted file mode 100644
index 2aa55a52cf95..000000000000
--- a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/"
-SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz"
-
-LICENSE="Boost-1.0"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-RDEPEND="dev-libs/boost:=[bzip2,zlib]"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.1.0-gentoo.patch
-	"${FILESDIR}"/${PN}-2.2.1-boost-1.65-tr1-removal.patch
-)
-
-src_configure() {
-	tc-export CXX
-
-	cat >> make.config <<- EOF || die
-		BOOST_LIB_DIR = "${EPREFIX}/usr/$(get_libdir)"
-		BOOST_INC_DIR = "${EPREFIX}/usr/include"
-	EOF
-}
-
-src_install() {
-	dobin mkdssp
-	dosym mkdssp /usr/bin/dssp
-	doman doc/mkdssp.1
-	dodoc README.txt changelog
-
-	doenvd "${FILESDIR}"/30-${PN}
-}
diff --git a/sci-chemistry/dssp/dssp-4.5.6.ebuild b/sci-chemistry/dssp/dssp-4.5.6.ebuild
deleted file mode 100644
index cae362ee3d3d..000000000000
--- a/sci-chemistry/dssp/dssp-4.5.6.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit cmake
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
-SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-# doc disabled as it only generates a PDF from the manpage for now
-# https://github.com/PDB-REDO/dssp/issues/64
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
-	dev-libs/boost:=[zlib]
-	>=dev-libs/libmcfp-1.4.2
-	>=sci-libs/libcifpp-9:=
-"
-BDEPEND="${CDEPEND}
-	dev-cpp/catch:0
-"
-#	doc? (
-#		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
-#		dev-python/weasyprint
-#	)
-RDEPEND="${CDEPEND}"
-
-#src_prepare() {
-#	# wkhtmltopdf is not available on Gentoo
-#	sed -i -e \
-#		's/-t html/-t html --pdf-engine=weasyprint/' \
-#		CMakeLists.txt
-#	cmake_src_prepare
-#}
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_LIBRARY=YES
-		#-DBUILD_DOCUMENTATION=$(usex doc)
-		-DBUILD_DOCUMENTATION=NO
-		-DBUILD_TESTING=$(usex test)
-	)
-	cmake_src_configure
-}
diff --git a/sci-chemistry/dssp/dssp-4.5.8.ebuild b/sci-chemistry/dssp/dssp-4.5.8.ebuild
deleted file mode 100644
index 24b75290b6b0..000000000000
--- a/sci-chemistry/dssp/dssp-4.5.8.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit cmake
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
-SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-# doc disabled as it only generates a PDF from the manpage for now
-# https://github.com/PDB-REDO/dssp/issues/64
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
-	>=dev-libs/boost-1.84:=[zlib]
-	>=dev-libs/libmcfp-1.4.2
-	>=sci-libs/libcifpp-9.0.6:=
-"
-BDEPEND="${CDEPEND}
-	dev-cpp/catch:0
-"
-#	doc? (
-#		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
-#		dev-python/weasyprint
-#	)
-RDEPEND="${CDEPEND}"
-
-#src_prepare() {
-#	# wkhtmltopdf is not available on Gentoo
-#	sed -i -e \
-#		's/-t html/-t html --pdf-engine=weasyprint/' \
-#		CMakeLists.txt
-#	cmake_src_prepare
-#}
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_LIBRARY=YES
-		#-DBUILD_DOCUMENTATION=$(usex doc)
-		-DBUILD_DOCUMENTATION=NO
-		-DBUILD_TESTING=$(usex test)
-	)
-	cmake_src_configure
-}
diff --git a/sci-chemistry/dssp/dssp-4.6.1.ebuild b/sci-chemistry/dssp/dssp-4.6.1.ebuild
deleted file mode 100644
index 5ea3099341df..000000000000
--- a/sci-chemistry/dssp/dssp-4.6.1.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit cmake
-
-DESCRIPTION="The protein secondary structure standard"
-HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
-SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-# doc disabled as it only generates a PDF from the manpage for now
-# https://github.com/PDB-REDO/dssp/issues/64
-IUSE="test"
-RESTRICT="!test? ( test )"
-
-CDEPEND="
-	>=dev-libs/boost-1.86:=[zlib]
-	>=dev-libs/libmcfp-1.4.2
-	>=sci-libs/libcifpp-9.0.6:=
-"
-BDEPEND="${CDEPEND}
-	dev-cpp/catch:0
-"
-#	doc? (
-#		|| ( app-text/pandoc-bin[pandoc-symlink] app-text/pandoc )
-#		dev-python/weasyprint
-#	)
-RDEPEND="${CDEPEND}"
-
-#src_prepare() {
-#	# wkhtmltopdf is not available on Gentoo
-#	sed -i -e \
-#		's/-t html/-t html --pdf-engine=weasyprint/' \
-#		CMakeLists.txt
-#	cmake_src_prepare
-#}
-
-src_configure() {
-	local mycmakeargs=(
-		-DINSTALL_LIBRARY=YES
-		#-DBUILD_DOCUMENTATION=$(usex doc)
-		-DBUILD_DOCUMENTATION=NO
-		-DBUILD_TESTING=$(usex test)
-	)
-	cmake_src_configure
-}
diff --git a/sci-chemistry/dssp/files/30-dssp b/sci-chemistry/dssp/files/30-dssp
deleted file mode 100644
index e0a5e0ce5626..000000000000
--- a/sci-chemistry/dssp/files/30-dssp
+++ /dev/null
@@ -1 +0,0 @@
-DSSP=/usr/bin/dssp
-\ No newline at end of file
diff --git a/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch b/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch
deleted file mode 100644
index 15198feaea19..000000000000
--- a/sci-chemistry/dssp/files/dssp-2.1.0-gentoo.patch
+++ /dev/null
@@ -1,60 +0,0 @@
- makefile | 21 +++++++++++----------
- 1 file changed, 11 insertions(+), 10 deletions(-)
-
-diff --git a/makefile b/makefile
-index d6f335e..68736c6 100644
---- a/makefile
-+++ b/makefile
-@@ -25,22 +25,23 @@ BOOST_LIBS			= thread filesystem program_options iostreams system
- LIBS				= $(BOOST_LIBS:%=boost_%$(BOOST_LIB_SUFFIX)) z bz2
- 
- DEFINES				= USE_COMPRESSION LINUX VERSION='"$(VERSION)"'
--CXX					= g++
-+CXX					?= g++
- 
--CFLAGS				+= $(INC_DIR:%=-I%) -iquote src -g -Wall -Wno-multichar -pthread
--LDOPTS				+= $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -g -pthread
-+CPPFLAGS				+= $(INC_DIR:%=-I%) -iquote src
-+CXXFLAGS				+= -Wall -Wno-multichar -pthread
-+LDOPTS				+= $(LIB_DIR:%=-L%) $(LIBS:%=-l%) -pthread
- 
- OBJ_DIR				= obj
- 
- ifeq ($(DEBUG),1)
- OBJ_DIR				:= $(OBJ_DIR).dbg
--CFLAGS				+= -g3
-+CFLAGS				+=
- else
- DEFINES				+= NDEBUG
--CFLAGS				+= -O3
-+CFLAGS				+=
- endif
- 
--CFLAGS				+= $(DEFINES:%=-D%)
-+CPPFLAGS				+= $(DEFINES:%=-D%)
- 
- DIST_NAME			= dssp-$(VERSION)
- 
-@@ -50,18 +51,18 @@ OBJECTS = $(OBJ_DIR)/mkdssp.o $(OBJ_DIR)/dssp.o $(OBJ_DIR)/primitives-3d.o $(OBJ
- 
- mkdssp: $(OBJECTS)
- 	@ echo linking $@
--	@ $(CXX) -static -o $@ $^ $(LDOPTS)
-+	$(CXX) $(LDFLAGS) -o $@ $^ $(LDOPTS)
- 
- include $(OBJECTS:%.o=%.d)
- 
- $(OBJECTS:.o=.d):
- 
--$(OBJ_DIR):
-+OBJ_DIR:
- 	@ mkdir -p $(OBJ_DIR)
- 
--$(OBJ_DIR)/%.o: %.cpp | $(OBJ_DIR)
-+$(OBJ_DIR)/%.o: %.cpp OBJ_DIR
- 	@ echo compiling $@
--	@ $(CXX) -MD -c -o $@ $< $(CFLAGS)
-+	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -MD -c -o $@ $<
- 
- clean:
- 	install -d $(BIN_DIR) $(MAN_DIR)
diff --git a/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch b/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch
deleted file mode 100644
index 4eee6b567349..000000000000
--- a/sci-chemistry/dssp/files/dssp-2.2.1-boost-1.65-tr1-removal.patch
+++ /dev/null
@@ -1,82 +0,0 @@
---- a/src/dssp.cpp
-+++ b/src/dssp.cpp
-@@ -73,7 +73,7 @@
- 
- 	double alpha;
- 	char chirality;
--	tr1::tie(alpha,chirality) = residue.Alpha();
-+	boost::tie(alpha,chirality) = residue.Alpha();
- 	
- 	uint32 bp[2] = {};
- 	char bridgelabel[2] = { ' ', ' ' };
---- a/src/primitives-3d.cpp
-+++ b/src/primitives-3d.cpp
-@@ -153,7 +153,7 @@
- 
- // --------------------------------------------------------------------
- 
--tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
-+boost::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q)
- {
- 	if (q.R_component_1() > 1)
- 		q = Normalize(q);
-@@ -169,7 +169,7 @@
- 	
- 	MPoint axis(q.R_component_2() / s, q.R_component_3() / s, q.R_component_4() / s);
- 
--	return tr1::make_tuple(angle, axis);
-+	return boost::make_tuple(angle, axis);
- }
- 
- MPoint CenterPoints(vector<MPoint>& points)
---- a/src/primitives-3d.h
-+++ b/src/primitives-3d.h
-@@ -9,7 +9,7 @@
- 
- #include <vector>
- 
--#include <boost/tr1/tuple.hpp>
-+#include <boost/tuple/tuple.hpp>
- #include <boost/math/quaternion.hpp>
- 
- typedef boost::math::quaternion<double> MQuaternion;
-@@ -64,7 +64,7 @@
- 
- MQuaternion Normalize(MQuaternion q);
- 
--std::tr1::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
-+boost::tuple<double,MPoint> QuaternionToAngleAxis(MQuaternion q);
- MPoint Centroid(std::vector<MPoint>& points);
- MPoint CenterPoints(std::vector<MPoint>& points);
- MQuaternion AlignPoints(const std::vector<MPoint>& a, const std::vector<MPoint>& b);
---- a/src/structure.cpp
-+++ b/src/structure.cpp
-@@ -544,7 +544,7 @@
- 	return result;
- }
- 
--tr1::tuple<double,char> MResidue::Alpha() const
-+boost::tuple<double,char> MResidue::Alpha() const
- {
- 	double alhpa = 360;
- 	char chirality = ' ';
-@@ -558,7 +558,7 @@
- 		else
- 			chirality = '+';
- 	}
--	return tr1::make_tuple(alhpa, chirality);
-+	return boost::make_tuple(alhpa, chirality);
- }
- 
- double MResidue::Kappa() const
---- a/src/structure.h
-+++ b/src/structure.h
-@@ -168,7 +168,7 @@
- 
- 	double				Phi() const;
- 	double				Psi() const;
--	std::tr1::tuple<double,char>
-+	boost::tuple<double,char>
- 						Alpha() const;
- 	double				Kappa() const;
- 	double				TCO() const;
diff --git a/sci-chemistry/dssp/metadata.xml b/sci-chemistry/dssp/metadata.xml
deleted file mode 100644
index e3c02bf1bb6f..000000000000
--- a/sci-chemistry/dssp/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>pacho@gentoo.org</email>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">PDB-REDO/dssp</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/easychem/Manifest b/sci-chemistry/easychem/Manifest
deleted file mode 100644
index 8041463530c5..000000000000
--- a/sci-chemistry/easychem/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST easychem-0.6.tar.gz 265458 BLAKE2B 673100e6d01653ea16a70a8384dc8c598c8e113e241851b19882b333c95e6118fc180a1123e770c021245417640310a05a9026e55a57ae589bde59cf9e5b4766 SHA512 83f877d1813287592a460f4dc3769feda88e45d8f77cd728c4055b60521babe253b4432033941ff429c753cfe675a642714052a01736534147398d6972e47051
diff --git a/sci-chemistry/easychem/easychem-0.6-r2.ebuild b/sci-chemistry/easychem/easychem-0.6-r2.ebuild
deleted file mode 100644
index a4655e28aea5..000000000000
--- a/sci-chemistry/easychem/easychem-0.6-r2.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Chemical structure drawing program - focused on presentation"
-HOMEPAGE="http://easychem.sourceforge.net/"
-SRC_URI="https://downloads.sourceforge.net/easychem/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-
-RDEPEND="
-	app-text/ghostscript-gpl
-	media-gfx/pstoedit
-	x11-libs/gtk+:2
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-lang/perl
-	virtual/pkgconfig
-"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-gentoo.patch
-	"${FILESDIR}"/${PN}-0.6-clang16-fix.patch
-)
-
-src_prepare() {
-	default
-	tc-export CC
-}
-
-src_compile() {
-	ln -s Makefile.linux Makefile || die
-	DGS_PATH="${EPREFIX}"/usr/bin DPSTOEDIT_PATH="${EPREFIX}"/usr/bin \
-		C_FLAGS="${CFLAGS}" emake -e
-}
-
-src_install() {
-	dobin easychem
-	dodoc TODO
-}
diff --git a/sci-chemistry/easychem/files/0.6-gentoo.patch b/sci-chemistry/easychem/files/0.6-gentoo.patch
deleted file mode 100644
index be6070603086..000000000000
--- a/sci-chemistry/easychem/files/0.6-gentoo.patch
+++ /dev/null
@@ -1,63 +0,0 @@
---- a/Makefile.linux
-+++ b/Makefile.linux
-@@ -1,5 +1,5 @@
- # The C compiler
--CC=gcc
-+CC ?= gcc
- 
- # The following line must be uncommented if you want to specify a place
- # where the 'gs' (or 'pstoedit') program is.
-@@ -25,11 +25,10 @@ GTK_LIBS=`pkg-config --libs gtk+-2.0`
- # The list of important files
- OBJECTS=auxi.o bonds.o easychem.o export.o dialogs.o detect.o library.o drawing.o
- 
--all: easychem po/
-+all: easychem po
- 
--easychem: postscript/ graph/ $(OBJECTS)
--	$(CC) -o easychem $(OBJECTS) $(GTK_LIBS) $(C_FLAGS)
--	strip easychem
-+easychem: postscript graph $(OBJECTS)
-+	$(CC) $(C_FLAGS) $(LDFLAGS) -o easychem $(OBJECTS) $(GTK_LIBS) -lm
- 
- clean: FORCE
- 	-cd graph; make clean
-@@ -37,7 +36,7 @@ clean: FORCE
- 	-cd po; make clean
- 	-rm $(OBJECTS) easychem
- 
--export.o: export.c common.h bonds.h postscript/
-+export.o: export.c common.h bonds.h postscript
- 	$(CC) $(GTK_FLAGS) $(C_FLAGS) -c export.c
- bonds.o: bonds.c common.h bonds.h
- 	$(CC) $(GTK_FLAGS) $(C_FLAGS) -c bonds.c
-@@ -49,20 +48,22 @@ library.o: library.c common.h library.h
- 	$(CC) $(GTK_FLAGS) $(C_FLAGS) -c library.c
- drawing.o: drawing.c common.h drawing.h
- 	$(CC) $(GTK_FLAGS) $(C_FLAGS) -c drawing.c
--dialogs.o: dialogs.c common.h dialogs.h graph/
-+dialogs.o: dialogs.c common.h dialogs.h graph
- 	$(CC) $(GTK_FLAGS) $(C_FLAGS) -c dialogs.c
- detect.o: detect.c common.h detect.h
- 	$(CC) $(GTK_FLAGS) $(C_FLAGS) -c detect.c
- 
- # The rules for subdirectories
--graph/: FORCE
--	cd graph; make all
-+graph:
-+	+make -C $@
- 
--postscript/: FORCE
--	cd postscript; make all
-+postscript:
-+	+make -C $@
- 
--po/: FORCE
--	cd po; make all
-+po:
-+	+make -C $@
- 
- # This is used to force an update
- FORCE:
-+
-+.PHONY: graph postscript po
diff --git a/sci-chemistry/easychem/files/easychem-0.6-clang16-fix.patch b/sci-chemistry/easychem/files/easychem-0.6-clang16-fix.patch
deleted file mode 100644
index a8a82f64de24..000000000000
--- a/sci-chemistry/easychem/files/easychem-0.6-clang16-fix.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-Bug: https://bugs.gentoo.org/886085
---- a/easychem.c
-+++ b/easychem.c
-@@ -34,6 +34,7 @@
- #include <stdlib.h>
- #include <string.h>
- #include <locale.h>
-+#include <libintl.h>
- #include <math.h>
- #include <errno.h>
- #include <gtk/gtk.h>
diff --git a/sci-chemistry/easychem/metadata.xml b/sci-chemistry/easychem/metadata.xml
deleted file mode 100644
index 7451327b470e..000000000000
--- a/sci-chemistry/easychem/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-		EasyChem is a program designed to draw chemical molecules, written under
-		Linux using Gtk+ 2.4. It is implemented with a strong focus on producing
-		press quality molecules. Easychem can be a little more difficult to learn to
-		use, but when mastered it can be very fast and powerful. It can draw
-		ornaments easily, and exports to EPS with LaTeX fonts among other things.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">easychem</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/elem/Manifest b/sci-chemistry/elem/Manifest
deleted file mode 100644
index 56d836adeddd..000000000000
--- a/sci-chemistry/elem/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST elem-src-1.0.3-Linux.tgz 58364 BLAKE2B bdedb844ca62f928fdae5b01b13b88e5f43f5e37f40b47f7b8b9b1a2cb11053b9aefa7b1b4bb78a8632f3329f37afeadfc34eddee1b9f7cd109bee89aa9cdf32 SHA512 24b163c5cc3019c1beb677ce7b432b21289352f7cdbad686ab9161c628d3aadbb90d8abf9bef49f1c7d077b706bbd4ea6b381f356cc85adf907f3c15a4f4893c
diff --git a/sci-chemistry/elem/elem-1.0.3-r3.ebuild b/sci-chemistry/elem/elem-1.0.3-r3.ebuild
deleted file mode 100644
index 7d06be84243b..000000000000
--- a/sci-chemistry/elem/elem-1.0.3-r3.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="periodic table of the elements"
-HOMEPAGE="http://elem.sourceforge.net/"
-SRC_URI="https://downloads.sourceforge.net/elem/${PN}-src-${PV}-Linux.tgz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-DEPEND="x11-libs/xforms"
-RDEPEND="${DEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-fix-build-system.patch
-	"${FILESDIR}"/${P}-missing-stdlib.patch
-	"${FILESDIR}"/${P}-fno-common.patch
-)
-
-src_configure() {
-	tc-export CC
-}
-
-src_compile() {
-	emake all
-}
-
-src_install() {
-	dobin elem elem-de elem-en
-
-	rm -rf doc/CVS || die
-	HTML_DOCS=( doc/. )
-	einstalldocs
-}
diff --git a/sci-chemistry/elem/files/elem-1.0.3-fix-build-system.patch b/sci-chemistry/elem/files/elem-1.0.3-fix-build-system.patch
deleted file mode 100644
index b89f226e46a7..000000000000
--- a/sci-chemistry/elem/files/elem-1.0.3-fix-build-system.patch
+++ /dev/null
@@ -1,65 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -1,8 +1,4 @@
--COMPILER=gcc
--LIBS = -lm -L./  -lforms -L/usr/X11R6/lib -lX11 -lnsl 
--INCLUDE=-I/usr/X11R6/include/X11 -I/usr/include -I/usr/X11R6/include -I/usr/local/X11/include/ -I/usr/X/include/
--FLAGS = -g -O2
--DESTDIR =
-+LIBS = -lm -L./ -lforms
- 
- 
- default:
-@@ -35,7 +31,7 @@
- 	@echo "erzeuge deutsche Version von elem"
- 
- elem-de: elem_main_de.o elem_cb_de.o elem_de.o deutsch.h
--	${COMPILER} ${FLAGS} -o elem-de elem_main_de.o elem_cb_de.o elem_de.o ${LIBS} -DDEUTSCH
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o elem-de elem_main_de.o elem_cb_de.o elem_de.o $(LIBS)
- 
- 
- 
-@@ -43,34 +39,34 @@
- 	@echo "creating english version of elem"
- 
- elem-en: elem_main_en.o elem_cb_en.o elem_en.o english.h
--	${COMPILER} ${FLAGS} -o elem-en elem_main_en.o elem_cb_en.o elem_en.o ${LIBS} -DENGLISH
-+	$(CC) $(LDFLAGS) $(CFLAGS) -o elem-en elem_main_en.o elem_cb_en.o elem_en.o $(LIBS)
- 
- static-de : elem_main_de.o elem_cb_de.o elem_de.o
--	${COMPILER} ${FLAGS} -static -o elem-static-de elem_main_de.o elem_cb_de.o elem_de.o  ${LIBS} -DDEUTSCH
-+	$(CC) $(LDFLAGS) $(CFLAGS) -static -o elem-static-de elem_main_de.o elem_cb_de.o elem_de.o $(LIBS)
- 
- static-en : elem_main_en.o elem_cb_en.o elem_en.o
--	${COMPILER} ${FLAGS} -static -o elem-static-en elem_main_en.o elem_cb_en.o elem_en.o  ${LIBS} -DENGLISH
-+	$(CC) $(LDFLAGS) $(CFLAGS) -static -o elem-static-en elem_main_en.o elem_cb_en.o elem_en.o $(LIBS)
- 
- 
- 
- 
- elem_main_de.o : elem_main.c elem.h deutsch.h
--	${COMPILER} ${FLAGS} -DDEUTSCH -o elem_main_de.o -c elem_main.c ${INCLUDE}
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -DDEUTSCH -o elem_main_de.o -c elem_main.c
- 
- elem_main_en.o : elem_main.c elem.h english.h
--	${COMPILER} ${FLAGS} -DENGLISH -o elem_main_en.o -c elem_main.c ${INCLUDE}
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -DENGLISH -o elem_main_en.o -c elem_main.c
- 
- 
- elem_cb_de.o : elem_cb.c elem.h deutsch.h
--	${COMPILER} ${FLAGS} -DDEUTSCH -o elem_cb_de.o -c elem_cb.c ${INCLUDE}
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -DDEUTSCH -o elem_cb_de.o -c elem_cb.c
- elem_cb_en.o : elem_cb.c elem.h english.h
--	${COMPILER} ${FLAGS} -DENGLISH -o elem_cb_en.o -c elem_cb.c ${INCLUDE}
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -DENGLISH -o elem_cb_en.o -c elem_cb.c
- 
- 
- elem_de.o : elem.c elem.h
--	${COMPILER} ${FLAGS} -DDEUTSCH  -o elem_de.o -c elem.c ${INCLUDE}
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -DDEUTSCH  -o elem_de.o -c elem.c
- elem_en.o : elem.c elem.h
--	${COMPILER} ${FLAGS} -DENGLISH  -o elem_en.o -c elem.c ${INCLUDE}
-+	$(CC) $(CFLAGS) $(CPPFLAGS) -DENGLISH  -o elem_en.o -c elem.c
- 
- 
- install-de: deutsch
diff --git a/sci-chemistry/elem/files/elem-1.0.3-fno-common.patch b/sci-chemistry/elem/files/elem-1.0.3-fno-common.patch
deleted file mode 100644
index 402ae0790587..000000000000
--- a/sci-chemistry/elem/files/elem-1.0.3-fno-common.patch
+++ /dev/null
@@ -1,24 +0,0 @@
---- a/elem.c
-+++ b/elem.c
-@@ -11,6 +11,9 @@
- #include "deutsch.h"
- #endif
- 
-+double amsumme;
-+FL_OBJECT *massensumme;
-+
- 
- 
- FD_Periodensystem *create_form_Periodensystem(void)
---- a/elem.h
-+++ b/elem.h
-@@ -154,7 +154,7 @@ typedef struct {
-   void *vdata;
-   long ldata;
- } FD_Periodensystem;
--double amsumme;
-+extern double amsumme;
- extern FD_Periodensystem * create_form_Periodensystem(void);
--        FL_OBJECT *massensumme;
-+extern FL_OBJECT *massensumme;
- #endif /* FD_Periodensystem_h_ */
diff --git a/sci-chemistry/elem/files/elem-1.0.3-missing-stdlib.patch b/sci-chemistry/elem/files/elem-1.0.3-missing-stdlib.patch
deleted file mode 100644
index e1937734a51c..000000000000
--- a/sci-chemistry/elem/files/elem-1.0.3-missing-stdlib.patch
+++ /dev/null
@@ -1,9 +0,0 @@
---- a/elem_cb.c
-+++ b/elem_cb.c
-@@ -1,5 +1,6 @@
- #include "forms.h"
- #include "elem.h"
-+#include <stdlib.h>
- #include <string.h>
- 
- 
diff --git a/sci-chemistry/elem/metadata.xml b/sci-chemistry/elem/metadata.xml
deleted file mode 100644
index 762d19498c85..000000000000
--- a/sci-chemistry/elem/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">elem</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/gelemental/Manifest b/sci-chemistry/gelemental/Manifest
deleted file mode 100644
index d9f9db82dac5..000000000000
--- a/sci-chemistry/gelemental/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gelemental-2.0.2.tar.gz 775839 BLAKE2B 642a868400ed362539182f7ebf1b034872018e93d7d797acbdef4ca4d2faafd44a72f16ff15273cd49152caf702b1e973a35ce6f119a85400b87664351c6ed56 SHA512 52304622df0c2edc002f17a21502875a7bd6b0d98ed7109363500e122e2947f364f2457c9425740ce4c5b063903eafd92ae04cfda05ddc8a3685c1ec92fdb8b1
diff --git a/sci-chemistry/gelemental/gelemental-2.0.2-r1.ebuild b/sci-chemistry/gelemental/gelemental-2.0.2-r1.ebuild
deleted file mode 100644
index 2cb434778c96..000000000000
--- a/sci-chemistry/gelemental/gelemental-2.0.2-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools flag-o-matic xdg
-
-DESCRIPTION="Periodic table viewer with detailed information on the chemical elements"
-HOMEPAGE="https://github.com/ginggs/gelemental/"
-SRC_URI="https://github.com/ginggs/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3 MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="
-	dev-cpp/gtkmm:2.4
-	dev-cpp/glibmm:2"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-util/intltool
-	sys-devel/gettext
-	virtual/pkgconfig
-	doc? ( app-text/doxygen[dot] )
-"
-
-PATCHES=(
-	)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	append-cxxflags -std=c++11 #566450
-
-	econf \
-		--disable-static \
-		$(use_enable doc api-docs)
-}
-
-src_install() {
-	default
-	find "${ED}" -name '*.la' -delete || die
-}
diff --git a/sci-chemistry/gelemental/gelemental-2.0.2.ebuild b/sci-chemistry/gelemental/gelemental-2.0.2.ebuild
deleted file mode 100644
index e24abba61afd..000000000000
--- a/sci-chemistry/gelemental/gelemental-2.0.2.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools flag-o-matic xdg
-
-DESCRIPTION="Periodic table viewer with detailed information on the chemical elements"
-HOMEPAGE="https://github.com/ginggs/gelemental/"
-SRC_URI="https://github.com/ginggs/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3 MIT"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="doc"
-
-RDEPEND="
-	dev-cpp/gtkmm:2.4
-	dev-cpp/glibmm:2"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-util/intltool
-	sys-devel/gettext
-	virtual/pkgconfig
-	doc? ( app-text/doxygen )
-"
-
-PATCHES=(
-	)
-
-src_prepare() {
-	default
-	eautoreconf
-}
-
-src_configure() {
-	append-cxxflags -std=c++11 #566450
-
-	econf \
-		--disable-static \
-		$(use_enable doc api-docs)
-}
-
-src_install() {
-	default
-	find "${ED}" -name '*.la' -delete || die
-}
diff --git a/sci-chemistry/gelemental/metadata.xml b/sci-chemistry/gelemental/metadata.xml
deleted file mode 100644
index a4a8fa434cf7..000000000000
--- a/sci-chemistry/gelemental/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>tamiko@gentoo.org</email>
-		<name>Matthias Maier</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">ginggs/gelemental</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/gnome-chemistry-utils/Manifest b/sci-chemistry/gnome-chemistry-utils/Manifest
deleted file mode 100644
index fc4b980a082b..000000000000
--- a/sci-chemistry/gnome-chemistry-utils/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST gnome-chemistry-utils-0.14.17.tar.xz 5911248 BLAKE2B 5d3bb4afbe3d3f620912e810717f08674d56a11c384b1fb239788cfbbb625797e8c52de2b6d940ae7f3d83847533afedd6ed961b1fa0ea1cec62dda88de1a6df SHA512 01bb964e1484e028c5965f1de74798422b448823047fcadf668dc76e98b3e214939a2f031d0182c717c4376f490e5969a4604ee66d1763e6b480032d7ae97468
-DIST gnome-chemistry-utils_0.14.17-6.debian.tar.xz 68528 BLAKE2B 2e4d318a5b91ca7963829c40c5d732a0ffa7fd9f4a32a6727f4926d2d4ec57989f50bd6839da49b4fa71dc533830bd0926205e952f08d04c08320e76ab51914c SHA512 8c6fad95c5d5e0895666fb9fb880364a9e3ab89761893b812c2cf835265acb40abe6b40def0960e1b38a0eea441310a3c1af608a2bcea37d5558533c9151e309
diff --git a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-disable_tests_man.patch b/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-disable_tests_man.patch
deleted file mode 100644
index 3cf549c4bfe0..000000000000
--- a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-disable_tests_man.patch
+++ /dev/null
@@ -1,26 +0,0 @@
-Disable tests for manpages, useless and it causes failures
-diff --git a/docs/man/Makefile.am b/docs/man/Makefile.am
-index eb8e3f5..fcddc85 100644
---- a/docs/man/Makefile.am
-+++ b/docs/man/Makefile.am
-@@ -40,20 +40,3 @@ if HAVE_XSLTPROC
- else
- 	echo "***** Cannot update the XML sources without `xsltproc'."
- endif
--
--
--check-local:
--	@echo "***** Correct any errors before making a distribution."
--if HAVE_XMLLINT
--	$(XMLLINT) $(XMLLINT_FLAGS) $(gcu_man_src)
--else
--	@echo "***** Cannot check the XML sources without `xmllint'."
--endif
--if HAVE_MAN
--	@for man in $(man_MANS) ; do \
--		LANG=C MANWIDTH=80 $(MAN) $(srcdir)/$${man} > /dev/null ; \
--	done
--else
--	@echo "***** Cannot check the manpages without `man'."
--endif	
--
diff --git a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_pointer_types.patch b/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_pointer_types.patch
deleted file mode 100644
index 256a008b9f7d..000000000000
--- a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_pointer_types.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-diff -Naur gnome-chemistry-utils-0.14.17_orig/libs/gccv/text.cc gnome-chemistry-utils-0.14.17_mod/libs/gccv/text.cc
---- gnome-chemistry-utils-0.14.17_orig/libs/gccv/text.cc	2017-02-12 10:10:09.000000000 +0100
-+++ gnome-chemistry-utils-0.14.17_mod/libs/gccv/text.cc	2024-09-02 22:58:57.724923903 +0200
-@@ -1126,7 +1126,7 @@
- 		if (event->state & GDK_CONTROL_MASK) {
- 			/* move to end of word */
- 			char const* s = m_Text.c_str ();
--			char *p = g_utf8_next_char (s + m_CurPos);
-+			char const* p = g_utf8_next_char (s + m_CurPos);
- 			while (*p && (!g_unichar_isgraph (g_utf8_get_char(p)) || g_unichar_ispunct (g_utf8_get_char(p))))
- 				p = g_utf8_next_char (p);
- 			while (g_unichar_isgraph (g_utf8_get_char(p)) && !g_unichar_ispunct (g_utf8_get_char(p)))
-@@ -1137,7 +1137,7 @@
- 			Invalidate ();
- 		} else {
- 			char const* s = m_Text.c_str ();
--			char *p = g_utf8_next_char (s + m_CurPos);
-+			char const* p = g_utf8_next_char (s + m_CurPos);
- 			if (!p)
- 				break;
- 			m_CurPos = p - s;
-@@ -1224,7 +1224,7 @@
- 		if (m_CurPos == m_Text.length ())
- 			break;
- 		char const* s = m_Text.c_str ();
--		char *p = g_utf8_next_char (s + m_CurPos);
-+		char const* p = g_utf8_next_char (s + m_CurPos);
- 		int new_pos = p - s;
- 		ReplaceText (empty_st, m_CurPos, new_pos - m_CurPos);
- 		if (client)
diff --git a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_underlinking.patch b/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_underlinking.patch
deleted file mode 100644
index 9b80a5590827..000000000000
--- a/sci-chemistry/gnome-chemistry-utils/files/gnome-chemistry-utils-fix_underlinking.patch
+++ /dev/null
@@ -1,30 +0,0 @@
-https://bugs.gentoo.org/913669
-fix underlinking with slibtool
---- a/plugins/loaders/cdx/Makefile.am
-+++ b/plugins/loaders/cdx/Makefile.am
-@@ -18,8 +18,9 @@ gcu_loader_cdx_LTLIBRARIES = cdx.la
- cdx_la_LDFLAGS = -module -avoid-version -no-undefined
- 
- cdx_la_LIBADD = \
--		$(gsf_LIBS) \
--		$(top_builddir)/libs/gcu/libgcu-@GCU_API_VER@.la
-+		$(gtk_LIBS) $(gsf_LIBS) \
-+ 		$(top_builddir)/libs/gcu/libgcu-@GCU_API_VER@.la \
-+		$(top_builddir)/libs/gcp/libgcp-@GCU_API_VER@.la
- 
- cdx_la_SOURCES =	\
- 	cdx.cc
---- a/plugins/loaders/cdxml/Makefile.am
-+++ b/plugins/loaders/cdxml/Makefile.am
-@@ -17,8 +17,9 @@ gcu_loader_cdxml_LTLIBRARIES = cdxml.la
- cdxml_la_LDFLAGS = -module -avoid-version -no-undefined
- 
- cdxml_la_LIBADD = \
--		$(gsf_LIBS) $(goffice_LIBS) \
--		$(top_builddir)/libs/gcu/libgcu-@GCU_API_VER@.la
-+ 		$(gtk_LIBS) $(gsf_LIBS) $(goffice_LIBS) \
-+		$(top_builddir)/libs/gcu/libgcu-@GCU_API_VER@.la \
-+		$(top_builddir)/libs/gcp/libgcp-@GCU_API_VER@.la
- 
- cdxml_la_SOURCES =	\
- 	cdxml.cc
diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r4.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r4.ebuild
deleted file mode 100644
index 54c80b7ee569..000000000000
--- a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.17_p6-r4.ebuild
+++ /dev/null
@@ -1,91 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit autotools flag-o-matic toolchain-funcs xdg
-
-DESCRIPTION="Programs and library containing GTK widgets and C++ classes related to chemistry"
-HOMEPAGE="https://gchemutils.nongnu.org/"
-SRC_URI="
-	https://download.savannah.gnu.org/releases/gchemutils/$(ver_cut 1-2)/${P/_p*}.tar.xz
-	mirror://debian/pool/main/${PN:0:1}/${PN}/${PN}_${PV/_p*}-${PV/*_p}.debian.tar.xz
-"
-S="${WORKDIR}/${P/_p*}"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="gnumeric"
-
-RDEPEND="
-	>=dev-libs/glib-2.36.0:2
-	>=dev-libs/libxml2-2.4.16:2=
-	>=gnome-extra/libgsf-1.14.9:=
-	media-libs/libglvnd[X]
-	>=sci-chemistry/bodr-5
-	>=sci-chemistry/chemical-mime-data-0.1.94
-	>=sci-chemistry/openbabel-2.3.0:0=
-	>=x11-libs/cairo-1.6.0
-	>=x11-libs/gdk-pixbuf-2.22.0:2
-	>=x11-libs/goffice-0.10.12:0.10
-	x11-libs/gtk+:3[X]
-	>=x11-libs/libX11-1.0.0
-	x11-libs/pango
-	gnumeric? ( >=app-office/gnumeric-1.12.42 )
-"
-DEPEND="${RDEPEND}
-	virtual/glu"
-BDEPEND="
-	app-text/doxygen
-	app-text/yelp-tools
-	dev-util/glib-utils
-	dev-util/intltool
-	virtual/pkgconfig
-"
-
-src_prepare() {
-	default
-
-	if has_version '<sci-chemistry/openbabel-3'; then
-		sed -i -e '/openbabel-v3/d' "${WORKDIR}"/debian/patches/series || die
-	fi
-
-	# Debian patches
-	for p in $(<"${WORKDIR}"/debian/patches/series) ; do
-		eapply -p1 "${WORKDIR}/debian/patches/${p}"
-	done
-
-	# From Fedora
-	eapply "${FILESDIR}"/${PN}-fix_pointer_types.patch
-
-	# Disable tests for manpages
-	eapply "${FILESDIR}"/${PN}-disable_tests_man.patch
-
-	# bug 913669 fix underlinking with slibtool
-	eapply "${FILESDIR}"/${PN}-fix_underlinking.patch
-
-	sed -e "s:pkg-config:$(tc-getPKG_CONFIG):g" \
-		-i configure.ac || die
-
-	eautoreconf
-}
-
-src_configure() {
-	# bug #790023
-	append-cxxflags -std=c++14
-
-	# lasem is not in the tree
-	econf \
-		--without-lasem \
-		--disable-mozilla-plugin \
-		--disable-update-databases
-}
-
-src_install() {
-	default
-
-	mv "${ED}"/usr/share/appdata "${ED}"/usr/share/metainfo || die
-	rm -rf "${ED}"/usr/share/mimelnk/ || die
-
-	find "${D}" -name '*.la' -type f -delete || die
-}
diff --git a/sci-chemistry/gnome-chemistry-utils/metadata.xml b/sci-chemistry/gnome-chemistry-utils/metadata.xml
deleted file mode 100644
index fcf8bc4bad08..000000000000
--- a/sci-chemistry/gnome-chemistry-utils/metadata.xml
+++ /dev/null
@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>pacho@gentoo.org</email>
-	</maintainer>
-	<use>
-		<flag name="gnumeric">Add a Gnumeric plugin to provide a molarmass function for the spreadsheet</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/gperiodic/Manifest b/sci-chemistry/gperiodic/Manifest
deleted file mode 100644
index 0f1c1543edc0..000000000000
--- a/sci-chemistry/gperiodic/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST gperiodic-3.0.3.tar.gz 451559 BLAKE2B b91995046b9905a534e3b6f530aee0ad2b4e6ac42cd11755ea182fdaaf8970f34b1aea8a33870abb8767837606a42a0cf0d76c9a689236aa39fba686e1521ee8 SHA512 7226063cf7977f4283a199d4a3d1842d6c9be60c53f5a005541eb26f35cd6538b29f086dc13c28225779e1849a12d1c39150897055c03902cb00adc011bc1ce8
diff --git a/sci-chemistry/gperiodic/files/gperiodic-3.0.3-incompatible-pointers.patch b/sci-chemistry/gperiodic/files/gperiodic-3.0.3-incompatible-pointers.patch
deleted file mode 100644
index b156532e9b54..000000000000
--- a/sci-chemistry/gperiodic/files/gperiodic-3.0.3-incompatible-pointers.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-https://bugs.gentoo.org/919213
-Cast pointer as it is cast everywhere around it
---- a/gperiodic.c
-+++ b/gperiodic.c
-@@ -137,7 +137,7 @@
- 	    if (col == 0) gtk_label_set_markup (GTK_LABEL (label), _(header.info[row]));
-             else {
- 	      gtk_label_set_markup (GTK_LABEL (label), _(entry->info[row]));
--	      gtk_label_set_selectable (label, TRUE);
-+	      gtk_label_set_selectable (GTK_LABEL (label), TRUE);
- 	    }
- 
- 	    gtk_misc_set_alignment(GTK_MISC(label), 0, 0);
diff --git a/sci-chemistry/gperiodic/gperiodic-3.0.3-r1.ebuild b/sci-chemistry/gperiodic/gperiodic-3.0.3-r1.ebuild
deleted file mode 100644
index f96d8c0b41f0..000000000000
--- a/sci-chemistry/gperiodic/gperiodic-3.0.3-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs xdg-utils
-
-DESCRIPTION="Periodic table application for Linux"
-HOMEPAGE="https://sourceforge.net/projects/gperiodic/"
-SRC_URI="https://downloads.sourceforge.net/project/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="nls"
-
-BDEPEND="
-	virtual/pkgconfig
-	nls? ( sys-devel/gettext )"
-RDEPEND="
-	sys-libs/ncurses:0
-	x11-libs/gtk+:2
-	x11-libs/cairo[X]"
-DEPEND="${RDEPEND}"
-
-PATCHES=( "${FILESDIR}/${P}-incompatible-pointers.patch" )
-
-src_compile() {
-	emake \
-		CFLAGS="${CFLAGS}" \
-		LDFLAGS="${LDFLAGS}" \
-		CC="$(tc-getCC)" "enable_nls=$(usex nls 1 0)"
-}
-
-src_install() {
-	emake DESTDIR="${D}" "enable_nls=$(usex nls 1 0)" install
-	dodoc AUTHORS ChangeLog README
-	newdoc po/README README.translation
-}
-
-pkg_postinst() {
-	xdg_icon_cache_update
-}
-
-pkg_postrm() {
-	xdg_icon_cache_update
-}
diff --git a/sci-chemistry/gperiodic/metadata.xml b/sci-chemistry/gperiodic/metadata.xml
deleted file mode 100644
index ca9404a805af..000000000000
--- a/sci-chemistry/gperiodic/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-		GPeriodic is a program for looking up various data about elements from the
-		periodic table, based on the GTK2 toolkit. It also features a command line
-		interface.
-	</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
deleted file mode 100644
index 841013ed827f..000000000000
--- a/sci-chemistry/gromacs/Manifest
+++ /dev/null
@@ -1,21 +0,0 @@
-DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c
-DIST gromacs-2024.6.tar.gz 42340289 BLAKE2B babba3ec83e8757d95733a51eebf780a2f0cf5da2fd3b2aa9410cdfca7901955cbd63d2ed0c61fde873b4438d85ae7769afa8f3d7ee1da26571d8989c516ecd4 SHA512 eb3d06df3e5c52d3dab801e5c2134fc05ded1bca8b1955f747e4efbb2b4cd1f50680f073592a5c5d580abff0a869ffd1c19c352bc6d9b4ab40465741ed7d001a
-DIST gromacs-2025.3.tar.gz 44407119 BLAKE2B 7e7385d5a83c02cb7152f789df6b86321b9ee22d7fb53e0e69fd01ba04ec197d1b725047f5c9983595ab124f23310f926e101d12a2113472f3b2aaa53f26b661 SHA512 8151bb0f72bf51d0368e40871b68d552c58ed69c0e431601afbf5c7923e7512d2458dfb22eb7fd79cc3c464434ca94a67c99a9f71c7e6b00d7d141789712c157
-DIST gromacs-2025.4.tar.gz 44406127 BLAKE2B 6a558e979574876bc0077e96733c0f7e267c39bff6afbf840ffc7ce0f2580ff0871136d43aa994f4bb44aa98ad4192cefac003d306c02b89aa026d46a47d2a84 SHA512 640bee4b499b06de7dc6a04c6448f174a0232afc2bc90a8e1a862842ea0cdc886eabe6d170d637ccfb9d8e979b74067ac0d52b760fd98c7d6dc47d32e5cd3733
-DIST gromacs-2026.0.tar.gz 45934287 BLAKE2B e9443a00a922355fd79e22855ce9512595aad6e3a2717e4b879796c722157a01ffff3d1d0e511654816f83c0dcea8bad1250564235ff37cf69cd7f66658e5dff SHA512 551ea9732bbebecc9ecd059dfdf8be37fe453bf75c1a75d17bffb1ba09e15fa5ee65ba48032cf411eb62acbec72108238ab2b0293f3aeeb303032f52da569bf7
-DIST gromacs-2026.1.tar.gz 45914061 BLAKE2B 18fe2fb93bb978954187505c45e984c967b58a8005e04e26d4a27e6e0a070f7734063bdfe9bf916d5d9cdd912c15a395b46905f054d7498d62e14baf788bfcf8 SHA512 6c9d97f0f0eeb936dbc228f403568c7bc3a06d64168bea93c2489b29d89715f9238339fe699f039c81e9d347c4ca5a692690e8efa60720c53401df5b98a9c2f0
-DIST gromacs-2026.2.tar.gz 45943914 BLAKE2B f14a30e043e5d8909ac7c4f452de12c083f1c41fe05df1dba8659f87c42b185ca897091ce5e28ef63674c447a1d736351a121f70b5fc70f5fbda08186170ffa4 SHA512 7865a48badeee3f45e308f70f8c336acebfefcaf47a454f4e360fad736bd15bb5fd2220dc7c0f23589f765bdbcdc8fd6c68b620c0649a0afa61afcfed53bd46f
-DIST manual-2023.5.pdf 13579081 BLAKE2B 42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc SHA512 0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb
-DIST manual-2024.6.pdf 13698340 BLAKE2B 7926fe0c09ab1a6027e6e5d2692e2a590ec31c061b0f3e0dd278ffc8bffe923d6342bd9f375758fe5b0ca9c7fd43a216e486c694ba8d644acceb6467aac37425 SHA512 9130bda473ddfc475f3c7a6946890189bf225609208fb9e84c81606a72d63383199ac5e05f3620e7d7f96916ee475e19528d03b4ddc4b339772af61825beec45
-DIST manual-2025.3.pdf 13822608 BLAKE2B 75ea8359a33941f1d44a6c471c03e268c707cdc4717ea43c455c25c5c60b7708e68849aba8fde7872aefa93691ef0bec531b7bd9cb0376b3ddee34c24058bdb5 SHA512 e0a3016eb6fc271d617795c1595a15e234c28a8492e2b0471b705c1f597b672ec05d0bb78ff3b977140c5f525dcc72c3b082cc74aee1e4207b9f1c2593a71bb5
-DIST manual-2025.4.pdf 13827071 BLAKE2B 8bc581f05fe80f1881efd7b3b5f87a34d153847fed92a4cb8b2d98666bd5b84ef46319f9f49f1c47b9940a5fa68b93d543fbf60318defc3884988a9942c1aeff SHA512 451360ba60f2c4fabe09851bdb1712a2273278f01b5b23b5afbf277b3822f8fed7eb64991a549fbac10878f366db15f12e3b93ae6285095fc30731761604f3fa
-DIST manual-2026.0.pdf 13895142 BLAKE2B 4bbdb564ee75b7187cae0ecbf1c11b6a0bac0a28bad6597163c479c103ba2bab37c2adbd7ac03abcee8947d0fcaf5824e415ea7ca33e91933c004f26a599a9ee SHA512 3d147b5f636d7a908892f37fc72953e7a9227cbf453e2dbb9c3bb01faf31a5e48defd30b4ced77a639e6727e62f52c615ac18336cf809a117d5429ba50541189
-DIST manual-2026.1.pdf 13908382 BLAKE2B 5f95cea9881575c6547fcbbe694c0515338108a03b0f31c9dfaed454e5920c45b6bad9cd9a6f6dcd091afc03db25847604d7bf5b4c75103475b0f0465d606180 SHA512 a3e2e9413ad94b60ee86d9c2dcf9e075e0b5687b32f16c1cba2afbe237327954f765ef9aa938f2ddca4f79da99c397cf764be67b642e98e8b3ebca69a41f5c29
-DIST manual-2026.2.pdf 13913299 BLAKE2B 24fc042ecaa56956a1b05f0cebec1424536ebc6ce26cc4b12a56cd9eb9a610b819f16c8eaa5e5ade10ac53f4027e731e6a420a7f7d8da0d92a3a4f451bce4179 SHA512 e9d2654ab955f5a9631b2f73db3e0d5456b92c24b6d7235f4a74be931d719f788b49ffe58517db6e306983c3e3981297d51312bf7c581af73b3425dd0d294aae
-DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f SHA512 3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a
-DIST regressiontests-2024.6.tar.gz 32776894 BLAKE2B 75dbf6a6ec5a1d0848a51335a1fb2e6777361d0b823e7f88c5145c881aa819abfc2eaaae1ae438538213c09659e9512bf77b4dc2f0ee63a28a1f213f49b5a47d SHA512 1150396a3c20b7747a4a58c22b26c0c40cf6e6f70b8daabfc71cbe00f2dce3ad1c02d89d264a7d7db3f3e7e9dd1c0b46a438d297cdeb074e50d8d6d3e916950b
-DIST regressiontests-2025.3.tar.gz 32653489 BLAKE2B 1396872d6ebe2756b02ca1a1d173edd29f4931d2b30280299723b24164e5576c14c59997c00d7919b262fb1a15083dc90541f9f7e48587090002fc7cca9e1332 SHA512 fb947dc148e21a69e1ef06258f6c2359156e4afb7c8bee9e659ea461f5e4e9fe3654bec86324e11fcd6624889490ec73cb213bf0111cf76ded966f43c1182a20
-DIST regressiontests-2025.4.tar.gz 32652577 BLAKE2B 7c4253499e94f5adeb17a17ebb93229b0a8dd0f6694af3b67a751d76e916d96bf461070b56774b331512cc351feb8889c6f843a386ac41e615f33af17d1baa2e SHA512 54c29741229a44e322b2e1445bb8d90ed4d790704d9b13fa392e78d6effa551f685e7c18e2c86ca613a85b34ebc3ddef512b406621d53471c6bbb0e1e8913ff0
-DIST regressiontests-2026.0.tar.gz 16580771 BLAKE2B 77fd30feb6a6df751f958e77433524831172c3fae333a008fa88419d88ebdd0abcf90cbaf75b9a4711ad0a1264aa29240d117d2044d74f7e2d2dfbf2a3e195bd SHA512 af8709010f150a1a988b6884ef0c37ebb8685a0e6d80f7b46ac03b697ecbe187e33b286afa0fa28eae4cbc8564872960e5275809324df5f06820801b36a89bca
-DIST regressiontests-2026.1.tar.gz 16580717 BLAKE2B e4535b881a18ee6fded9a6f53256eb05e611449ddcba9b6c96a0d8d67f7f371a8a52f9234535fed610fb9063db774316c07b92f5a0b813a3671304e205dfdf2e SHA512 bdefb5c0156f5ac13ee36a0256d8b568872e9e668bf736c9b0a147ef03384ee7d1e250c7df59bf5bc4cd5c37a31051784bc491dce861c10994c81dd5fcecd305
-DIST regressiontests-2026.2.tar.gz 16580813 BLAKE2B 31f464ff992ab5dd81a0e6449ab67a9e2bc9d0afe7b72f17dc1ee01c4877ebb4f07521e1a582bee4188a375d61f0acf3265ed85667f50643bb2671d63e73a961 SHA512 e2262737100736f9614a6d88583b36a82359c486d5139300667c47fd0248ee5a81ecebb2e82c4219e6f9fa5281bcc2272913a661a71ee5873c8c2c2ff1345657
diff --git a/sci-chemistry/gromacs/files/gromacs-gcc-15.patch b/sci-chemistry/gromacs/files/gromacs-gcc-15.patch
deleted file mode 100644
index c0168ba9f21e..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-gcc-15.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/gromacs/mdtypes/energyhistory.h b/src/gromacs/mdtypes/energyhistory.h
-index 0c8fecfae70605d64613a2408755e715e5f9b6c5..f80d4c56b95caf6942b35222d8983c8ed8f10e1e 100644
---- a/src/gromacs/mdtypes/energyhistory.h
-+++ b/src/gromacs/mdtypes/energyhistory.h
-@@ -47,6 +47,8 @@
- #ifndef GMX_MDLIB_ENERGYHISTORY_H
- #define GMX_MDLIB_ENERGYHISTORY_H
- 
-+#include <cstdint>
-+
- #include <memory>
- #include <vector>
- 
diff --git a/sci-chemistry/gromacs/files/gromacs-musl.patch b/sci-chemistry/gromacs/files/gromacs-musl.patch
deleted file mode 100644
index 52a1748ea3d0..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-musl.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-From 611bf005f64d7d21258462e520111144f14b2db8 Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxyum@gmail.com>
-Date: Mon, 4 May 2026 18:28:43 +0300
-Subject: [PATCH] Fix build with musl based systems
-
-Bug: https://bugs.gentoo.org/968018
-
-Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com>
----
- api/gmxapi/include/gmxapi/gmxapicompat.h | 2 ++
- 1 file changed, 2 insertions(+)
-
-diff --git a/api/gmxapi/include/gmxapi/gmxapicompat.h b/api/gmxapi/include/gmxapi/gmxapicompat.h
-index 837dc2ed1f..de51dabc02 100644
---- a/api/gmxapi/include/gmxapi/gmxapicompat.h
-+++ b/api/gmxapi/include/gmxapi/gmxapicompat.h
-@@ -47,6 +47,8 @@
- #ifndef GMXAPICOMPAT_H
- #define GMXAPICOMPAT_H
- 
-+#include <cstdint>
-+
- #include <map>
- #include <string>
- 
--- 
-2.54.0
-
diff --git a/sci-chemistry/gromacs/gromacs-2023.5.ebuild b/sci-chemistry/gromacs/gromacs-2023.5.ebuild
deleted file mode 100644
index afdae334eed1..000000000000
--- a/sci-chemistry/gromacs/gromacs-2023.5.ebuild
+++ /dev/null
@@ -1,341 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	KEYWORDS="amd64 -arm arm64 ~x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2024.6.ebuild b/sci-chemistry/gromacs/gromacs-2024.6.ebuild
deleted file mode 100644
index 6aed3da979af..000000000000
--- a/sci-chemistry/gromacs/gromacs-2024.6.ebuild
+++ /dev/null
@@ -1,346 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	KEYWORDS="amd64 -arm arm64 ~riscv -x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-PATCHES=(
-	"${FILESDIR}/${PN}-gcc-15.patch"
-	"${FILESDIR}/${PN}-musl.patch"
-)
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2025.3.ebuild b/sci-chemistry/gromacs/gromacs-2025.3.ebuild
deleted file mode 100644
index 16470374ded5..000000000000
--- a/sci-chemistry/gromacs/gromacs-2025.3.ebuild
+++ /dev/null
@@ -1,362 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	# since 2025 x86-32 support was dropped
-	KEYWORDS="amd64 -arm arm64 ~riscv -x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	nnpot? ( sci-ml/caffe2[cuda=,opencl=] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-	local nnpot="OFF"
-
-	if use nnpot; then
-		nnpot="TORCH"
-	fi
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_USE_HDF5=off
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_BUILD_HELP=$(usex doc)
-		-DGMX_SIMD="$acce"
-		-DGMX_NNPOT="$nnpot"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	# fix sandbox violation bug #965866
-	addwrite /proc/mtrr
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile man
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2025.4.ebuild b/sci-chemistry/gromacs/gromacs-2025.4.ebuild
deleted file mode 100644
index 5a9d1127ed40..000000000000
--- a/sci-chemistry/gromacs/gromacs-2025.4.ebuild
+++ /dev/null
@@ -1,364 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	# since 2025 x86-32 support was dropped
-	KEYWORDS="amd64 -arm ~arm64 ~riscv -x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	nnpot? ( sci-ml/caffe2[cuda=,opencl=] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-PATCHES=( "${FILESDIR}/${PN}-musl.patch" )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-	local nnpot="OFF"
-
-	if use nnpot; then
-		nnpot="TORCH"
-	fi
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_USE_HDF5=off
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_BUILD_HELP=$(usex doc)
-		-DGMX_SIMD="$acce"
-		-DGMX_NNPOT="$nnpot"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	# fix sandbox violation bug #965866
-	addwrite /proc/mtrr
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile man
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2026.0.ebuild b/sci-chemistry/gromacs/gromacs-2026.0.ebuild
deleted file mode 100644
index fbe7250f2334..000000000000
--- a/sci-chemistry/gromacs/gromacs-2026.0.ebuild
+++ /dev/null
@@ -1,365 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	# since 2025 x86-32 support was dropped
-	KEYWORDS="amd64 -arm arm64 ~riscv -x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hdf5? ( sci-libs/hdf5 )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	nnpot? ( sci-ml/caffe2[cuda=,opencl=] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-PATCHES=( "${FILESDIR}/${PN}-musl.patch" )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-	local nnpot="OFF"
-
-	if use nnpot; then
-		nnpot="TORCH"
-	fi
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_USE_HDF5=$(usex hdf5)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_BUILD_HELP=$(usex doc)
-		-DGMX_SIMD="$acce"
-		-DGMX_NNPOT="$nnpot"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	# fix sandbox violation bug #965866
-	addwrite /proc/mtrr
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile man
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2026.1.ebuild b/sci-chemistry/gromacs/gromacs-2026.1.ebuild
deleted file mode 100644
index 008c38e106d6..000000000000
--- a/sci-chemistry/gromacs/gromacs-2026.1.ebuild
+++ /dev/null
@@ -1,365 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	# since 2025 x86-32 support was dropped
-	KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hdf5? ( sci-libs/hdf5 )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	nnpot? ( sci-ml/caffe2[cuda=,opencl=] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-PATCHES=( "${FILESDIR}/${PN}-musl.patch" )
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-	local nnpot="OFF"
-
-	if use nnpot; then
-		nnpot="TORCH"
-	fi
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_USE_HDF5=$(usex hdf5)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_BUILD_HELP=$(usex doc)
-		-DGMX_SIMD="$acce"
-		-DGMX_NNPOT="$nnpot"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	# fix sandbox violation bug #965866
-	addwrite /proc/mtrr
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile man
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2026.2.ebuild b/sci-chemistry/gromacs/gromacs-2026.2.ebuild
deleted file mode 100644
index d77fc54eea2b..000000000000
--- a/sci-chemistry/gromacs/gromacs-2026.2.ebuild
+++ /dev/null
@@ -1,363 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	# since 2025 x86-32 support was dropped
-	KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hdf5? ( sci-libs/hdf5 )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	nnpot? ( sci-ml/caffe2[cuda=,opencl=] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-	local nnpot="OFF"
-
-	if use nnpot; then
-		nnpot="TORCH"
-	fi
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_USE_HDF5=$(usex hdf5)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_BUILD_HELP=$(usex doc)
-		-DGMX_SIMD="$acce"
-		-DGMX_NNPOT="$nnpot"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	# fix sandbox violation bug #965866
-	addwrite /proc/mtrr
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile man
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2026.9999.ebuild b/sci-chemistry/gromacs/gromacs-2026.9999.ebuild
deleted file mode 100644
index d77fc54eea2b..000000000000
--- a/sci-chemistry/gromacs/gromacs-2026.9999.ebuild
+++ /dev/null
@@ -1,363 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	# since 2025 x86-32 support was dropped
-	KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hdf5? ( sci-libs/hdf5 )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	nnpot? ( sci-ml/caffe2[cuda=,opencl=] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-	local nnpot="OFF"
-
-	if use nnpot; then
-		nnpot="TORCH"
-	fi
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_USE_HDF5=$(usex hdf5)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_BUILD_HELP=$(usex doc)
-		-DGMX_SIMD="$acce"
-		-DGMX_NNPOT="$nnpot"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	# fix sandbox violation bug #965866
-	addwrite /proc/mtrr
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile man
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
deleted file mode 100644
index d77fc54eea2b..000000000000
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ /dev/null
@@ -1,363 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_OPTIONAL=1
-DISTUTILS_USE_PEP517=no
-DISTUTILS_SINGLE_IMPL=1
-
-inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ ${PV} = *9999* ]]; then
-	EGIT_REPO_URI="
-		https://gitlab.com/gromacs/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		"
-	[[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="
-		https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-		test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	# since 2022 arm support was dropped (but not arm64)
-	# since 2025 x86-32 support was dropped
-	KEYWORDS="~amd64 -arm ~arm64 ~riscv -x86 ~x64-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="https://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="blas clang clang-cuda cuda  +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy hdf5 +hwloc lapack mkl mpi nnpot +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] )
-	opencl? ( virtual/opencl )
-	openmp? (
-		|| (
-			sys-devel/gcc[openmp]
-			llvm-runtimes/clang-runtime[openmp]
-		)
-	)
-	fftw? ( sci-libs/fftw:3.0= )
-	hdf5? ( sci-libs/hdf5 )
-	hwloc? ( sys-apps/hwloc:= )
-	lapack? ( virtual/lapack )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi[cxx] )
-	nnpot? ( sci-ml/caffe2[cuda=,opencl=] )
-	sci-libs/lmfit:=
-	>=dev-cpp/muParser-2.3:=
-	${PYTHON_DEPS}
-	"
-BDEPEND="${CDEPEND}
-	virtual/pkgconfig
-	clang? ( >=llvm-core/clang-6:* )
-	$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-	build-manual? (
-		app-text/doxygen
-		$(python_gen_cond_dep '
-			dev-python/sphinx[${PYTHON_USEDEP}]
-			dev-python/sphinx-copybutton[${PYTHON_USEDEP}]
-			dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}]
-			dev-python/sphinx-argparse[${PYTHON_USEDEP}]
-			dev-python/sphinxcontrib-autoprogram[${PYTHON_USEDEP}]
-		')
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	doc? ( !build-manual )
-	cuda? ( single-precision )
-	opencl? ( single-precision )
-	cuda? ( !opencl )
-	clang-cuda? ( clang cuda )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-	python-single-r1_pkg_setup
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	# we can use clang as default
-	if use clang && ! tc-is-clang ; then
-		export CC=${CHOST}-clang
-		export CXX=${CHOST}-clang++
-	else
-		tc-export CXX CC
-	fi
-	# clang-cuda need to filter mfpmath
-	if use clang-cuda ; then
-		filter-mfpmath sse
-		filter-mfpmath i386
-	fi
-
-	cmake_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-	if use build-manual; then
-		# try to create policy for imagemagik
-		mkdir -p "${HOME}"/.config/ImageMagick
-		cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF
-		<?xml version="1.0" encoding="UTF-8"?>
-		<!DOCTYPE policymap [
-		<!ELEMENT policymap (policy)+>
-		!ATTLIST policymap xmlns CDATA #FIXED ''>
-		<!ELEMENT policy EMPTY>
-		<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-		]>
-		<policymap>
-			<policy domain="coder" rights="read | write" pattern="PS" />
-			<policy domain="coder" rights="read | write" pattern="PS2" />
-			<policy domain="coder" rights="read | write" pattern="PS3" />
-			<policy domain="coder" rights="read | write" pattern="EPS" />
-			<policy domain="coder" rights="read | write" pattern="PDF" />
-			<policy domain="coder" rights="read | write" pattern="XPS" />
-		</policymap>
-		EOF
-	fi
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-	local acce="AUTO"
-	local nnpot="OFF"
-
-	if use nnpot; then
-		nnpot="TORCH"
-	fi
-
-	if use custom-cflags; then
-		#go from slowest to fastest acceleration
-		acce="None"
-		if (use amd64 || use x86); then
-			use cpu_flags_x86_sse2 && acce="SSE2"
-			use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-			use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-			use cpu_flags_x86_avx && acce="AVX_256"
-			use cpu_flags_x86_avx2 && acce="AVX2_256"
-			use cpu_flags_x86_avx512f && acce="AVX_512"
-		elif (use arm); then
-			use cpu_flags_arm_neon && acce="ARM_NEON"
-		elif (use arm64); then
-			use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD"
-		fi
-	else
-		strip-flags
-	fi
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_USE_LMFIT=EXTERNAL
-		-DGMX_USE_MUPARSER=EXTERNAL
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex build-manual)
-		-DGMX_USE_HDF5=$(usex hdf5)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_BUILD_HELP=$(usex doc)
-		-DGMX_SIMD="$acce"
-		-DGMX_NNPOT="$nnpot"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local gpu=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" )
-		[[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" )
-		use opencl && gpu=( "-DGMX_GPU=OPENCL" )
-		local mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=$(usex mpi)
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
-			"${gpu[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			-DGMX_PYTHON_PACKAGE=$(usex python)
-		)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	# fix sandbox violation bug #965866
-	addwrite /proc/mtrr
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile man
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile	python_packaging/all
-			BUILD_DIR="${WORKDIR}/${P}" \
-				distutils-r1_src_compile
-		fi
-		# not 100% necessary for rel ebuilds as available from website
-		if use build-manual; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake_src_compile manual
-		fi
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_compile check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake_src_install
-		if use python; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}" \
-				cmake_src_install	python_packaging/install
-		fi
-		if use build-manual; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-
-		if use doc; then
-			if [[ ${PV} != *9999* ]]; then
-				newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
-			fi
-		fi
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"/usr/bin/GMXRC* || die
-	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"/usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite gromacs related papers from list:"
-	einfo  "https://www.gromacs.org/articles.html"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
deleted file mode 100644
index c9f06ca19ba2..000000000000
--- a/sci-chemistry/gromacs/metadata.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-		<name>Alexey Shvetsov</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="build-manual">Build manual instead of downloading it</flag>
-		<flag name="clang">Build gromacs with Clang instead of default compiler</flag>
-		<flag name="clang-cuda">Use clang for cuda units compilation</flag>
-		<flag name="cuda">Enable cuda non-bonded kernels</flag>
-		<flag name="double-precision">More precise calculations at the expense of speed</flag>
-		<flag name="gmxapi">Add support for gmxapi library</flag>
-		<flag name="gmxapi-legacy">Enable installing lagacy headers</flag>
-		<flag name="hwloc">Enable HWLoc lib support</flag>
-		<flag name="nnpot">Allow to use <pkg>sci-ml/caffe2</pkg> for NN Potentials</flag>
-		<flag name="opencl">Enable opencl non-bonded kernels</flag>
-		<flag name="single-precision">Single precision version of gromacs (default)</flag>
-		<flag name="tng">Enable new trajectory format - tng</flag>
-		<flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag>
-		<flag name="offensive">Enable gromacs partly offensive quotes</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/ksdssp/Manifest b/sci-chemistry/ksdssp/Manifest
deleted file mode 100644
index 2b2e2efc1e3b..000000000000
--- a/sci-chemistry/ksdssp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ksdssp-040728.shar 104347 BLAKE2B f77ba1fd83e9dd959dabf49818c541605eb8fba895880dbd8324cd02a0528d7961ced200de4b64c18c897a18e9f78474293a9f95fee9beace36f5faba61fcaa2 SHA512 17c32bea1f32acfd31353d0378fe2a664a8922db8b929da4b9b10ac279013946911acd2a26ab3ab227ae160352c8313dcf742fae8c139a90ac11f772f17a1689
diff --git a/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild b/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild
deleted file mode 100644
index 0b787554f7ed..000000000000
--- a/sci-chemistry/ksdssp/ksdssp-040728-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="An open source implementation of sci-chemistry/dssp"
-HOMEPAGE="http://www.cgl.ucsf.edu/Overview/software.html"
-SRC_URI="mirror://gentoo/${P}.shar"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="sci-libs/libpdb++"
-DEPEND="${RDEPEND}"
-BDEPEND="app-arch/sharutils"
-
-S="${WORKDIR}/${PN}"
-
-src_unpack() {
-	unshar "${DISTDIR}"/${A} || die
-}
-
-src_compile() {
-	emake \
-		CXX="$(tc-getCXX)" \
-		PDBINCDIR="${EPREFIX}/usr/include/libpdb++" \
-		BINDIR="${EPREFIX}/usr/bin" \
-		.TARGET="${PN}.csh" \
-		.CURDIR="${S}" \
-		CC="$(tc-getCXX)" \
-		LINKER="$(tc-getCXX)" \
-		OPT="${CXXFLAGS}" \
-		LFLAGS="${LDFLAGS}" \
-		${PN} ${PN}.csh
-}
-
-src_install() {
-	dobin ksdssp{,.csh}
-
-	HTML_DOCS=( ksdssp.html )
-	einstalldocs
-
-	doman ksdssp.1
-}
diff --git a/sci-chemistry/ksdssp/metadata.xml b/sci-chemistry/ksdssp/metadata.xml
deleted file mode 100644
index d4ff1000a775..000000000000
--- a/sci-chemistry/ksdssp/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mdtraj/Manifest b/sci-chemistry/mdtraj/Manifest
deleted file mode 100644
index ff4637c4aaa6..000000000000
--- a/sci-chemistry/mdtraj/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST mdtraj-1.10.3.gh.tar.gz 21993979 BLAKE2B a9d6e0bfb073c3a0f4852123ffa72d7b812d01e9d5c7130bcb9f0d7ff5f029f293ba08e417c404f876d62a592c264a5a540a2f55f7af3a8535decae214619bf4 SHA512 ff3b2959dfe21a633d99a8ae27520c8b582fc3384182bfb6653a4ffa4fb13b83f25e4e75ddd30ecf1b6ad36afe5c9580faa158f2069383563a46868d2dea0ed4
-DIST mdtraj-1.11.1_p1.gh.tar.gz 22729985 BLAKE2B b3dd05da0c685c44ae33f2b2be58d2c8ff6b1585d29b70e1a72acd36f8b10a0e06d35e3c4eeb150e16fae2d0f9490913aa8fad7eb221de8cb328f458ae61ccc2 SHA512 7de695fb4b2c160913a7c1344e2b2719d6b265ff1724a83d233c49427e58fe3a5add9a076fc2850e05dcf956ffc4b2b6730e8f169449e954703be39125262948
diff --git a/sci-chemistry/mdtraj/files/mdtraj-1.10.3-tests.py b/sci-chemistry/mdtraj/files/mdtraj-1.10.3-tests.py
deleted file mode 100644
index 7150090d9b0c..000000000000
--- a/sci-chemistry/mdtraj/files/mdtraj-1.10.3-tests.py
+++ /dev/null
@@ -1,134 +0,0 @@
-diff '--color=auto' -urN mdtraj-1.10.3.orig/tests/test_distance.py mdtraj-1.10.3/tests/test_distance.py
---- mdtraj-1.10.3.orig/tests/test_distance.py	2025-04-04 01:29:47.406044779 +0300
-+++ mdtraj-1.10.3/tests/test_distance.py	2025-04-04 01:30:29.880088967 +0300
-@@ -301,13 +301,13 @@
-         compute_distances_t(ptraj, pairs, incorrect_times)
- 
- 
--def test_distances_t(get_fn):
--    a = compute_distances_t(ptraj, pairs, times, periodic=True, opt=True)
--    b = compute_distances_t(ptraj, pairs, times, periodic=True, opt=False)
--    eq(a, b)
--    c = compute_distances_t(ptraj, pairs, times, periodic=False, opt=True)
--    d = compute_distances_t(ptraj, pairs, times, periodic=False, opt=False)
--    eq(c, d)
-+#def test_distances_t(get_fn):
-+#    a = compute_distances_t(ptraj, pairs, times, periodic=True, opt=True)
-+#    b = compute_distances_t(ptraj, pairs, times, periodic=True, opt=False)
-+#    eq(a, b)
-+#    c = compute_distances_t(ptraj, pairs, times, periodic=False, opt=True)
-+#    d = compute_distances_t(ptraj, pairs, times, periodic=False, opt=False)
-+#    eq(c, d)
- 
- 
- def test_distances_t_at_0(get_fn):
-diff '--color=auto' -urN mdtraj-1.10.3.orig/tests/test_rdf.py mdtraj-1.10.3/tests/test_rdf.py
---- mdtraj-1.10.3.orig/tests/test_rdf.py	2025-04-04 01:29:47.406044779 +0300
-+++ mdtraj-1.10.3/tests/test_rdf.py	2025-04-04 01:31:45.613894761 +0300
-@@ -216,20 +216,20 @@
-     mean_g_r_t = np.mean(g_r_t, axis=0)
-     compare_gromacs_xvg(get_fn("tip3p_300K_1ATM_O-O_rdf.xvg"), r_t, mean_g_r_t)
- 
--@pytest.mark.skipif(np.__version__ < "2.0", reason="Expected failure for NumPy < 2.0 due to histogram output differences")
--def test_compare_rdf_t_master(get_fn):
--    traj = md.load(get_fn("tip3p_300K_1ATM.xtc"), top=get_fn("tip3p_300K_1ATM.pdb"))
--
--    times = [[0,j] for j in range(100)]
--
--    pairs = traj.top.select_pairs("name O", "name O")
--    r_t, rdf_O_O = mdtraj.geometry.rdf.compute_rdf_t(traj, pairs, times)
--
--    master_r_t = np.loadtxt(get_fn("r_O_O_rdf_t.txt"))
--    master_g_r_t = np.loadtxt(get_fn("O_O_rdf_t.txt")) 
--
--    assert eq(r_t, master_r_t)
--    assert eq(rdf_O_O, master_g_r_t, decimal=5)
-+#@pytest.mark.skipif(np.__version__ < "2.0", reason="Expected failure for NumPy < 2.0 due to histogram output differences")
-+#def test_compare_rdf_t_master(get_fn):
-+#    traj = md.load(get_fn("tip3p_300K_1ATM.xtc"), top=get_fn("tip3p_300K_1ATM.pdb"))
-+#
-+#    times = [[0,j] for j in range(100)]
-+#
-+#    pairs = traj.top.select_pairs("name O", "name O")
-+#    r_t, rdf_O_O = mdtraj.geometry.rdf.compute_rdf_t(traj, pairs, times)
-+#
-+#    master_r_t = np.loadtxt(get_fn("r_O_O_rdf_t.txt"))
-+#    master_g_r_t = np.loadtxt(get_fn("O_O_rdf_t.txt")) 
-+#
-+#    assert eq(r_t, master_r_t)
-+#    assert eq(rdf_O_O, master_g_r_t, decimal=5)
- 
- 
- def test_compare_n_concurrent_pairs(get_fn):
-diff '--color=auto' -urN mdtraj-1.10.3.orig/tests/test_sasa.py mdtraj-1.10.3/tests/test_sasa.py
---- mdtraj-1.10.3.orig/tests/test_sasa.py	2025-04-04 01:29:47.406044779 +0300
-+++ mdtraj-1.10.3/tests/test_sasa.py	2025-04-04 01:32:20.243021996 +0300
-@@ -103,14 +103,14 @@
-     np.testing.assert_approx_equal(true_frame_0_sasa, val2)
- 
- 
--def test_sasa_3(get_fn):
--    traj_ref = np.loadtxt(get_fn("gmx_sasa.dat"))
--    traj = md.load(get_fn("frame0.h5"))
--    traj_sasa = md.geometry.shrake_rupley(traj, probe_radius=0.14, n_sphere_points=960)
--
--    # the algorithm used by gromacs' g_sas is slightly different than the one
--    # used here, so the results are not exactly the same
--    np.testing.assert_array_almost_equal(traj_sasa, traj_ref, decimal=1)
-+#def test_sasa_3(get_fn):
-+#    traj_ref = np.loadtxt(get_fn("gmx_sasa.dat"))
-+#    traj = md.load(get_fn("frame0.h5"))
-+#    traj_sasa = md.geometry.shrake_rupley(traj, probe_radius=0.14, n_sphere_points=960)
-+#
-+#    # the algorithm used by gromacs' g_sas is slightly different than the one
-+#    # used here, so the results are not exactly the same
-+#    np.testing.assert_array_almost_equal(traj_sasa, traj_ref, decimal=1)
- 
- 
- def test_sasa_4(get_fn):
-diff '--color=auto' -urN mdtraj-1.10.3.orig/tests/test_trajectory.py mdtraj-1.10.3/tests/test_trajectory.py
---- mdtraj-1.10.3.orig/tests/test_trajectory.py	2025-04-04 01:29:47.406044779 +0300
-+++ mdtraj-1.10.3/tests/test_trajectory.py	2025-04-04 01:32:58.690788000 +0300
-@@ -871,24 +871,24 @@
-     assert hash(t1) == hash(t2)
- 
- 
--def test_smooth(get_fn):
--    from scipy.signal import butter, filtfilt, lfilter, lfilter_zi
--
--    pad = 5
--    order = 3
--    b, a = butter(order, 2.0 / pad)
--    zi = lfilter_zi(b, a)
--
--    signal = np.sin(np.arange(100))
--    padded = np.r_[signal[pad - 1 : 0 : -1], signal, signal[-1:-pad:-1]]
--
--    z, _ = lfilter(b, a, padded, zi=zi * padded[0])
--    z2, _ = lfilter(b, a, z, zi=zi * z[0])
--
--    output = filtfilt(b, a, padded)
--    test = np.loadtxt(get_fn("smooth.txt"))
--
--    eq(output, test)
-+#def test_smooth(get_fn):
-+#    from scipy.signal import butter, filtfilt, lfilter, lfilter_zi
-+#
-+#    pad = 5
-+#    order = 3
-+#    b, a = butter(order, 2.0 / pad)
-+#    zi = lfilter_zi(b, a)
-+#
-+#    signal = np.sin(np.arange(100))
-+#    padded = np.r_[signal[pad - 1 : 0 : -1], signal, signal[-1:-pad:-1]]
-+#
-+#    z, _ = lfilter(b, a, padded, zi=zi * padded[0])
-+#    z2, _ = lfilter(b, a, z, zi=zi * z[0])
-+#
-+#    output = filtfilt(b, a, padded)
-+#    test = np.loadtxt(get_fn("smooth.txt"))
-+#
-+#    eq(output, test)
- 
- 
- @pytest.mark.skip(reason="Broken, maybe only on Python 3.11")
diff --git a/sci-chemistry/mdtraj/mdtraj-1.10.3.ebuild b/sci-chemistry/mdtraj/mdtraj-1.10.3.ebuild
deleted file mode 100644
index 61c5ded6bf15..000000000000
--- a/sci-chemistry/mdtraj/mdtraj-1.10.3.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
-HOMEPAGE="https://mdtraj.org"
-SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
-LICENSE="LGPL-2.1+"
-
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/pyparsing[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/scipy[${PYTHON_USEDEP}]
-	dev-python/tables[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
-		dev-python/pytest-datadir[${PYTHON_USEDEP}]
-		dev-python/ipykernel[${PYTHON_USEDEP}]
-		dev-python/jupyter-client[${PYTHON_USEDEP}]
-		dev-python/nbformat[${PYTHON_USEDEP}]
-		dev-python/scikit-learn[${PYTHON_USEDEP}]
-	)
-"
-BDEPEND="
-	dev-python/cython[${PYTHON_USEDEP}]
-"
-
-PATCHES=( "${FILESDIR}/${PN}-1.10.3-tests.py" )
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
-	sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
-		-i basesetup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	rm -rf mdtraj* || die
-	epytest tests
-	epytest examples
-}
diff --git a/sci-chemistry/mdtraj/mdtraj-1.11.1_p1.ebuild b/sci-chemistry/mdtraj/mdtraj-1.11.1_p1.ebuild
deleted file mode 100644
index 35bc8c788826..000000000000
--- a/sci-chemistry/mdtraj/mdtraj-1.11.1_p1.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-PYTHON_COMPAT=( python3_{13..14} )
-
-DISTUTILS_EXT=1
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="Read, write and analyze MD trajectories with only a few lines of Python code"
-HOMEPAGE="https://mdtraj.org"
-SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/${PV/_p/.post}.tar.gz -> ${P}.gh.tar.gz"
-S="${WORKDIR}/${PN}-${PV/_p/.post}"
-
-LICENSE="LGPL-2.1+"
-
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/pandas[${PYTHON_USEDEP}]
-	dev-python/pyparsing[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/scipy[${PYTHON_USEDEP}]
-	dev-python/tables[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}
-	test? (
-		dev-python/pytest-rerunfailures[${PYTHON_USEDEP}]
-		dev-python/pytest-datadir[${PYTHON_USEDEP}]
-		dev-python/ipykernel[${PYTHON_USEDEP}]
-		dev-python/jupyter-client[${PYTHON_USEDEP}]
-		dev-python/nbformat[${PYTHON_USEDEP}]
-		dev-python/scikit-learn[${PYTHON_USEDEP}]
-	)
-"
-BDEPEND="
-	dev-python/cython[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
-	sed -e "s:re.match('build.*(mdtraj.*)', output_dir).group(1):'.':g" \
-		-i basesetup.py || die
-	distutils-r1_python_prepare_all
-}
-
-python_test() {
-	rm -rf mdtraj* || die
-	epytest tests
-	epytest examples
-}
diff --git a/sci-chemistry/mdtraj/metadata.xml b/sci-chemistry/mdtraj/metadata.xml
deleted file mode 100644
index b91aca7d360a..000000000000
--- a/sci-chemistry/mdtraj/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">mdtraj/mdtraj</remote-id>
-		<remote-id type="pypi">mdtraj</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/metadata.xml b/sci-chemistry/metadata.xml
deleted file mode 100644
index 3f779c2ba92b..000000000000
--- a/sci-chemistry/metadata.xml
+++ /dev/null
@@ -1,37 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE catmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<catmetadata>
-	<longdescription lang="en">
-		The sci-chemistry category contains software that can be used
-		in chemistral scientific environments.
-	</longdescription>
-	<longdescription lang="de">
-		Die Kategorie sci-chemistry enthält Software, welche in chemischen
-		und chemietechnischen Umgebungen genutzt werden kann.
-	</longdescription>
-	<longdescription lang="es">
-		La categoría sci-chemistry contiene programas que pueden ser utilizados
-		en entornos relacionados con la química.
-	</longdescription>
-	<longdescription lang="ja">
-		sci-chemistryカテゴリーには化学の科学的な分野に利用される
-		フトウェアが含まれています。
-	</longdescription>
-	<longdescription lang="nl">
-		De sci-chemistry categorie bevat software die in scheikundige omgevingen
-		gebruikt kan worden.
-	</longdescription>
-	<longdescription lang="vi">
-		Nhóm sci-chemistry chứa các phần mềm dùng trong hoá học.
-	</longdescription>
-	<longdescription lang="it">
-		La categoria sci-chemistry contiene programmi per la chimica.
-	</longdescription>
-	<longdescription lang="pt">
-		A categoria sci-chemistry contém programas que podem ser usados
-		em ambientes relacionados a química.
-	</longdescription>
-	<longdescription lang="pl">
-		Kategoria sci-chemistry zawiera programy naukowe związane z chemią.
-	</longdescription>
-</catmetadata>
diff --git a/sci-chemistry/moldy/Manifest b/sci-chemistry/moldy/Manifest
deleted file mode 100644
index c492c32f9de6..000000000000
--- a/sci-chemistry/moldy/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST moldy-2.16e.tar.gz 488410 BLAKE2B 44ff1dacc66922ba11297ca54c645f209b782b8cde50e427d54d1d249a93b718eeb865357ea47b820801fdbca325d5f0d6027fe11ce6e0a842e77d1970a0467c SHA512 b672f4e5c8843277d1b66eedf5f7ad87be0b4c014e0d6bfda4ef941cd9bfeec68d94a361e28531cc3794ee2e4a6937f15c462c69f9adcfcfe5254c3c677fe877
diff --git a/sci-chemistry/moldy/files/2.16e-as-needed.patch b/sci-chemistry/moldy/files/2.16e-as-needed.patch
deleted file mode 100644
index 67399e08560e..000000000000
--- a/sci-chemistry/moldy/files/2.16e-as-needed.patch
+++ /dev/null
@@ -1,65 +0,0 @@
-diff --git a/Makefile.in b/Makefile.in
-index 0b02f00..ec588a8 100644
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -115,25 +115,25 @@ VMSBUILD=	compile_moldy.com link_moldy.com defcomm.com\
- 
- DOSBUILD=	Makefile.mak OFILES.RSP SHAKOBJS.RSP Makefile.w32
- 
--all:		moldy utilities Makefile
-+all:		moldy utilities
- 
- moldy:		$(OFILES) $(EXTRA_OBJ) $(HFILES)
--		$(CC) -o moldy $(LDFLAGS) $(OFILES) $(EXTRA_OBJ)  $(LIBS)
-+		$(CC) $(LDFLAGS) -o moldy $(LDFLAGS) $(OFILES) $(EXTRA_OBJ)  $(LIBS)
- 
- moldyext:	moldyext.c $(LIBOBJS) $(HFILES)
--		$(CC) $(CFLAGS) -o moldyext $(OPT) $(DEFS) $(LDFLAGS1) moldyext.c $(LIBOBJS) $(LDFLAGS) $(LIBS)
-+		$(CC) $(LDFLAGS) $(CFLAGS) -o moldyext $(OPT) $(DEFS) $(LDFLAGS1) moldyext.c $(LIBOBJS) $(LIBS)
- 
- manalyze:	manalyze.c $(HFILES)
--		$(CC) $(CFLAGS)  -o manalyze $(OPT) $(DEFS) $(LDFLAGS1) manalyze.c $(LDFLAGS) $(LIBS)
-+		$(CC) $(LDFLAGS) $(CFLAGS)  -o manalyze $(OPT) $(DEFS) $(LDFLAGS1) manalyze.c $(LIBS)
- 
- dumpanal:	dumpanal.c xdr.o $(HFILES)
--		$(CC) $(CFLAGS) -o dumpanal $(OPT) $(DEFS) $(LDFLAGS1) dumpanal.c xdr.o  $(LDFLAGS) $(LIBS)
-+		$(CC) $(LDFLAGS) $(CFLAGS) -o dumpanal $(OPT) $(DEFS) $(LDFLAGS1) dumpanal.c xdr.o $(LIBS)
- 
- dumpext:	dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(HFILES)
--		$(CC) $(CFLAGS) -o dumpext $(OPT) $(DEFS) $(LDFLAGS1) dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(LDFLAGS) $(LIBS)
-+		$(CC) $(LDFLAGS) $(CFLAGS) -o dumpext $(OPT) $(DEFS) $(LDFLAGS1) dumpext.c xdr.o utlsup.o matrix.o $(LIBOBJS) $(LIBS)
- 
- dumpconv:	dumpconv.c xdr.o $(HFILES)
--		$(CC) $(CFLAGS) -o dumpconv $(OPT) $(DEFS) $(LDFLAGS1) dumpconv.c xdr.o $(LDFLAGS) $(LIBS)
-+		$(CC) $(LDFLAGS) $(CFLAGS) -o dumpconv $(OPT) $(DEFS) $(LDFLAGS1) dumpconv.c xdr.o $(LIBS)
- 
- #mdtraj:		mdtraj.o $(SHAKOBJS) $(LIBOBJS) 
- #		$(CC) -o mdtraj $(LDFLAGS) mdtraj.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
-@@ -142,21 +142,21 @@ mdshak:		mdshak.o $(SHAKOBJS) $(LIBOBJS)
- 		$(CC) -o mdshak $(LDFLAGS) mdshak.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
- 
- msd:		msd.o $(SHAKOBJS) $(LIBOBJS) 
--		$(CC) -o msd $(LDFLAGS1) msd.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS)
-+		$(CC) $(LDFLAGS) -o msd $(LDFLAGS1) msd.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
- 
- mdvaf:		mdvaf.o $(SHAKOBJS) $(LIBOBJS) 
--		$(CC) -o mdvaf $(LDFLAGS1) mdvaf.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS) $(LIBS)
-+		$(CC) $(LDFLAGS) -o mdvaf $(LDFLAGS1) mdvaf.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
- mdavpos:	mdavpos.o $(SHAKOBJS) $(LIBOBJS) 
--		$(CC) -o mdavpos $(LDFLAGS1) mdavpos.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS)  $(LIBS)
-+		$(CC) $(LDFLAGS) -o mdavpos $(LDFLAGS1) mdavpos.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
- 
- mdbond:	mdbond.o $(SHAKOBJS) $(LIBOBJS) 
--		$(CC) -o mdbond $(LDFLAGS1) mdbond.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS)  $(LIBS)
-+		$(CC) $(LDFLAGS) -o mdbond $(LDFLAGS1) mdbond.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
- 
- bdist:	bdist.c $(HFILES)
--		$(CC) $(CFLAGS)  -o bdist $(OPT) $(DEFS) $(LDFLAGS1) bdist.c $(LIBOBJS) $(LDFLAGS) $(LIBS)
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o bdist $(OPT) $(DEFS) $(LDFLAGS1) bdist.c $(LIBOBJS) $(LIBS)
- 
- ransub:	ransub.o $(SHAKOBJS) $(LIBOBJS) 
--		$(CC) -o ransub $(LDFLAGS1) ransub.o $(SHAKOBJS) $(LIBOBJS) $(LDFLAGS)  $(LIBS)
-+		$(CC) $(LDFLAGS) -o ransub $(LDFLAGS1) ransub.o $(SHAKOBJS) $(LIBOBJS) $(LIBS)
- 
- utilities:	$(UTILS) $(UTILS2)
- 
diff --git a/sci-chemistry/moldy/metadata.xml b/sci-chemistry/moldy/metadata.xml
deleted file mode 100644
index d4ff1000a775..000000000000
--- a/sci-chemistry/moldy/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild b/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
deleted file mode 100644
index 65272b35cf77..000000000000
--- a/sci-chemistry/moldy/moldy-2.16e-r2.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Molecular dynamics simulations platform"
-HOMEPAGE="http://www.ccp5.ac.uk/moldy/moldy.html"
-SRC_URI="ftp://ftp.earth.ox.ac.uk/pub/keith/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-IUSE="doc"
-
-BDEPEND="doc? ( virtual/latex-base )"
-
-S="${WORKDIR}"
-
-PATCHES=( "${FILESDIR}"/${PV}-as-needed.patch )
-
-src_prepare() {
-	default
-	sed \
-		-e 's:-O2::g' \
-		-e 's:-ffast-math::g' \
-		-i configure || die
-}
-
-src_configure() {
-	# bug #944874
-	append-cflags -std=gnu17
-
-	#Individuals may want to edit the OPT* variables below.
-	#From the READ.ME:
-	#You may need to  "hand-tune" compiler or optimization options,
-	#which may be specified by setting the OPT and OPT2 environment
-	#variables.  OPT2 is used to compile only the most performance-critical
-	#modules and usually will select a very high level of optimization.
-	#It should be safe to select an optimization which means "treat all
-	#function arguments as restricted pointers which are not aliased to
-	#any other object".  OPT is used for less preformance-critical modules
-	#and may be set to a lower level of optimization than OPT2.
-
-	OPT="${CFLAGS}" \
-	OPT2="${CFLAGS} ${CFLAGS_OPT}" \
-	CC="$(tc-getCC)" \
-	econf
-}
-
-src_compile() {
-	emake
-
-	# To prevent sandbox violations by metafont
-	if use doc; then
-		VARTEXFONTS="${T}"/fonts emake moldy.pdf
-	fi
-}
-
-src_install() {
-	dodir /usr/bin
-	emake prefix="${ED}"/usr install
-	dodoc BENCHMARK READ.ME RELNOTES
-
-	rm Makefile.in configure.in config.h.in || die
-	insinto /usr/share/${PN}/examples/
-	doins *.in *.out control.*
-
-	if use doc; then
-		docinto pdf
-		newdoc moldy.pdf moldy-manual.pdf
-	fi
-}
diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
deleted file mode 100644
index 917a0546bb34..000000000000
--- a/sci-chemistry/molmol/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c50304348f76759dd3125cd74d02e629383d4a566f28ac77ab89ecf5e17a82617b8f61525e6f454689840b27899827399d866 SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe
-DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b
-DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287
-DIST molmol_256.png 22668 BLAKE2B c7d75b8e0d738b48790bea25e21ec60d57a8181253518c70d6f18d93c64eef3c9acf90213fdbdf2dde272e85a04a6442e4e4a9c375829f369380d88c9c0ca57c SHA512 5e7975f54a7462161dc630ee973e9a8126b9c120e0d8d6b62007384c970ce39792e52300edc25dc7a85209845801d749d9ecba02899f3e18b18f5a5fdbc28a97
diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch b/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch
deleted file mode 100644
index 7041ced28efe..000000000000
--- a/sci-chemistry/molmol/files/molmol-2k_p2-gcc14-fix.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Bug: https://bugs.gentoo.org/923325
---- a/src/motogl/MotOGLDump.c
-+++ b/src/motogl/MotOGLDump.c
-@@ -245,7 +245,7 @@ jpegErrHand(j_common_ptr jpegInfoP)
- 
- #ifdef PNG_SUPPORT
- static void
--pngErrHand(png_structp pngStrucP, char *errMsg)
-+pngErrHand(png_structp pngStrucP, const char *errMsg)
- {
-   IORaiseError(errMsg);
-   longjmp(png_jmpbuf(pngStrucP), 1);
diff --git a/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch b/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch
deleted file mode 100644
index 6129ed03b3ab..000000000000
--- a/sci-chemistry/molmol/files/molmol-2k_p2-transform-makefiles.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-Transformed multiple seds to this patch. `MOLMOLHOME` is the runtime variable
-that depends on knowledge of paths that I didn't think of how to correctly
-pass beyond editing it with sed. For everything else, it is here and changed
-to work correctly with build system.
-Rolled up sed transformations were to made build system non-parallel,
-fix environmental variables, remove sleep and add use right shell and
-build dependencies in startup script.
---- a/makedef.lnx
-+++ b/makedef.lnx
-@@ -11,12 +11,12 @@
- 
- XINCL   = -I/usr/X11R6/include
- 
--CC=gcc
-+CC ?= gcc
- MCPPFLAGS =
--MCFLAGS =-pipe -O3 -ffast-math -march=i686 -mcpu=i686
-+MCFLAGS := $(CFLAGS)
- 
- RANLIB   = /bin/true
--WAIT     = sleep 2
-+WAIT     = sleep 0
- SHELL    = /bin/sh
- CPP      = /lib/cpp
- 
---- a/molmol
-+++ b/molmol
-@@ -1,9 +1,10 @@
--#!/bin/ksh
-+#!/bin/sh
- #
- # startup script for MOLMOL
- #
- 
--MOLMOLHOME=/opt/group/MOLMOL
-+MOLMOLHOME=/;
-+MOLMOLDEV="Motif/OpenGL"
- export MOLMOLHOME
- export MOLMOLDEV
- 
diff --git a/sci-chemistry/molmol/metadata.xml b/sci-chemistry/molmol/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/molmol/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild
deleted file mode 100644
index 045af390992a..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild
+++ /dev/null
@@ -1,103 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit desktop toolchain-funcs flag-o-matic
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-
-# Original page dead
-#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-HOMEPAGE="
-	http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html
-	http://pjf.net/science/molmol.html
-"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2
-	https://dev.gentoo.org/~pacho/${PN}/${PN}_256.png
-"
-S="${WORKDIR}"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-
-RDEPEND="
-	|| (
-		(
-			media-libs/mesa[X(+)]
-			x11-libs/libGLw
-		)
-		media-libs/mesa[motif(-),X(+)]
-	)
-	media-libs/libjpeg-turbo:=
-	media-libs/libpng:=
-	media-libs/tiff:=
-	virtual/zlib:=
-	virtual/glu
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo
-	media-fonts/font-adobe-100dpi
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc14-fix.patch
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	"${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-	"${WORKDIR}"/patches/ldflags.patch
-	"${WORKDIR}"/patches/opengl.patch
-	"${WORKDIR}"/patches/cast.patch
-	# patch from fink
-	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	"${WORKDIR}"/patches/${P}-fink.patch
-	"${WORKDIR}"/patches/wild.patch
-
-	"${FILESDIR}"/${P}-transform-makefiles.patch
-)
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-}
-
-src_prepare() {
-	default
-	eapply -p0 "${WORKDIR}"/patches/libpng15.patch
-	rm -rf tiff*
-
-	sed \
-		-e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR}|" \
-		-i "${S}"/molmol || die
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	# Parallel build fails (#880621) and cannot be disabled by MAKEOPTS
-	# (#880621, #941488).
-	find . -name Makefile -exec sed -i -e "1i .NOTPARALLEL:" {} + || die
-
-	# https://bugs.gentoo.org/944200
-	# uses C polymorphism. Can't be trivially patched
-	append-cflags -std=gnu17
-	tc-export AR CC
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	doexe src/main/molmol
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	make_desktop_entry "${PN}" MOLMOL
-	newicon "${DISTDIR}/${PN}_256.png" "${PN}.png"
-
-	einstalldocs
-	dodoc HISTORY
-}
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
deleted file mode 100644
index 508f37f78209..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r9.ebuild
+++ /dev/null
@@ -1,109 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-inherit desktop toolchain-funcs
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-
-# Original page dead
-#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-HOMEPAGE="
-	http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html
-	http://pjf.net/science/molmol.html
-"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2
-	https://dev.gentoo.org/~pacho/${PN}/${PN}_256.png
-"
-S="${WORKDIR}"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86"
-
-RDEPEND="
-	|| (
-		(
-			media-libs/mesa[X(+)]
-			x11-libs/libGLw
-		)
-		media-libs/mesa[motif(-),X(+)]
-	)
-	media-libs/libjpeg-turbo:=
-	media-libs/libpng:=
-	media-libs/tiff:=
-	virtual/zlib:=
-	virtual/glu
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gcc14-fix.patch
-)
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-}
-
-src_prepare() {
-	default
-
-	rm -rf tiff*
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	eapply "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-
-	eapply "${WORKDIR}"/patches/ldflags.patch
-	eapply "${WORKDIR}"/patches/opengl.patch
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	sed \
-		-e "s|ksh|sh|" \
-		-e "s|^MOLMOLHOME.*|MOLMOLHOME=${EPREFIX}/${MMDIR};MOLMOLDEV=\"Motif/OpenGL\"|" \
-		-i "${S}"/molmol || die
-	sed \
-		-e "s|^MCFLAGS.*|MCFLAGS = ${CFLAGS}|" \
-		-e "s|^CC.*|CC = $(tc-getCC)|" \
-		-i "${S}"/makedef || die
-
-	eapply "${WORKDIR}"/patches/cast.patch
-	eapply -p0 "${WORKDIR}"/patches/libpng15.patch
-
-	# patch from fink
-	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	eapply "${WORKDIR}"/patches/${P}-fink.patch
-
-	eapply "${WORKDIR}"/patches/wild.patch
-	tc-export AR
-
-	# Parallel build fails (#880621) and cannot be disabled by MAKEOPTS
-	# (#880621, #941488).
-	find . -name Makefile -exec sed -i -e "1i .NOTPARALLEL:" {} + || die
-	# Try to drop the ugly hardcoded sleep now that make is really
-	# serial
-	sed -i -e 's/sleep 2/sleep 0/g' makedef || die
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	doexe src/main/molmol
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	make_desktop_entry "${PN}" MOLMOL
-	newicon "${DISTDIR}/${PN}_256.png" "${PN}.png"
-
-	einstalldocs
-	dodoc HISTORY
-}
diff --git a/sci-chemistry/molsketch/Manifest b/sci-chemistry/molsketch/Manifest
deleted file mode 100644
index f0a4638205b6..000000000000
--- a/sci-chemistry/molsketch/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST Molsketch-0.8.3-src.tar.gz 1855805 BLAKE2B 6f221c170d8f6c9af6ab5b9db479c9a1052047331455b13c7aaf00b851793ed0db9b6de66954734858a56c5a6bf0009582aa084c612161925315352c2e5401ab SHA512 336266f59ca119972bb3820b366abe57a524016658e715524d48570e2077dc4a211711e4de2df24b3f760a4e4826fff8966af53d2b4aad91f2755471c45cc728
-DIST Molsketch-0.8.4-src.tar.gz 1855977 BLAKE2B 4cf2e7ae26da1b15a5feb7843a853557d0e8b1594ea080767a234ba2cc238f837e46651ba4eb5698330c5c56fc39695c5596278033d4287772dd22b6b26ee501 SHA512 14f544c8fc30ee9b11ff056c248890ca33bbc02a19d93142ae0106539cbba73eae04ba3c6506df8a3e6d997ef4a1f75c7a3490467a2023cd32c20e186e8a0188
diff --git a/sci-chemistry/molsketch/metadata.xml b/sci-chemistry/molsketch/metadata.xml
deleted file mode 100644
index 180494b54d2f..000000000000
--- a/sci-chemistry/molsketch/metadata.xml
+++ /dev/null
@@ -1,20 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription lang="en">
-		Molsketch is a 2D molecular editing tool. Its goal is to help you draw
-		molecules quick and easily. Of course you're creation can be exported
-		afterwards in high quality in a number of vector and bitmap formats.
-	</longdescription>
-	<use>
-		<flag name="openbabel">Interface for <pkg>sci-chemistry/openbabel</pkg> to support many file formats</flag>
-	</use>
-	<upstream>
-		<remote-id type="sourceforge">molsketch</remote-id><!-- old -->
-		<remote-id type="github">hvennekate/Molsketch</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/molsketch/molsketch-0.8.3.ebuild b/sci-chemistry/molsketch/molsketch-0.8.3.ebuild
deleted file mode 100644
index 50ba01864559..000000000000
--- a/sci-chemistry/molsketch/molsketch-0.8.3.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake optfeature xdg
-
-DESCRIPTION="Drawing tool for 2D molecular structures"
-HOMEPAGE="https://molsketch.sourceforge.io/ https://github.com/hvennekate/Molsketch/"
-SRC_URI="https://downloads.sourceforge.net/project/${PN}/Molsketch/${P^}-src.tar.gz"
-S="${WORKDIR}/${P^}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="openbabel"
-
-DEPEND="
-	dev-qt/qtbase:6[gui,network,widgets]
-	dev-qt/qtsvg:6
-	openbabel? ( >=sci-chemistry/openbabel-3:= )
-"
-RDEPEND="${DEPEND}"
-BDEPEND="dev-qt/qttools:6[linguist]"
-
-src_configure() {
-	local mycmakeargs=(
-		-DMSK_OBABELIFACE="$(usex openbabel)"
-		-DMSK_QT6=ON
-	)
-	cmake_src_configure
-}
-
-pkg_postinst() {
-	xdg_pkg_postinst
-
-	use openbabel && optfeature "wikiquery support through openbabel inchi interface" "sci-chemistry/openbabel[inchi]"
-}
diff --git a/sci-chemistry/molsketch/molsketch-0.8.4.ebuild b/sci-chemistry/molsketch/molsketch-0.8.4.ebuild
deleted file mode 100644
index 50ba01864559..000000000000
--- a/sci-chemistry/molsketch/molsketch-0.8.4.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake optfeature xdg
-
-DESCRIPTION="Drawing tool for 2D molecular structures"
-HOMEPAGE="https://molsketch.sourceforge.io/ https://github.com/hvennekate/Molsketch/"
-SRC_URI="https://downloads.sourceforge.net/project/${PN}/Molsketch/${P^}-src.tar.gz"
-S="${WORKDIR}/${P^}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="openbabel"
-
-DEPEND="
-	dev-qt/qtbase:6[gui,network,widgets]
-	dev-qt/qtsvg:6
-	openbabel? ( >=sci-chemistry/openbabel-3:= )
-"
-RDEPEND="${DEPEND}"
-BDEPEND="dev-qt/qttools:6[linguist]"
-
-src_configure() {
-	local mycmakeargs=(
-		-DMSK_OBABELIFACE="$(usex openbabel)"
-		-DMSK_QT6=ON
-	)
-	cmake_src_configure
-}
-
-pkg_postinst() {
-	xdg_pkg_postinst
-
-	use openbabel && optfeature "wikiquery support through openbabel inchi interface" "sci-chemistry/openbabel[inchi]"
-}
diff --git a/sci-chemistry/mpqc/Manifest b/sci-chemistry/mpqc/Manifest
deleted file mode 100644
index 014f43df34f4..000000000000
--- a/sci-chemistry/mpqc/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mpqc-2.3.1.tar.bz2 2521392 BLAKE2B 0c2cd9ac2fe32791ab5f0226972b5f1376e5f0ed368e12f6e89f8ff44cb11e4e2cf150f24b3768eb119e94289aca989a5287fef9b51dbd67e2856e944b61c299 SHA512 34f24f72c6c0024e72d47c7fd17927ca2a88020b30d22a791954fbc933f67ed6dd6741ee8a80ddd4fdb007f1a357b5f5ea7fc284cab85474bf60e9f29aaaa747
diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-MPI-3.0.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-MPI-3.0.patch
deleted file mode 100644
index d03d1f9b0566..000000000000
--- a/sci-chemistry/mpqc/files/mpqc-2.3.1-MPI-3.0.patch
+++ /dev/null
@@ -1,37 +0,0 @@
-https://bugs.gentoo.org/801682
-rename MPI 1.0 to 3.0+ functions:
-- MPI_Errhandler_set -> MPI_Comm_set_errhandler
-
---- a/src/lib/util/group/memmtmpi.cc
-+++ b/src/lib/util/group/memmtmpi.cc
-@@ -241,8 +241,8 @@
-   MPI_Comm_dup(comm, &comp_comm_);
-   MPI_Comm_dup(comm, &comm_comm_);
- 
--  MPI_Errhandler_set(comp_comm_, MPI_ERRORS_ARE_FATAL);
--  MPI_Errhandler_set(comm_comm_, MPI_ERRORS_ARE_FATAL);
-+  MPI_Comm_set_errhandler(comp_comm_, MPI_ERRORS_ARE_FATAL);
-+  MPI_Comm_set_errhandler(comm_comm_, MPI_ERRORS_ARE_FATAL);
- 
-   serial_ = 0;
-   req_tag_ = 15001;
---- a/src/lib/util/group/messmpi.cc
-+++ b/src/lib/util/group/messmpi.cc
-@@ -129,7 +129,7 @@
-   if (keyval->booleanvalue("errors_return")) {
-       if (me()==0)
-           ExEnv::outn() << indent << "MPIMessageGrp: errors_return is true" << endl;
--      MPI_Errhandler_set(commgrp, MPI_ERRORS_RETURN);
-+      MPI_Comm_set_errhandler(commgrp, MPI_ERRORS_RETURN);
-     }
- 
-   if (debug_) {
-@@ -200,7 +200,7 @@
-   MPI_Comm_dup(comm, &commgrp);
-   global_commgrp = commgrp;
- 
--  MPI_Errhandler_set(commgrp, MPI_ERRORS_ARE_FATAL);
-+  MPI_Comm_set_errhandler(commgrp, MPI_ERRORS_ARE_FATAL);
- 
-    if (!nmpi_grps) {
-       threadgrp = ThreadGrp::get_default_threadgrp();
diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch
deleted file mode 100644
index a917c0aaff70..000000000000
--- a/sci-chemistry/mpqc/files/mpqc-2.3.1-as-needed.patch
+++ /dev/null
@@ -1,163 +0,0 @@
---- mpqc-2.3.1.orig/src/lib/chemistry/molecule/Makefile	2005-05-26 08:00:29.000000000 +0200
-+++ mpqc-2.3.1/src/lib/chemistry/molecule/Makefile	2010-02-13 14:28:46.514285918 +0100
-@@ -66,6 +66,12 @@
- interface:: $(DEPENDINCLUDE)
- 
- LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/LIBS.h)
-+LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCcontainer.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCclass.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCoptimize.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCscmat.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCsymmetry.la
- 
- LD = $(CXX)
- 
---- mpqc-2.3.1.orig/src/lib/chemistry/qc/wfn/Makefile	2004-06-12 06:50:35.000000000 +0200
-+++ mpqc-2.3.1/src/lib/chemistry/qc/wfn/Makefile	2010-02-13 14:20:06.911896080 +0100
-@@ -48,6 +48,12 @@
- 
- LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/../dft/LIBS.h)
- 
-+LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCisosurf.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCsolvent.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCbasis.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCdft.la \
-+	$(SRCDIR)/$(TOPDIR)/lib/libSCintv3.la
-+
- wfntest:: wfntest.$(OBJSUF) $(LIBS)
- 	$(LTLINK) $(CXX) $(LDFLAGS) -o wfntest $^ $(SYSLIBS) $(LTLINKBINOPTS)
- 
---- mpqc-2.3.1.orig/src/lib/chemistry/qc/intv3/Makefile	2002-04-04 01:08:04.000000000 +0200
-+++ mpqc-2.3.1/src/lib/chemistry/qc/intv3/Makefile	2010-02-13 14:04:15.393432311 +0100
-@@ -52,6 +52,8 @@
- LIBOBJ = $(LIBSRC:%.c=%.$(OBJSUF))
- LIBOBJ := $(LIBOBJ:%.cc=%.$(OBJSUF))
- 
-+LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCoint3.la
-+
- DISTFILES = $(TESTCSRC) $(INC) atoms.sgen Makefile LIBS.h
- 
- DEPENDINCLUDE = $(INC) $(GENINC) $(SGENINC)
---- mpqc-2.3.1.orig/src/lib/chemistry/qc/mbpt/Makefile	2005-07-07 17:54:05.000000000 +0200
-+++ mpqc-2.3.1/src/lib/chemistry/qc/mbpt/Makefile	2010-02-13 14:12:38.975370147 +0100
-@@ -44,6 +44,7 @@
- CSRCS = bzerofast.c
- 
- LIBOBJ= $(CXXSRCS:%.cc=%.$(OBJSUF)) $(CSRCS:%.c=%.$(OBJSUF))
-+LIBADD= $(SRCDIR)/$(TOPDIR)/lib/libSCsymmetry.la
- 
- default:: $(DEPENDINCLUDE)
- 
---- mpqc-2.3.1.orig/src/lib/chemistry/qc/basis/Makefile	2004-02-11 01:24:43.000000000 +0100
-+++ mpqc-2.3.1/src/lib/chemistry/qc/basis/Makefile	2010-02-13 14:04:15.395432868 +0100
-@@ -59,6 +59,7 @@
- DISTFILES = $(CXXSRC) $(INC) Makefile $(TESTSRC) $(TESTFILES)
- 
- LIBOBJ= $(CXXSRC:%.cc=%.$(OBJSUF))
-+LIBADD = $(SYSLIBS)
- 
- default:: $(DEPENDINCLUDE)
- 
---- mpqc-2.3.1.orig/src/lib/math/scmat/Makefile	2003-09-16 17:07:03.000000000 +0200
-+++ mpqc-2.3.1/src/lib/math/scmat/Makefile	2010-02-13 14:27:36.028370446 +0100
-@@ -75,6 +75,8 @@
- DISTFILES = $(CXXSRC) $(INC) scmat.h $(WEBSRC) Makefile LIBS.h \
-             $(TESTSRC) $(TESTFILES)
- 
-+LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCgroup.la $(SYSLIBS)
-+
- LIBS = $(shell $(LISTLIBS) $(INCLUDE) $(SRCDIR)/LIBS.h)
- 
- matrixtest:
---- mpqc-2.3.1.orig/src/lib/util/class/Makefile	2005-05-26 08:00:49.000000000 +0200
-+++ mpqc-2.3.1/src/lib/util/class/Makefile	2010-02-13 14:04:15.396433004 +0100
-@@ -41,6 +41,7 @@
- 
- BIN_OR_LIB = LIB
- TARGET_TO_MAKE = libSCclass
-+LIBADD = $(SYSLIBS)
- 
- TESTCXXSRC = classtest.cc scextest.cc
- DISTFILES = $(CXXSRC) $(INC) Makefile LIBS.h $(TESTCXXSRC)
---- mpqc-2.3.1.orig/src/lib/util/state/Makefile	2005-05-26 08:00:51.000000000 +0200
-+++ mpqc-2.3.1/src/lib/util/state/Makefile	2010-02-13 14:22:06.302369965 +0100
-@@ -50,6 +50,7 @@
- 
- BIN_OR_LIB = LIB
- TARGET_TO_MAKE = libSCstate
-+LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la
- 
- default:: $(DEPENDINCLUDE)
- 
---- mpqc-2.3.1.orig/src/lib/util/group/Makefile	2005-07-30 02:30:18.000000000 +0200
-+++ mpqc-2.3.1/src/lib/util/group/Makefile	2010-02-13 14:21:38.582370124 +0100
-@@ -61,6 +61,7 @@
- 
- BIN_OR_LIB = LIB
- TARGET_TO_MAKE = libSCgroup
-+LIBADD = $(SRCDIR)/$(TOPDIR)/lib/libSCkeyval.la
- 
- TESTCXXSRC = pooltest.cc messtest.cc rnglocktest.cc thrtest.cc prttest.cc
- DISTFILES = $(REQUIREDCXXSRC) $(OPTIONALCXXSRC) $(INC) \
---- mpqc-2.3.1.orig/src/lib/util/Makefile	2001-08-07 00:29:56.000000000 +0200
-+++ mpqc-2.3.1/src/lib/util/Makefile	2010-02-13 14:40:23.611369920 +0100
-@@ -5,7 +5,7 @@
- 
- include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile
- 
--SUBDIRS = options ref container class state misc keyval group render
-+SUBDIRS = options keyval ref container class state misc group render
- 
- include $(SRCDIR)/$(TOPDIR)/lib/GlobalSubDirs
- 
---- mpqc-2.3.1.orig/lib/GlobalRules	2010-02-13 19:47:19.019432588 +0100
-+++ mpqc-2.3.1/lib/GlobalRules	2010-02-13 19:47:57.760370198 +0100
-@@ -75,7 +75,7 @@
- 	$(RANLIB) $@
- 
- $(TOPDIR)/lib/$(TARGET_TO_MAKE).la: $(LIBOBJ)
--	$(LTLINK) $(CXX) -o $@ $^ $(wildcard $(TMPLREPO)/*.o) $(LTLINKLIBOPTS)
-+	$(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(wildcard $(TMPLREPO)/*.o) $(LTLINKLIBOPTS) $(LIBADD)
- 
- else
- 
-@@ -104,7 +104,7 @@
- endif
- 
- $(TOPDIR)/lib/$(TARGET_TO_MAKE).la: $(LIBOBJ)
--	$(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS)
-+	$(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS) $(LIBADD)
- 
- endif
- 
---- mpqc-2.3.1.orig/doc/devsamp/Makefile	2004-04-28 22:45:14.000000000 +0200
-+++ mpqc-2.3.1/doc/devsamp/Makefile	2010-02-13 19:58:56.958452043 +0100
-@@ -9,4 +9,4 @@
- LTLINKBINOPTS := $(shell $(SCCONFIG) --ltlinkbinopts)
- 
- mp2: mp2.o
--	$(LTLINK) $(CXX) $(CXXFLAGS) -o $@ $^ -L$(LIBDIR) -lmpqc $(LIBS) $(LTLINKBINOPTS)
-+	$(LTLINK) $(CXX) $(LDFLAGS) $(CXXFLAGS) -o $@ $^ -L$(LIBDIR) -lmpqc $(LIBS) $(LTLINKBINOPTS)
---- mpqc-2.3.1.orig/src/bin/mpqc/Makefile	2005-07-28 18:57:47.000000000 +0200
-+++ mpqc-2.3.1/src/bin/mpqc/Makefile	2010-02-13 19:57:40.484216235 +0100
-@@ -82,7 +82,7 @@
- 	$(RANLIB) $@
- 
- $(TOPDIR)/lib/libmpqc.la: $(BINOBJ)
--	$(LTLINK) $(CXX) -o $@ $^ $(LTLINKLIBOPTS)
-+	$(LTLINK) $(CXX) $(LDFLAGS) -o $@ $^ $(LTLINKLIBOPTS)
- 
- install_devel:: $(TOPDIR)/lib/libmpqc.$(LIBSUF)
- 	$(INSTALL) $(INSTALLDIROPT) $(installroot)$(libdir)
---- mpqc-2.3.1.orig/src/lib/chemistry/qc/Makefile.orig	2010-06-18 18:09:58.192621760 +0000
-+++ mpqc-2.3.1/src/lib/chemistry/qc/Makefile	2010-06-18 18:10:10.350261767 +0000
-@@ -33,7 +33,7 @@
- include $(SRCDIR)/$(TOPDIR)/lib/GlobalMakefile
- include $(TOPDIR)/lib/Makedirlist
- 
--SUBDIRS = basis oint3 intv3 wfn scf dft mbpt
-+SUBDIRS = basis oint3 intv3 dft wfn scf mbpt
- ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_PSI),yes)
- SUBDIRS := $(SUBDIRS) psi
- endif
diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch
deleted file mode 100644
index b99c82fb71da..000000000000
--- a/sci-chemistry/mpqc/files/mpqc-2.3.1-blas.patch
+++ /dev/null
@@ -1,55 +0,0 @@
- configure.in |   36 +++---------------------------------
- 1 files changed, 3 insertions(+), 33 deletions(-)
-
-diff --git a/configure.in b/configure.in
-index ee82977..caae1f9 100644
---- a/configure.in
-+++ b/configure.in
-@@ -1487,44 +1487,14 @@ AC_LANG_CPLUSPLUS
- LIBSSAV="$LIBS"
- LIBS="$LIBSSAV $FLIBS"
- 
--LIBBLAS=""
--F77_DGEMM=`$PERL $srcdir/bin/mkf77sym.pl.in -method $F77_SYMBOLS DAXPY`
--AC_CHECK_FUNC($F77_DGEMM,HAVE_BLAS=yes,[
--  AC_CHECK_LIB(essl,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lessl"],
--    AC_CHECK_LIB(blas,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lblas"])
--  )]
--)
--if test X$HAVE_BLAS != Xyes; then
--  LIBSSAV2="$LIBS"
--  LIBS="-latlas $LIBS"
--  AC_CHECK_LIB(f77blas,$F77_DGEMM,[HAVE_BLAS=yes;LIBBLAS="-lf77blas -latlas"],
--               LIBS="$LIBSSAV2")
--fi
--AC_SUBST(HAVE_BLAS)
--if test X$HAVE_BLAS != Xyes; then
--  echo "WARNING: Could not link to the BLAS library.  It can be obtained at"
--  echo "http://www.netlib.org/blas.  Use --with-libdirs and/or --with-libs"
--  echo "to specify the name of the library."
--  AC_MSG_ERROR([BLAS is required to complete the build])
--fi
-+PKG_CHECK_MODULES([BLAS], [blas], [LIBBLAS="${BLAS_LIBS}"])
- 
- LIBS="$LIBSSAV $LIBBLAS $FLIBS"
- 
--LIBLAPACK=""
--F77_DGESVD=`$PERL $srcdir/bin/mkf77sym.pl.in -method $F77_SYMBOLS DGESVD`
--AC_CHECK_FUNC($F77_DGESVD,HAVE_LAPACK=yes,[
--  AC_CHECK_LIB(lapack,$F77_DGESVD,[HAVE_LAPACK=yes;LIBLAPACK="-llapack"]
--  )]
--)
--AC_SUBST(HAVE_LAPACK)
--if test X$HAVE_LAPACK != Xyes; then
--  echo "Could not link to the LAPACK library.  It can be obtained at"
--  echo "http://www.netlib.org/lapack.  Use --with-libdirs and/or --with-libs"
--  echo "to specify the name of the library."
--  AC_MSG_ERROR([LAPACK is required to complete the build])
--fi
-+PKG_CHECK_MODULES([LAPACK], [lapack], [LIBLAPACK="${LAPACK_LIBS}"])
- 
- FLIBS="$LIBLAPACK $LIBBLAS $FLIBS"
-+
- AC_LANG_RESTORE
- 
- dnl ----------- check for Scalable BLAS library --------------
diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch
deleted file mode 100644
index c38c9579ddde..000000000000
--- a/sci-chemistry/mpqc/files/mpqc-2.3.1-respect-ldflags.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- mpqc-2.3.1.orig/configure.in	2006-03-22 19:04:54.000000000 +0100
-+++ mpqc-2.3.1/configure.in	2010-02-13 17:46:19.545557872 +0100
-@@ -10,6 +10,8 @@
- AC_CONFIG_HEADER(src/lib/scconfig.h)
- AC_CONFIG_AUX_DIR(bin)
- 
-+m4_include([lib/autoconf/cca.m4])
-+m4_include([lib/autoconf/acinclude.m4])
- AC_CANONICAL_SYSTEM
- 
- AC_DEFINE_UNQUOTED(HOST_ARCH, "$host")
-@@ -473,12 +473,10 @@
- echo Using FORTRAN runtime libraries: $withval
- )
- 
--LDFLAGS=
--LIBDIRS=
- AC_ARG_WITH(libdirs,
- [  --with-libdirs          Specifies library directories (-Ldir1 -Ldir2).],
- LIBDIRS=$withval
--LDFLAGS=$withval
-+LDFLAGS="$LDFLAGS $withval"
- echo Using extra library directories: $withval
- )
- 
diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch
deleted file mode 100644
index 91fcc30d0d90..000000000000
--- a/sci-chemistry/mpqc/files/mpqc-2.3.1-test-failure-hack.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- mpqc-2.3.1.orig/src/bin/mpqc/validate/Makefile	2006-03-22 19:03:51.000000000 +0100
-+++ mpqc-2.3.1/src/bin/mpqc/validate/Makefile	2010-02-13 20:26:12.496370219 +0100
-@@ -52,7 +52,7 @@
- # Also need to see if --mpqc was specified.  If not, then add
- # --mpqc ../../mpqc.
- ifeq ($(filter --mpqc%, $(ALL_MPQCRUN_ARGS)),)
--ALL_MPQCRUN_ARGS:=--mpqc ../../mpqc $(ALL_MPQCRUN_ARGS)
-+ALL_MPQCRUN_ARGS:=--mpqc "LD_LIBRARY_PATH=\"../../../../../lib/.libs/\" ../../mpqc" $(ALL_MPQCRUN_ARGS)
- endif
- 
- ifeq ($(HAVE_SC_SRC_LIB_CHEMISTRY_QC_MBPTR12),yes)
diff --git a/sci-chemistry/mpqc/files/mpqc-2.3.1-wformat-security.patch b/sci-chemistry/mpqc/files/mpqc-2.3.1-wformat-security.patch
deleted file mode 100644
index 7f25a92ad891..000000000000
--- a/sci-chemistry/mpqc/files/mpqc-2.3.1-wformat-security.patch
+++ /dev/null
@@ -1,71 +0,0 @@
-Fix -Werror=format-security errors
-https://bugs.gentoo.org/show_bug.cgi?id=542278
-
---- mpqc-2.3.1/src/lib/chemistry/molecule/atominfo.cc
-+++ mpqc-2.3.1/src/lib/chemistry/molecule/atominfo.cc
-@@ -493,7 +493,7 @@
-   if (iname != symbol_to_Z_.end()) return iname->second;
- 
-   if (allow_exceptions) {
--      ExEnv::err0() << sprintf("AtomInfo: invalid name: %s\n",name.c_str());
-+      ExEnv::err0() << fprintf(stderr, "AtomInfo: invalid name: %s\n",name.c_str());
-       throw std::runtime_error("invalid atom name");
-     }
- 
---- mpqc-2.3.1/src/lib/chemistry/molecule/atominfo.h
-+++ mpqc-2.3.1/src/lib/chemistry/molecule/atominfo.h
-@@ -49,8 +49,8 @@
-     struct atom
-     {
-       int Z;
--      char *name;
--      char *symbol;
-+      const char *name;
-+      const char *symbol;
-     };
- 
-     static struct atom elements_[Nelement];
---- mpqc-2.3.1/src/lib/chemistry/molecule/simple.cc
-+++ mpqc-2.3.1/src/lib/chemistry/molecule/simple.cc
-@@ -214,7 +214,7 @@
-       os << scprintf(" %4d", atoms[i]);
- 
-   if (mol.nonnull()) {
--      char *separator = " ";
-+      const char *separator = " ";
-       os << "  ";
-       for (i=0; i<(4-natoms()); i++) {
-           os << "   ";
---- mpqc-2.3.1/src/lib/chemistry/qc/psi/psiexenv.cc
-+++ mpqc-2.3.1/src/lib/chemistry/qc/psi/psiexenv.cc
-@@ -147,7 +147,7 @@
-   return 0;
- }
- 
--int PsiExEnv::run_psi_module(char *module)
-+int PsiExEnv::run_psi_module(const char *module)
- {
-   int errcod;
-   char *module_cmd = new char[2*cwd_.size()+strlen(module)+psiprefix_.size()+fileprefix_.size()+stdout_.size()+stderr_.size()+40];
---- mpqc-2.3.1/src/lib/chemistry/qc/psi/psiexenv.h
-+++ mpqc-2.3.1/src/lib/chemistry/qc/psi/psiexenv.h
-@@ -57,7 +57,7 @@
-     /// Executes Psi input+driver
-     int run_psi();
-     /// Executes a Psi module
--    int run_psi_module(char *);
-+    int run_psi_module(const char *);
- 
-     /// Returns current working directory
-     string get_cwd() const { return cwd_;};
---- mpqc-2.3.1/src/lib/chemistry/qc/psi/psiwfn.cc
-+++ mpqc-2.3.1/src/lib/chemistry/qc/psi/psiwfn.cc
-@@ -44,7 +44,7 @@
-     bytes = 2000000;
-   int bytes_str_len = (int)ceil(log10((long double)bytes));
-   memory_ = new char[bytes_str_len+5];
--  sprintf(memory_,"(%ld B)",bytes);
-+  sprintf(memory_,"(%d B)",bytes);
- }
- 
- PsiWavefunction::~PsiWavefunction()
diff --git a/sci-chemistry/mpqc/metadata.xml b/sci-chemistry/mpqc/metadata.xml
deleted file mode 100644
index f010ff6d55a9..000000000000
--- a/sci-chemistry/mpqc/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">mpqc</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/mpqc/mpqc-2.3.1-r4.ebuild b/sci-chemistry/mpqc/mpqc-2.3.1-r4.ebuild
deleted file mode 100644
index 609035e9b4f3..000000000000
--- a/sci-chemistry/mpqc/mpqc-2.3.1-r4.ebuild
+++ /dev/null
@@ -1,105 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools toolchain-funcs
-
-DESCRIPTION="The Massively Parallel Quantum Chemistry Program"
-HOMEPAGE="http://www.mpqc.org/"
-SRC_URI="https://downloads.sourceforge.net/mpqc/${P}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86"
-IUSE="doc mpi threads tk"
-
-RDEPEND="
-	virtual/blas
-	virtual/lapack
-	mpi? ( virtual/mpi[cxx] )
-	tk? ( dev-lang/tk:0 )"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-lang/perl
-	app-alternatives/lex
-	virtual/pkgconfig
-	doc? (
-		app-text/doxygen
-		media-gfx/graphviz
-	)"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-as-needed.patch
-	"${FILESDIR}"/${P}-respect-ldflags.patch
-	"${FILESDIR}"/${P}-test-failure-hack.patch
-	"${FILESDIR}"/${P}-blas.patch
-	"${FILESDIR}"/${P}-wformat-security.patch
-	"${FILESDIR}"/${P}-MPI-3.0.patch
-)
-
-src_prepare() {
-	# do not install tkmolrender if not requested
-	if ! use tk; then
-		sed \
-			-e "s:.*/bin/molrender/tkmolrender.*::" \
-			-e "s:.*\$(INSTALLBINOPT) tkmolrender.*::" \
-			-e "s:/bin/rm -f tkmolrender::" \
-			-i "./src/bin/molrender/Makefile" \
-			|| die "failed to disable tkmolrender"
-	fi
-	default
-
-	eautoreconf
-}
-
-src_configure() {
-	tc-export CC CXX
-	if use mpi; then
-		export CC=mpicc
-		export CXX=mpicxx
-	fi
-
-	econf \
-		--enable-shared \
-		$(use_enable threads) \
-		$(use_enable mpi parallel)
-
-	sed \
-		-e "s|^CFLAGS =.*$|CFLAGS=${CFLAGS}|" \
-		-e "s|^FFLAGS =.*$|FFLAGS=${FFLAGS:- -O2}|" \
-		-e "s|^CXXFLAGS =.*$|CXXFLAGS=${CXXFLAGS}|" \
-		-i lib/LocalMakefile || die
-}
-
-src_test() {
-	# we'll only run the small test set, since the
-	# medium and large ones take >10h and >24h on my
-	# 1.8Ghz P4M
-	emake -C src/bin/mpqc/validate -j1 check1
-}
-
-src_install() {
-	emake installroot="${D}" install install_devel install_inc
-	dodoc CHANGES CITATION README
-
-	# make extended docs
-	if use doc; then
-		cd doc || die
-		emake all
-		doman man/man1/* man/man3/*
-		dodoc -r html
-	fi
-
-	find "${ED}" -name '*.la' -delete || die
-}
-
-pkg_postinst() {
-	einfo "MPQC can be picky with regard to compilation flags."
-	einfo "If during mpqc runs you have trouble converging or "
-	einfo "experience oscillations during SCF interations, "
-	einfo "consider recompiling with less aggressive CFLAGS/CXXFLAGS."
-	einfo "Particularly, replacing -march=pentium4 by -march=pentium3"
-	einfo "might help if you encounter problems with correlation "
-	einfo "consistent basis sets."
-}
diff --git a/sci-chemistry/msms-bin/Manifest b/sci-chemistry/msms-bin/Manifest
deleted file mode 100644
index 6816196e5e48..000000000000
--- a/sci-chemistry/msms-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST msms_i86Linux2_2.6.1.tar.gz 112762 BLAKE2B 8ceb55eef29234b38d631ea4aa63c7f11e4a606b8f14526412ed64d2ac9174604fd6ecb8c11c8e7629fd570b2298ee81d4f364c75ee64a41b1bc9fd9c661277b SHA512 814a5b5fa760b57c773f6900d42cacc5b68a2bf16d8792aa63cfa779aeabdab4e05064b86de6fb2551194543db925d83e07cf4ef74be8c08935ef5ecc8dcfe73
-DIST msms_i86_64Linux2_2.6.1.tar.gz 593147 BLAKE2B b66430303f732bc66c62577950671a947c2a81efa139857a255522fa5dc73f042b571e7756e76246aaeac30cb8cf3ac7383645b35a70bb08a15572de1c5fb2af SHA512 630da1ae57b2d8d072247b650636a71e5ef6f07a245c8c4d07b26e20618d9c5dbaffcff563d0504b9b899ca263ba5f3458447f0e649bbfb895aea34305c1c8f8
diff --git a/sci-chemistry/msms-bin/metadata.xml b/sci-chemistry/msms-bin/metadata.xml
deleted file mode 100644
index 9a643a85e7bb..000000000000
--- a/sci-chemistry/msms-bin/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>alexxy@gentoo.org</email>
-	</maintainer>
-<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild b/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild
deleted file mode 100644
index 1994e41d15c5..000000000000
--- a/sci-chemistry/msms-bin/msms-bin-2.6.1-r1.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="MSMS very efficiently computes triangulations of Solvent Excluded Surfaces"
-HOMEPAGE="http://mgl.scripps.edu/people/sanner/html/msms_home.html"
-SRC_URI="
-	amd64? ( msms_i86_64Linux2_2.6.1.tar.gz )
-	x86? ( msms_i86Linux2_2.6.1.tar.gz )"
-
-LICENSE="MSMS"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-RESTRICT="fetch"
-
-S="${WORKDIR}"
-
-QA_PREBUILT="opt/bin/*"
-
-pkg_nofetch() {
-	einfo "Please download ${A} from https://ccsb.scripps.edu/msms/downloads/ and"
-	einfo "place it into your DISTDIR directory."
-}
-
-src_install() {
-	dobin pdb_to_xyz*
-
-	exeinto /opt/bin
-	newexe ${PN%-bin}.$(usex amd64 x86_64Linux2 i86Linux2).${PV} msms
-
-	dodoc README msms.html ReleaseNotes
-	doman msms.1
-
-	insinto /usr/share/${PN}/
-	doins atmtypenumbers
-	sed \
-		-e 's:nawk:awk:g' \
-		-e "s:./atmtypenumbers:${EPREFIX}/usr/share/${PN}/atmtypenumbers:g" \
-		-i pdb_to_xyz* || die
-}
diff --git a/sci-chemistry/mustang/Manifest b/sci-chemistry/mustang/Manifest
deleted file mode 100644
index e053c2f20e0c..000000000000
--- a/sci-chemistry/mustang/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST mustang_v3.2.2.tgz 141940 BLAKE2B b90b42df782bd1dbdb387d0d0ab42430c5212b439da84f56a33ca2c746c8937ae330dfb8d634e7d1c5ffd0f6959cd9e4be0efe8f569c452930a3481894c68ec5 SHA512 cb862f860f3cdb3349743c6005a29acc14cde5269df9d61f1100ffdc9a22c1d8e3dd46771371557b823724e79783f8fcb7356c63c6f0c0a09aac09bee407a26d
diff --git a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
deleted file mode 100644
index 20bd300db89e..000000000000
--- a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/superpose_on_core_2.cpp
-+++ b/src/superpose_on_core_2.cpp
-@@ -55,6 +55,8 @@ using std::ofstream ;
- #include "multiple_superposition.h"
- #include "3D_manip_functions.h"
- 
-+#include <unistd.h>
-+
- int **core_columns ;
- int *core_columns_2 , NCORE = 0 ;
- int **algn_to_seq_hash ;
diff --git a/sci-chemistry/mustang/metadata.xml b/sci-chemistry/mustang/metadata.xml
deleted file mode 100644
index d4ff1000a775..000000000000
--- a/sci-chemistry/mustang/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/mustang/mustang-3.2.2.ebuild b/sci-chemistry/mustang/mustang-3.2.2.ebuild
deleted file mode 100644
index 99b831fda7e2..000000000000
--- a/sci-chemistry/mustang/mustang-3.2.2.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-MY_PN="MUSTANG"
-SRC_P="${PN}_v${PV}"
-MY_P="${MY_PN}_v${PV}"
-
-DESCRIPTION="MUltiple STructural AligNment AlGorithm"
-HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html"
-SRC_URI="http://www.csse.monash.edu.au/~karun/${PN}/${PN}_v${PV}.tgz"
-S="${WORKDIR}/${MY_P}"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-PATCHES=( "${FILESDIR}"/${PN}-3.2.1-gcc-4.7.patch )
-
-src_prepare() {
-	default
-	sed -e 's:3.2.1:3.2.2:g' -i Makefile || die
-}
-
-src_compile() {
-	emake \
-		CPP="$(tc-getCXX)" \
-		CPPFLAGS="${CXXFLAGS}" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_test() {
-	./bin/${P} -f ./data/test/test_zf-CCHH || die
-}
-
-src_install() {
-	newbin bin/${P} ${PN}
-	doman man/${PN}.1
-	dodoc README
-}
-
-pkg_postinst() {
-	elog "If you use this program for an academic paper, please cite:"
-	elog "Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey, and Arthur M. Lesk"
-	elog "Proteins: Structure, Function, and Bioinformatics. 64(3):559-574, Aug. 2006"
-}
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
deleted file mode 100644
index 336f074b2917..000000000000
--- a/sci-chemistry/openbabel/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST openbabel-3.1.1_p20241221.tar.gz 36864825 BLAKE2B 55e6fbdd5c50a557c40fd5ffaca41753f73175b2b4eea22abe5c2b0031363e3c133acf9a8daf5b1cb362a3adb6398204497af036b9a7ba3630c1d8ccbce0f9d3 SHA512 44340c3d08b22783cf6a702c192480869b73fef21104641feaf5cbcd51f693fd17bb05ad31a3520f330aa57733d6f4be707b3c1243b3010d6ceccca8974e732f
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-cmake4.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-cmake4.patch
deleted file mode 100644
index 822213a7bddb..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-cmake4.patch
+++ /dev/null
@@ -1,78 +0,0 @@
-https://github.com/openbabel/openbabel/pull/2784.patch
-From fda825d390af8b5eaf79d7b7c39c19ab5ce317ac Mon Sep 17 00:00:00 2001
-From: Nicolas PARLANT <nicolas.parlant@parhuet.fr>
-Date: Wed, 26 Mar 2025 10:24:42 +0000
-Subject: [PATCH] cmake4 compat :
-
-* up cmake_minimum_required to 3.10
-* delete CMP0042 because OLD behavior is removed in cmake-4 and
-is no longer used.
-* set ENABLE_EXPORTS for test_runner (OLD behavior for CMP0065 is removed
-in cmake4)
-
-Signed-off-by: Nicolas PARLANT <nicolas.parlant@parhuet.fr>
----
- CMakeLists.txt                                | 7 ++-----
- doc/examples/static_executable/CMakeLists.txt | 2 +-
- scripts/CMakeLists.txt                        | 2 +-
- test/CMakeLists.txt                           | 1 +
- 4 files changed, 5 insertions(+), 7 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 9d2a9f143e..f8440e412e 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,6 +1,6 @@
--# Please ensure that any changes remain compliant with 3.1.
-+# Please ensure that any changes remain compliant with 3.10.
- if(NOT EMBED_OPENBABEL)
--  cmake_minimum_required(VERSION 3.1)
-+  cmake_minimum_required(VERSION 3.10)
- endif()
- 
- project(openbabel)
-@@ -10,9 +10,6 @@ set (CMAKE_CXX_STANDARD 11)
- 
- if(COMMAND cmake_policy)
-   cmake_policy(SET CMP0003 NEW)
--  if(POLICY CMP0042)
--    cmake_policy(SET CMP0042 OLD)
--  endif()
- endif()
- 
- include (CheckCXXCompilerFlag)
-diff --git a/doc/examples/static_executable/CMakeLists.txt b/doc/examples/static_executable/CMakeLists.txt
-index 0ed21beaaf..63dae2a468 100644
---- a/doc/examples/static_executable/CMakeLists.txt
-+++ b/doc/examples/static_executable/CMakeLists.txt
-@@ -25,7 +25,7 @@
- #
- 
- # This line is required for cmake backwards compatibility.
--cmake_minimum_required(VERSION 2.6)
-+cmake_minimum_required(VERSION 3.10)
- 
- # Name of your project
- project(myproject)
-diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
-index 792e4592d0..eafda66c5a 100644
---- a/scripts/CMakeLists.txt
-+++ b/scripts/CMakeLists.txt
-@@ -1,4 +1,4 @@
--cmake_minimum_required(VERSION 2.6.0)
-+cmake_minimum_required(VERSION 3.10.0)
- # Library versioning (used in Mac Python bindings)x
- set(SOVERSION 4)
- 
-diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
-index 2ecf0dbe22..280eac471f 100644
---- a/test/CMakeLists.txt
-+++ b/test/CMakeLists.txt
-@@ -152,6 +152,7 @@ endif()
- 
- add_executable(test_runner ${srclist} obtest.cpp)
- target_link_libraries(test_runner ${libs})
-+set_target_properties(test_runner PROPERTIES ENABLE_EXPORTS TRUE)
- 
- if(NOT BUILD_SHARED AND NOT BUILD_MIXED)
-   set_target_properties(test_runner PROPERTIES LINK_SEARCH_END_STATIC TRUE)
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch
deleted file mode 100644
index b61d3bc29b98..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-prevent installation of examples in /usr/bin
-all files from examples are 'RUNTIME', no lib
---- a/doc/examples/CMakeLists.txt
-+++ b/doc/examples/CMakeLists.txt
-@@ -7,7 +7,7 @@
-   add_executable(${example} ${example}.cpp)
-   target_link_libraries(${example} ${BABEL_LIBRARY})
-   install(TARGETS ${example}
--    RUNTIME DESTINATION bin
-+    RUNTIME DESTINATION ${CMAKE_INSTALL_DOCDIR}/examples
-     LIBRARY DESTINATION lib
-     ARCHIVE DESTINATION lib
-   )
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch
deleted file mode 100644
index ab1a24499306..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- a/scripts/CMakeLists.txt
-+++ b/scripts/CMakeLists.txt
-@@ -69,13 +69,9 @@
- 
- if (DO_PYTHON_BINDINGS)
- 
--    include_directories(
--        ${PYTHON_INCLUDE_PATH}
--    )
--
-     if(RUN_SWIG)
-       add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel.py
--      COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
-+	      COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${PYTHON_INCLUDE_PATH} -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
-               MAIN_DEPENDENCY openbabel-python.i
-               VERBATIM
-               )
-@@ -84,6 +80,7 @@
-     configure_file(${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
-                    ${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py)
-     add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp)
-+    target_include_directories(bindings_python PRIVATE ${PYTHON_INCLUDE_PATH})
- 
-     if(APPLE)
-       # Don't link against Python library on Mac
diff --git a/sci-chemistry/openbabel/files/openbabel-python-r2.cmake b/sci-chemistry/openbabel/files/openbabel-python-r2.cmake
deleted file mode 100644
index a16970deb0b1..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-python-r2.cmake
+++ /dev/null
@@ -1,103 +0,0 @@
-# The following is a cmake fragment taken from scripts/CMakeLists.txt and
-# edited for Gentoo python multibuild compatibility.
-
-if (DO_PYTHON_BINDINGS)
-	# Tags should be edited to reflect the active python implementation
-	set(EPYTHON @@EPYTHON@@)
-	set(PYTHON_INCLUDE_DIR @@PYTHON_INCLUDE_DIR@@)
-	set(PYTHON_LIBS @@PYTHON_LIBS@@)
-	set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@)
-
-	add_custom_command(
-		OUTPUT ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
-		COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${PYTHON_INCLUDE_DIR} -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_BINARY_DIR}/include -o ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${eigen_define} -outdir ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON} ${CMAKE_SOURCE_DIR}/scripts/openbabel-python.i
-		MAIN_DEPENDENCY openbabel-python.i
-		VERBATIM
-	)
-
-	configure_file(${CMAKE_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
-		${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py)
-
-	add_library(bindings_python_${EPYTHON} MODULE ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp)
-    	target_include_directories(bindings_python_${EPYTHON} PRIVATE ${PYTHON_INCLUDE_DIR})
-	target_link_libraries(bindings_python_${EPYTHON} ${PYTHON_LIBS} ${BABEL_LIBRARY})
-
-	set_target_properties(bindings_python_${EPYTHON}
-		PROPERTIES
-		OUTPUT_NAME _openbabel
-		LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel
-		PREFIX ""
-		SUFFIX .so )
-
-	add_dependencies(bindings_python_${EPYTHON} openbabel)
-
-	install(TARGETS bindings_python_${EPYTHON}
-		LIBRARY DESTINATION ${PYTHON_SITEDIR}/openbabel
-		COMPONENT bindings_python)
-	install(FILES ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py
-		DESTINATION ${PYTHON_SITEDIR}/openbabel
-		COMPONENT bindings_python)
-	install(FILES ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
-		DESTINATION ${PYTHON_SITEDIR}/openbabel
-		COMPONENT bindings_python)
-	install(FILES ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py
-		DESTINATION ${PYTHON_SITEDIR}/openbabel
-		COMPONENT bindings_python)
-
-	if (ENABLE_TESTS)
-		# Make sure all module files are together in the same directory for testing
-		add_custom_command(TARGET bindings_python_${EPYTHON} POST_BUILD
-			COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/
-			COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/)
-		set(TEST_SOURCE_DIR ${CMAKE_SOURCE_DIR}/test)
-		# define TESTDATADIR for tests that need input files
-		add_definitions(-DTESTDATADIR="${TEST_SOURCE_DIR}/files/")
-		# define FORMATDIR for location of format plugin binaries
-		set(FORMATDIR "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/")
-		add_definitions(-DFORMATDIR="${FORMATDIR}/")
-		include_directories(${TEST_SOURCE_DIR})
-
-		# The macro is modified from cmake/modules/UsePythonTest.cmake
-		MACRO(ADD_PYTHON_TEST TESTNAME FILENAME)
-			GET_SOURCE_FILE_PROPERTY(loc ${FILENAME} LOCATION)
-			STRING(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}")
-			FILE(WRITE ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake
-"
-	MESSAGE(\"${PYTHONPATH}\")
-	EXECUTE_PROCESS(
-		COMMAND ${EPYTHON} ${loc} ${wo_semicolumn}
-		RESULT_VARIABLE import_res
-		OUTPUT_VARIABLE import_output
-		ERROR_VARIABLE  import_output
-	)
-
-	# Pass the output back to ctest
-	IF(import_output)
-		MESSAGE(\${import_output})
-	ENDIF(import_output)
-	IF(import_res)
-		MESSAGE(SEND_ERROR \${import_res})
-	ENDIF(import_res)
-"
-			)
-			ADD_TEST(${TESTNAME} ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake)
-		ENDMACRO(ADD_PYTHON_TEST)
-
-		set(pybindtests
-			bindings
-			_pybel
-			example 
-			obconv_writers
-			cdjsonformat
-			pcjsonformat
-			roundtrip
-			)
-		foreach(pybindtest ${pybindtests})
-			ADD_PYTHON_TEST(pybindtest_${pybindtest}_${EPYTHON} ${TEST_SOURCE_DIR}/test${pybindtest}.py)
-			set_tests_properties(pybindtest_${pybindtest}_${EPYTHON} PROPERTIES
-				ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX};LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}:\$ENV{LD_LIBRARY_PATH};BABEL_LIBDIR=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/;BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data"
-				FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed"
-			)
-		endforeach(pybindtest ${pybindtests})
-	endif (ENABLE_TESTS)
-endif(DO_PYTHON_BINDINGS)
diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml
deleted file mode 100644
index a81d304be773..000000000000
--- a/sci-chemistry/openbabel/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<longdescription>
-		Open Babel is a chemical toolbox designed to speak the many languages of
-		chemical data. It's an open, collaborative project allowing anyone to
-		search, convert, analyze, or store data from molecular modeling, chemistry,
-		solid-state materials, biochemistry, or related areas.
-	</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">openbabel</remote-id>
-		<remote-id type="github">openbabel/openbabel</remote-id>
-	</upstream>
-	<use>
-		<flag name="inchi">Build support for IUPAC International Chemical Identifier format</flag>
-		<flag name="json">Build support for JSON formats (ChemDoodle, PubChem, etc...)</flag>
-	</use>
-</pkgmetadata>
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild
deleted file mode 100644
index 1cc66e2c7a02..000000000000
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild
+++ /dev/null
@@ -1,238 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-WX_GTK_VER=3.2-gtk3
-
-inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
-
-if [[ "${PV}" == *9999* ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
-else
-	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
-		# Set to commit hash
-		OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
-		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
-		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
-	else
-		MY_P="${PN}-$(ver_rs 1- -)"
-		SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
-		S="${WORKDIR}/${PN}-${MY_P}"
-	fi
-	KEYWORDS="amd64 ~arm ~x86"
-fi
-
-LICENSE="GPL-2"
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
-IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="
-	python? ( ${PYTHON_REQUIRED_USE} )
-	test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
-"
-
-RDEPEND="
-	dev-cpp/eigen:=
-	virtual/zlib:=
-	inchi? ( sci-libs/inchi )
-	json? ( >=dev-libs/rapidjson-1.1.0 )
-	!minimal? (
-		dev-libs/libxml2:2=
-		png? ( x11-libs/cairo )
-	)
-	perl? ( dev-lang/perl:= )
-	python? ( ${PYTHON_DEPS} )
-	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}=[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-lang/perl
-	doc? (
-		app-text/doxygen
-		dev-texlive/texlive-latex
-	)
-	perl? ( dev-lang/swig )
-	python? ( dev-lang/swig )
-	test? ( dev-lang/python )
-"
-
-PATCHES=(
-	# Set include dir only for global implementation
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
-	# prevent installation of examples in /usr/bin
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
-	# cmake4-compat
-	"${FILESDIR}"/${PN}-3.1.1_p2024-cmake4.patch
-)
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-gen_python_bindings() {
-	mkdir -p scripts/${EPYTHON} || die
-	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
-	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
-		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
-			-e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
-			-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
-			-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
-				scripts/CMakeLists.txt || die
-}
-
-src_prepare() {
-	cmake_src_prepare
-
-	# Prevent bundled inchi as fallback
-	rm -r include/inchi || die
-
-	use python && python_foreach_impl gen_python_bindings
-}
-
-src_configure() {
-	if use json; then
-		# -DOPTIMIZE_NATIVE=ON also forces -march=native so use
-		# cpu_flags to set defines instead
-		use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2
-		use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42
-		use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON
-	fi
-
-	use wxwidgets && setup-wxwidgets
-
-	use_bindings() {
-		(use perl || use python) && (echo 'yes' || die) || (echo 'no' || die)
-	}
-
-	local mycmakeargs=(
-		$(cmake_use_find_package png Cairo)
-		$(cmake_use_find_package wxwidgets wxWidgets)
-		-DCMAKE_SKIP_RPATH=ON
-		-DBUILD_DOCS=$(usex doc)
-		-DBUILD_EXAMPLES=$(usex examples)
-		-DBUILD_GUI=$(usex wxwidgets)
-		-DENABLE_OPENMP=$(usex openmp)
-		-DENABLE_TESTS=$(usex test)
-		-DMINIMAL_BUILD=$(usex minimal)
-		# All three required to comply w/ useflag and prevent bundled lib
-		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
-		-DADD_INCHI_FORMAT=$(usex inchi)
-		-DWITH_INCHI=$(usex inchi)
-		-DOPTIMIZE_NATIVE=OFF
-		-DPERL_BINDINGS=$(usex perl)
-		-DPYTHON_BINDINGS=$(usex python)
-		-DRUN_SWIG=$(use_bindings)
-		-DWITH_COORDGEN=false
-		-DWITH_JSON=$(usex json)
-		# MEAPARSER
-		-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
-		-DWITH_MAEPARSER=false
-	)
-
-	if use perl; then
-		perl_set_version
-		mycmakeargs+=(
-			-DPERL_INSTDIR="${VENDOR_ARCH}"
-		)
-	fi
-
-	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built
-		# without native-symlinks support.
-		python_setup
-		mycmakeargs+=(
-			-DPYTHON_EXECUTABLE="${PYTHON}"
-		)
-	fi
-
-	cmake_src_configure
-}
-
-src_test() {
-	local CMAKE_SKIP_TESTS=(
-		# https://github.com/openbabel/openbabel/issues/2766
-		test_align_{4,5}
-	)
-	! use wxwidgets && CMAKE_SKIP_TESTS+=(
-		test_tautomer_{22,27}
-	)
-
-	# Weird deadlock causes system_load to keep rising
-	cmake_src_test -j1
-}
-
-openbabel-optimize() {
-	python_optimize "${D}/$(python_get_sitedir)"/openbabel || die
-}
-
-src_install() {
-	cmake_src_install
-
-	docinto html
-	for x in doc/*.html; do
-		[[ ${x} != doc/api*.html ]] && dodoc ${x}
-	done
-
-	if use doc; then
-		cmake_src_install docs
-		docinto html/API
-		dodoc -r doc/API/html/.
-	fi
-
-	if use examples; then
-		# no compression since we want ready-to-run scripts
-		docompress -x /usr/share/doc/${PF}/examples
-
-		# ${PV} doesn't correspond to the internal BABEL_VERSION for
-		# live or patch release builds so we grep it
-		local babel_ver=$(
-			grep '^#define BABEL_VERSION' < \
-				"${BUILD_DIR}"/include/openbabel/babelconfig.h | \
-				cut -d \" -f 2 || die
-		)
-		docinto examples/povray
-		dodoc doc/dioxin.* doc/README*.pov*
-		# Needed by the povray example
-		dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
-			/usr/share/doc/${PF}/examples/povray/babel31.inc
-	fi
-
-	if use perl; then
-		docinto /
-		newdoc scripts/perl/Changes Changes.perl
-		newdoc scripts/perl/README README.perl
-		if use examples; then
-			docinto examples/perl
-			dodoc -r scripts/perl/examples/.
-		fi
-	fi
-
-	if use python; then
-		python_foreach_impl openbabel-optimize
-		docinto /
-		newdoc scripts/python/README.rst README.python.rst
-		docinto html
-		dodoc scripts/python/*.html
-		if use examples; then
-			docinto examples/python
-			dodoc -r scripts/python/examples/.
-		fi
-	fi
-
-	if use wxwidgets; then
-		make_desktop_entry obgui "Open Babel" ${PN}
-		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
-	fi
-}
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r4.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r4.ebuild
deleted file mode 100644
index e9ea539cde58..000000000000
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r4.ebuild
+++ /dev/null
@@ -1,247 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-GENTOO_DEPEND_ON_PERL="no"
-PYTHON_COMPAT=( python3_{13..14} )
-WX_GTK_VER=3.2-gtk3
-
-inherit cmake desktop flag-o-matic perl-module python-r1 toolchain-funcs wxwidgets xdg
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
-
-if [[ "${PV}" == *9999* ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
-else
-	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
-		# Set to commit hash
-		OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
-		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
-		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
-	else
-		MY_P="${PN}-$(ver_rs 1- -)"
-		SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
-		S="${WORKDIR}/${PN}-${MY_P}"
-	fi
-	KEYWORDS="amd64 ~arm ~x86"
-fi
-
-LICENSE="GPL-2"
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
-IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets ${GENTOO_PERL_USESTRING}"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="
-	python? ( ${PYTHON_REQUIRED_USE} )
-	test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
-"
-
-RDEPEND="
-	dev-cpp/eigen:=
-	virtual/zlib:=
-	inchi? ( sci-libs/inchi )
-	json? ( >=dev-libs/rapidjson-1.1.0 )
-	!minimal? (
-		dev-libs/libxml2:2=
-		png? ( x11-libs/cairo )
-	)
-	perl? (
-		${GENTOO_PERL_DEPSTRING}
-		dev-lang/perl:=
-	)
-	python? ( ${PYTHON_DEPS} )
-	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}=[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-lang/perl
-	doc? (
-		app-text/doxygen
-		dev-texlive/texlive-latex
-	)
-	perl? ( dev-lang/swig )
-	python? ( dev-lang/swig )
-	test? ( dev-lang/python )
-"
-
-PATCHES=(
-	# Set include dir only for global implementation
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
-	# prevent installation of examples in /usr/bin
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
-	# cmake4-compat
-	"${FILESDIR}"/${PN}-3.1.1_p2024-cmake4.patch
-)
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-gen_python_bindings() {
-	mkdir -p scripts/${EPYTHON} || die
-	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
-	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
-		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
-			-e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
-			-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
-			-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
-				scripts/CMakeLists.txt || die
-}
-
-src_prepare() {
-	cmake_src_prepare
-
-	# Prevent bundled inchi as fallback
-	rm -r include/inchi || die
-
-	use python && python_foreach_impl gen_python_bindings
-}
-
-src_configure() {
-	if use json; then
-		# -DOPTIMIZE_NATIVE=ON also forces -march=native so use
-		# cpu_flags to set defines instead
-		use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2
-		use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42
-		use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON
-	fi
-
-	use wxwidgets && setup-wxwidgets
-
-	use_bindings() {
-		(use perl || use python) && (echo 'yes' || die) || (echo 'no' || die)
-	}
-
-	local mycmakeargs=(
-		$(cmake_use_find_package png Cairo)
-		$(cmake_use_find_package wxwidgets wxWidgets)
-		-DCMAKE_SKIP_RPATH=ON
-		-DBUILD_DOCS=$(usex doc)
-		-DBUILD_EXAMPLES=$(usex examples)
-		-DBUILD_GUI=$(usex wxwidgets)
-		-DENABLE_OPENMP=$(usex openmp)
-		-DENABLE_TESTS=$(usex test)
-		-DMINIMAL_BUILD=$(usex minimal)
-		# All three required to comply w/ useflag and prevent bundled lib
-		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
-		-DADD_INCHI_FORMAT=$(usex inchi)
-		-DWITH_INCHI=$(usex inchi)
-		-DOPTIMIZE_NATIVE=OFF
-		-DPERL_BINDINGS=$(usex perl)
-		-DPYTHON_BINDINGS=$(usex python)
-		-DRUN_SWIG=$(use_bindings)
-		-DWITH_COORDGEN=false
-		-DWITH_JSON=$(usex json)
-		# MEAPARSER
-		-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
-		-DWITH_MAEPARSER=false
-	)
-
-	if use perl; then
-		perl_set_version
-		mycmakeargs+=(
-			-DPERL_INSTDIR="${VENDOR_ARCH}"
-		)
-	fi
-
-	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built
-		# without native-symlinks support.
-		python_setup
-		mycmakeargs+=(
-			-DPYTHON_EXECUTABLE="${PYTHON}"
-		)
-	fi
-
-	cmake_src_configure
-}
-
-src_compile() {
-	# Avoid perl-module_src_compile (bug #963096)
-	cmake_src_compile
-}
-
-src_test() {
-	local CMAKE_SKIP_TESTS=(
-		# https://github.com/openbabel/openbabel/issues/2766
-		test_align_{4,5}
-	)
-	! use wxwidgets && CMAKE_SKIP_TESTS+=(
-		test_tautomer_{22,27}
-	)
-
-	# Weird deadlock causes system_load to keep rising
-	cmake_src_test -j1
-}
-
-openbabel-optimize() {
-	python_optimize "${D}/$(python_get_sitedir)"/openbabel || die
-}
-
-src_install() {
-	cmake_src_install
-
-	docinto html
-	for x in doc/*.html; do
-		[[ ${x} != doc/api*.html ]] && dodoc ${x}
-	done
-
-	if use doc; then
-		cmake_src_install docs
-		docinto html/API
-		dodoc -r doc/API/html/.
-	fi
-
-	if use examples; then
-		# no compression since we want ready-to-run scripts
-		docompress -x /usr/share/doc/${PF}/examples
-
-		# ${PV} doesn't correspond to the internal BABEL_VERSION for
-		# live or patch release builds so we grep it
-		local babel_ver=$(
-			grep '^#define BABEL_VERSION' < \
-				"${BUILD_DIR}"/include/openbabel/babelconfig.h | \
-				cut -d \" -f 2 || die
-		)
-		docinto examples/povray
-		dodoc doc/dioxin.* doc/README*.pov*
-		# Needed by the povray example
-		dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
-			/usr/share/doc/${PF}/examples/povray/babel31.inc
-	fi
-
-	if use perl; then
-		docinto /
-		newdoc scripts/perl/Changes Changes.perl
-		newdoc scripts/perl/README README.perl
-		if use examples; then
-			docinto examples/perl
-			dodoc -r scripts/perl/examples/.
-		fi
-	fi
-
-	if use python; then
-		python_foreach_impl openbabel-optimize
-		docinto /
-		newdoc scripts/python/README.rst README.python.rst
-		docinto html
-		dodoc scripts/python/*.html
-		if use examples; then
-			docinto examples/python
-			dodoc -r scripts/python/examples/.
-		fi
-	fi
-
-	if use wxwidgets; then
-		make_desktop_entry --eapi9 obgui -n "Open Babel" -i ${PN}
-		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
-	fi
-}
diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild
deleted file mode 100644
index 780e60991924..000000000000
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ /dev/null
@@ -1,245 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-GENTOO_DEPEND_ON_PERL="no"
-PYTHON_COMPAT=( python3_{13..14} )
-WX_GTK_VER=3.2-gtk3
-
-inherit cmake desktop flag-o-matic perl-module python-r1 toolchain-funcs wxwidgets xdg
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
-
-if [[ "${PV}" == *9999* ]]; then
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
-else
-	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
-		# Set to commit hash
-		OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
-		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
-		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
-	else
-		MY_P="${PN}-$(ver_rs 1- -)"
-		SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
-		S="${WORKDIR}/${PN}-${MY_P}"
-	fi
-	KEYWORDS="~amd64 ~arm ~x86"
-fi
-
-LICENSE="GPL-2"
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
-IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets ${GENTOO_PERL_USESTRING}"
-RESTRICT="!test? ( test )"
-REQUIRED_USE="
-	python? ( ${PYTHON_REQUIRED_USE} )
-	test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
-"
-
-RDEPEND="
-	dev-cpp/eigen:=
-	virtual/zlib:=
-	inchi? ( sci-libs/inchi )
-	json? ( >=dev-libs/rapidjson-1.1.0 )
-	!minimal? (
-		dev-libs/libxml2:2=
-		png? ( x11-libs/cairo )
-	)
-	perl? (
-		${GENTOO_PERL_DEPSTRING}
-		dev-lang/perl:=
-	)
-	python? ( ${PYTHON_DEPS} )
-	wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}=[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-lang/perl
-	doc? (
-		app-text/doxygen
-		dev-texlive/texlive-latex
-	)
-	perl? ( dev-lang/swig )
-	python? ( dev-lang/swig )
-	test? ( dev-lang/python )
-"
-
-PATCHES=(
-	# Set include dir only for global implementation
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
-	# prevent installation of examples in /usr/bin
-	"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
-)
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
-}
-
-gen_python_bindings() {
-	mkdir -p scripts/${EPYTHON} || die
-	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
-	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
-		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
-			-e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
-			-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
-			-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
-				scripts/CMakeLists.txt || die
-}
-
-src_prepare() {
-	cmake_src_prepare
-
-	# Prevent bundled inchi as fallback
-	rm -r include/inchi || die
-
-	use python && python_foreach_impl gen_python_bindings
-}
-
-src_configure() {
-	if use json; then
-		# -DOPTIMIZE_NATIVE=ON also forces -march=native so use
-		# cpu_flags to set defines instead
-		use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2
-		use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42
-		use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON
-	fi
-
-	use wxwidgets && setup-wxwidgets
-
-	use_bindings() {
-		(use perl || use python) && (echo 'yes' || die) || (echo 'no' || die)
-	}
-
-	local mycmakeargs=(
-		$(cmake_use_find_package png Cairo)
-		$(cmake_use_find_package wxwidgets wxWidgets)
-		-DCMAKE_SKIP_RPATH=ON
-		-DBUILD_DOCS=$(usex doc)
-		-DBUILD_EXAMPLES=$(usex examples)
-		-DBUILD_GUI=$(usex wxwidgets)
-		-DENABLE_OPENMP=$(usex openmp)
-		-DENABLE_TESTS=$(usex test)
-		-DMINIMAL_BUILD=$(usex minimal)
-		# All three required to comply w/ useflag and prevent bundled lib
-		-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
-		-DADD_INCHI_FORMAT=$(usex inchi)
-		-DWITH_INCHI=$(usex inchi)
-		-DOPTIMIZE_NATIVE=OFF
-		-DPERL_BINDINGS=$(usex perl)
-		-DPYTHON_BINDINGS=$(usex python)
-		-DRUN_SWIG=$(use_bindings)
-		-DWITH_COORDGEN=false
-		-DWITH_JSON=$(usex json)
-		# MEAPARSER
-		-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
-		-DWITH_MAEPARSER=false
-	)
-
-	if use perl; then
-		perl_set_version
-		mycmakeargs+=(
-			-DPERL_INSTDIR="${VENDOR_ARCH}"
-		)
-	fi
-
-	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built
-		# without native-symlinks support.
-		python_setup
-		mycmakeargs+=(
-			-DPYTHON_EXECUTABLE="${PYTHON}"
-		)
-	fi
-
-	cmake_src_configure
-}
-
-src_compile() {
-	# Avoid perl-module_src_compile (bug #963096)
-	cmake_src_compile
-}
-
-src_test() {
-	local CMAKE_SKIP_TESTS=(
-		# https://github.com/openbabel/openbabel/issues/2766
-		test_align_{4,5}
-	)
-	! use wxwidgets && CMAKE_SKIP_TESTS+=(
-		test_tautomer_{22,27}
-	)
-
-	# Weird deadlock causes system_load to keep rising
-	cmake_src_test -j1
-}
-
-openbabel-optimize() {
-	python_optimize "${D}/$(python_get_sitedir)"/openbabel || die
-}
-
-src_install() {
-	cmake_src_install
-
-	docinto html
-	for x in doc/*.html; do
-		[[ ${x} != doc/api*.html ]] && dodoc ${x}
-	done
-
-	if use doc; then
-		cmake_src_install docs
-		docinto html/API
-		dodoc -r doc/API/html/.
-	fi
-
-	if use examples; then
-		# no compression since we want ready-to-run scripts
-		docompress -x /usr/share/doc/${PF}/examples
-
-		# ${PV} doesn't correspond to the internal BABEL_VERSION for
-		# live or patch release builds so we grep it
-		local babel_ver=$(
-			grep '^#define BABEL_VERSION' < \
-				"${BUILD_DIR}"/include/openbabel/babelconfig.h | \
-				cut -d \" -f 2 || die
-		)
-		docinto examples/povray
-		dodoc doc/dioxin.* doc/README*.pov*
-		# Needed by the povray example
-		dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
-			/usr/share/doc/${PF}/examples/povray/babel31.inc
-	fi
-
-	if use perl; then
-		docinto /
-		newdoc scripts/perl/Changes Changes.perl
-		newdoc scripts/perl/README README.perl
-		if use examples; then
-			docinto examples/perl
-			dodoc -r scripts/perl/examples/.
-		fi
-	fi
-
-	if use python; then
-		python_foreach_impl openbabel-optimize
-		docinto /
-		newdoc scripts/python/README.rst README.python.rst
-		docinto html
-		dodoc scripts/python/*.html
-		if use examples; then
-			docinto examples/python
-			dodoc -r scripts/python/examples/.
-		fi
-	fi
-
-	if use wxwidgets; then
-		make_desktop_entry obgui "Open Babel" ${PN}
-		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
-	fi
-}
diff --git a/sci-chemistry/pdbcat/Manifest b/sci-chemistry/pdbcat/Manifest
deleted file mode 100644
index 9d17e65c82b9..000000000000
--- a/sci-chemistry/pdbcat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pdbcat-1.3.tar.gz 12750 BLAKE2B 45a229af85665bcdc82d8407eab69e2a3827988202401a2d1c5201647ececc76d4c5c908e001305fcb12b5dc0f5788989aa3fb87840711c9970db571c3bd263d SHA512 369ac0c4c1d8396eaa0450feb9852d2d75ebd9862a2e403ccd42a2801e924f99c28c5d71c0b66feb4588076a8948b503823d2c75420128dd04d020253f821f4c
diff --git a/sci-chemistry/pdbcat/files/CMakeLists.txt b/sci-chemistry/pdbcat/files/CMakeLists.txt
deleted file mode 100644
index f3fa1f9d817c..000000000000
--- a/sci-chemistry/pdbcat/files/CMakeLists.txt
+++ /dev/null
@@ -1,13 +0,0 @@
-cmake_minimum_required (VERSION 3.31)
-project (pdbcat)
-
-include(GNUInstallDirs)
-
-add_executable(pdbcat
-	Common.C
-	Common.h
-	pdbcat.C
-	PDBData.C
-	PDBData.h)
-
-install (TARGETS pdbcat DESTINATION ${CMAKE_INSTALL_BINDIR})
diff --git a/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch b/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch
deleted file mode 100644
index b45c36bd8a8d..000000000000
--- a/sci-chemistry/pdbcat/files/pdbcat-1.3-gcc.patch
+++ /dev/null
@@ -1,17 +0,0 @@
- pdbcat.C | 3 ++-
- 1 file changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/pdbcat.C b/pdbcat.C
-index 0786d9b..387edf9 100644
---- a/pdbcat.C
-+++ b/pdbcat.C
-@@ -17,7 +17,8 @@
- #include <stdlib.h> // for exit
- #include <stdio.h>  // for feof() and other file manip stuff
- #include <string.h> // for strcasecmp
--#include <iostream.h>
-+#include <iostream>
-+using namespace std;
- #include "Common.h"
- #include "PDBData.h"
- 
diff --git a/sci-chemistry/pdbcat/metadata.xml b/sci-chemistry/pdbcat/metadata.xml
deleted file mode 100644
index 9f9da7cbec86..000000000000
--- a/sci-chemistry/pdbcat/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-  The Brookhaven Protein Data Bank stores atomic coordinate information
-  for protein structures in a column based format.  This is designed to
-  be read easily read by FORTRAN programs.  Indeed, if you get the
-  format description (from anonymous ftp to ftp.pdb.bnl.gov, the file
-  /pub/format.desc.ps) they show the single input line needed to read
-  each record type.
-  However, I am a C/C++ programmer in the Unix environment.  It is a
-  easier for me to deal with field based input than column based ones.
-  If the fields are white space delimited I can easily use awk and perl
-  to manipulate the coordinate information.  So I needed some way to
-  convert the ATOM and HETATM records of PDB files from the standard
-  column based format to a field based one and back again.  It needed
-  to denote missing fields if they exist.
-  That converter is `pdbcat'.
-  </longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/pdbcat/pdbcat-1.3-r1.ebuild b/sci-chemistry/pdbcat/pdbcat-1.3-r1.ebuild
deleted file mode 100644
index c07ab32f95f6..000000000000
--- a/sci-chemistry/pdbcat/pdbcat-1.3-r1.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake
-
-DESCRIPTION="Manipulate and process PDB files using tools such as Perl, awk, etc"
-HOMEPAGE="https://www.ks.uiuc.edu/Development/MDTools/pdbcat/"
-SRC_URI="https://www.ks.uiuc.edu/Development/MDTools/${PN}/files/${P}.tar.gz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-BDEPEND=">=dev-build/cmake-3.31"
-
-DOCS=( README )
-
-PATCHES=( "${FILESDIR}"/${P}-gcc.patch )
-
-src_prepare() {
-	cp "${FILESDIR}"/CMakeLists.txt . || die
-
-	cmake_src_prepare
-}
diff --git a/sci-chemistry/pdbcns/Manifest b/sci-chemistry/pdbcns/Manifest
deleted file mode 100644
index c56d0ca5c00e..000000000000
--- a/sci-chemistry/pdbcns/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pdbcns.2.0.010504.perl.tgz 6806 BLAKE2B a7501b818c7b32f9116a3407234f2ceb39602032a47338772dc7bdf146f4b829091da4caba40045118f52e562f5b62fc270525fc880f80bf0bee50cd7ad4fe88 SHA512 5174cb51dbe3ead405fa1005d81a7ee063bf4be4268b0e728f1ca0aa3e6cbc005fb0bac3e21e06f872c6f4d42c23f50b6e6130391e3b825260c890070e6f766b
diff --git a/sci-chemistry/pdbcns/metadata.xml b/sci-chemistry/pdbcns/metadata.xml
deleted file mode 100644
index d4ff1000a775..000000000000
--- a/sci-chemistry/pdbcns/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild b/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild
deleted file mode 100644
index fe20291abf7e..000000000000
--- a/sci-chemistry/pdbcns/pdbcns-2.0.010504.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Convert atom names for amino acids/nucleic acid bases between PDB and CNS format"
-HOMEPAGE="http://www.mybiosoftware.com/3d-molecular-model/314/"
-#SRC_URI="http://kinemage.biochem.duke.edu/php/downlode.php?filename=/downloads/software/scripts/${PN}.${PV}.perl.tgz"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${PN}.${PV}.perl.tgz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-lang/perl"
-
-S="${WORKDIR}"/${PN}
-
-src_install() {
-	newbin ${PN}*.pl ${PN}
-
-	docinto html
-	dodoc *html
-}
diff --git a/sci-chemistry/pdbmat/Manifest b/sci-chemistry/pdbmat/Manifest
deleted file mode 100644
index 53f52bdcf046..000000000000
--- a/sci-chemistry/pdbmat/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pdbmat-3.89.tar.gz 124727 BLAKE2B ed74b4278d85d21f97a6268f2554478e5da0c871be6d071d54edf964b10f92518f1869a77a6718e2c2b6b8c61b8e4659ccb84f9ee829d4351f23abd727c113cf SHA512 2c7f8f32344fe1abc662878c2556c10bd6671e683787231827399866f485389c3a63253b00d5a5bdbe8d0b8b779891e846962c9372d927b94c45f0fac59a4fb6
diff --git a/sci-chemistry/pdbmat/files/CMakeLists.txt b/sci-chemistry/pdbmat/files/CMakeLists.txt
deleted file mode 100644
index 3a1911c81155..000000000000
--- a/sci-chemistry/pdbmat/files/CMakeLists.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-cmake_minimum_required (VERSION 3.31)
-project (PDBMAT Fortran)
-
-include(GNUInstallDirs)
-
-option (EXAMPLES "Install additional example files" OFF)
-
-add_executable(diagstd diagstd.f)
-add_executable(pdbmat pdbmat.f)
-
-install (TARGETS diagstd pdbmat DESTINATION ${CMAKE_INSTALL_BINDIR})
-install (FILES diagstd.README pdbmat.README DESTINATION ${CMAKE_INSTALL_DOCDIR})
-
-if ( EXAMPLES )
-	install (DIRECTORY ../Try_ENM2011 DESTINATION ${CMAKE_INSTALL_DOCDIR}/examples)
-endif (EXAMPLES)
diff --git a/sci-chemistry/pdbmat/metadata.xml b/sci-chemistry/pdbmat/metadata.xml
deleted file mode 100644
index d9ad115f4e77..000000000000
--- a/sci-chemistry/pdbmat/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-  A fortran program in which Tirion's model (also called the Elastic Network
-  Model) is implemented. Within the frame of this model, atoms (particles)
-  less than cutoff (angstroms) away from each others are linked by springs of
-  same strength. Alternatively, a list of interacting atoms can be given to the
-  program.
-  Requirements: a file with the coordinates of the system, in PDB (Protein Data
-  Bank) or "x y z mass" format.
-
-  Output: the hessian (the mass-weighted second derivatives of energy matrix),
-  in the "i j non-zero-ij-matrix-element" format.
-
-  Diagstd, a fortran program with a standard diagonalization routine, can next
-  be used in order to obtain the corresponding normal modes of the system. If
-  the system is large, the RTB approximation can prove usefull (see below).
-  </longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/pdbmat/pdbmat-3.89-r1.ebuild b/sci-chemistry/pdbmat/pdbmat-3.89-r1.ebuild
deleted file mode 100644
index 500893811395..000000000000
--- a/sci-chemistry/pdbmat/pdbmat-3.89-r1.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake fortran-2
-
-DESCRIPTION="Calculate Tirion's model from pdb structures"
-HOMEPAGE="http://ecole.modelisation.free.fr/modes.html"
-SRC_URI="http://ecole.modelisation.free.fr/enm2011.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"/Source_ENM2011
-
-LICENSE="CeCILL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-BDEPEND=">=dev-build/cmake-3.31"
-
-src_prepare() {
-	cp "${FILESDIR}"/CMakeLists.txt . || die
-
-	cmake_src_prepare
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DEXAMPLES=$(usex examples)
-	)
-
-	cmake_src_configure
-}
diff --git a/sci-chemistry/probe/Manifest b/sci-chemistry/probe/Manifest
deleted file mode 100644
index 99f05261298e..000000000000
--- a/sci-chemistry/probe/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST probe.2.13.110909.src.zip 131063 BLAKE2B da2cc9f43c96043b4cba0c628856e32aa7d5d9ca49d58d4e3f02c8d3aa106955d562c6212240d3d977940fc7301ce2bd27c86915517d5e5a313e5a7e459479ca SHA512 5efa066873d0e139da66bf8edb541fe42df94e99cab171ad8d06a8a6f5caada982ef5b18481e748b224dbed86f63c99237d04ecd107c82855b44de91fb6d2b16
diff --git a/sci-chemistry/probe/files/as-needed.patch b/sci-chemistry/probe/files/as-needed.patch
deleted file mode 100644
index 9ddecf5f569e..000000000000
--- a/sci-chemistry/probe/files/as-needed.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 68d7469..bcb821c 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,6 +1,6 @@
- MACHINEFLAGS = 
- CFLAGS = $(MACHINEFLAGS)
--LFLAGS = -lm $(MACHINEFLAGS)
-+LFLAGS = -lm
- OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
- 	 parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
- 
-@@ -8,7 +8,7 @@ OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
- 	cc -c $*.c $(CFLAGS)
- 
- probe: probe.o $(OBJLIST)
--	cc -o $@ probe.o $(OBJLIST) $(LFLAGS)
-+	cc $(MACHINEFLAGS) -o $@ probe.o $(OBJLIST) $(LFLAGS)
- 
- clean:
- 	@rm -f *.o *.ckp
diff --git a/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch b/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch
deleted file mode 100644
index df7040c3ba1d..000000000000
--- a/sci-chemistry/probe/files/probe-2.13.110909-as-needed.patch
+++ /dev/null
@@ -1,25 +0,0 @@
- Makefile |    8 +++-----
- 1 files changed, 3 insertions(+), 5 deletions(-)
-
-diff --git a/Makefile b/Makefile
-index 9031bd0..8f74d6a 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,14 +1,12 @@
--MACHINEFLAGS = 
--CFLAGS = $(MACHINEFLAGS)
--LFLAGS = -static -lm $(MACHINEFLAGS)
-+LIBS = -lm
- OBJLIST = dots.o abin.o readPDBrecs.o geom3d.o utility.o select.o \
- 	 parse.o atomprops.o stdconntable.o autobondrot.o hybrid_36_c.o
- 
- .c.o:
--	cc -c $*.c $(CFLAGS)
-+	$(CC) $(CFLAGS) -c $*.c
- 
- probe: probe.o $(OBJLIST)
--	cc -o $@ probe.o $(OBJLIST) $(LFLAGS)
-+	$(CC) $(CFLAGS) $(LDFLAGS) -o $@ probe.o $(OBJLIST) $(LIBS)
- 
- clean:
- 	@rm -f *.o *.ckp
diff --git a/sci-chemistry/probe/metadata.xml b/sci-chemistry/probe/metadata.xml
deleted file mode 100644
index d4ff1000a775..000000000000
--- a/sci-chemistry/probe/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/probe/probe-2.13.110909.ebuild b/sci-chemistry/probe/probe-2.13.110909.ebuild
deleted file mode 100644
index feb69db12cec..000000000000
--- a/sci-chemistry/probe/probe-2.13.110909.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-MY_P="${PN}.${PV}"
-
-DESCRIPTION="Evaluates atomic packing within or between molecules"
-HOMEPAGE="http://kinemage.biochem.duke.edu/software/probe.php"
-SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/probe/${MY_P}.src.zip"
-
-LICENSE="richardson"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ~x86 ~x64-macos"
-
-BDEPEND="app-arch/unzip"
-
-S="${WORKDIR}/${MY_P}.src"
-
-PATCHES=( "${FILESDIR}"/${P}-as-needed.patch )
-
-src_configure() {
-	tc-export CC
-}
-
-src_install() {
-	dobin probe
-	einstalldocs
-}
diff --git a/sci-chemistry/propka/Manifest b/sci-chemistry/propka/Manifest
deleted file mode 100644
index 7e914c08740d..000000000000
--- a/sci-chemistry/propka/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST propka-3.5.1.gh.tar.gz 376176 BLAKE2B ef4f5f51a6d08da566aa8dc4d2ec73ca028137031dbe49ca329589fe9ceb7cdda672cac755735a11bed79db1f31be5401b083239214177c2d459207ae998ae29 SHA512 3a9a7fd773700850f14c3ef1cc4ef7614242ea1191001fdca6afd44953486f208cbc067b84752c89e97e82ef6bac5561907b2aeafbee80c4d83cbf3ab443aaa2
diff --git a/sci-chemistry/propka/metadata.xml b/sci-chemistry/propka/metadata.xml
deleted file mode 100644
index 5153791d2361..000000000000
--- a/sci-chemistry/propka/metadata.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="pypi">propka</remote-id>
-		<remote-id type="github">jensengroup/propka</remote-id>
-	</upstream>
-	<stabilize-allarches/>
-</pkgmetadata>
diff --git a/sci-chemistry/propka/propka-3.5.1.ebuild b/sci-chemistry/propka/propka-3.5.1.ebuild
deleted file mode 100644
index 1bd6a6ee0c65..000000000000
--- a/sci-chemistry/propka/propka-3.5.1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-DISTUTILS_USE_PEP517=setuptools
-
-inherit distutils-r1
-
-DESCRIPTION="pKa-value prediction of ionizable groups in protein and protein-ligand complexes"
-HOMEPAGE="https://github.com/jensengroup/propka"
-SRC_URI="https://github.com/jensengroup/propka/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-
-distutils_enable_tests pytest
-
-python_prepare_all() {
-	# Do not install the tests
-	sed -e "/exclude/s:scripts:\', \'tests:g" \
-		-i setup.py || die
-	distutils-r1_python_prepare_all
-}
diff --git a/sci-chemistry/psi/Manifest b/sci-chemistry/psi/Manifest
deleted file mode 100644
index 3dac2d2dedea..000000000000
--- a/sci-chemistry/psi/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST psi-3.4.0.tar.gz 7413072 BLAKE2B de8b5e0fb1692780446385bf13f6b9984f5be8d441730babacf6f59dd18be6e13b1cff17170cec87def1f743d7e634354b57afbc046e6f34c79c9fc52c31b146 SHA512 b13d2464502545cceec3a3b6048b505b918da26730c1614617b04ee6c1d637c9f799ef7fd92ad9554fa2db87617004aa810a6a81400a04df3c06787d51654ca6
diff --git a/sci-chemistry/psi/files/3.4.0-destdir.patch b/sci-chemistry/psi/files/3.4.0-destdir.patch
deleted file mode 100644
index 45db9529aa4d..000000000000
--- a/sci-chemistry/psi/files/3.4.0-destdir.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff --git a/Makefile.in b/Makefile.in
-index aca5a16..2e49f0a 100644
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -8,6 +8,7 @@ subdirs = lib include src
- 
- top_srcdir = @top_srcdir@
- srcdir = @srcdir@
-+datarootdir = @datarootdir@
- VPATH = @srcdir@
- top_objdir = .
- 
-diff --git a/lib/ruby/Makefile.in b/lib/ruby/Makefile.in
-index b31ce7f..e099e1b 100644
---- a/lib/ruby/Makefile.in
-+++ b/lib/ruby/Makefile.in
-@@ -29,10 +29,10 @@ ccenergy.rb    cclambda.rb    chkpt.rb       color.rb       deriv2.rb      frequ
- cceom.rb       ccsort.rb      cints.rb       cphf.rb        detci.rb       input.rb       optking.rb     psi3.rb        testcases.rb 
- 
- install: $(RUBYSRC)
--	$(MKDIRS) $(rubydatadir)
-+	$(MKDIRS) $(DESTDIR)/$(rubydatadir)
- 	for rbfile in $(RUBYSRC); \
-           do \
--            ($(INSTALL_DATA) $(srcdir)/$${rbfile} $(rubydatadir)) || exit 1; \
-+            ($(INSTALL_DATA) $(srcdir)/$${rbfile} $(DESTDIR)/$(rubydatadir)) || exit 1; \
-           done
- 
- install_man: 
-diff --git a/src/bin/Makefile.in b/src/bin/Makefile.in
-index e1abb46..4eddf8d 100644
---- a/src/bin/Makefile.in
-+++ b/src/bin/Makefile.in
-@@ -65,6 +65,7 @@ targetclean:
- 
- top_srcdir = @top_srcdir@
- srcdir = @srcdir@
-+datarootdir = @datarootdir@
- top_objdir = ../..
- 
- $(top_srcdir)/configure: $(top_srcdir)/configure.ac $(top_srcdir)/aclocal.m4
diff --git a/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch b/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch
deleted file mode 100644
index 0d65cee8a1a9..000000000000
--- a/sci-chemistry/psi/files/3.4.0-dont-build-libint.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/src/lib/Makefile.in b/src/lib/Makefile.in
-index 42e025d..b098a36 100644
---- a/src/lib/Makefile.in
-+++ b/src/lib/Makefile.in
-@@ -2,7 +2,7 @@
- .PHONY:	default all install depend clean dclean targetclean
- 
- subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd libutil \
--          liboptions libmoinfo libint libderiv libr12 libbasis libmints
-+          liboptions libmoinfo libbasis libmints
- 
- all: default
- 
diff --git a/sci-chemistry/psi/files/3.4.0-fortify.patch b/sci-chemistry/psi/files/3.4.0-fortify.patch
deleted file mode 100644
index 5f098399ad3f..000000000000
--- a/sci-chemistry/psi/files/3.4.0-fortify.patch
+++ /dev/null
@@ -1,58 +0,0 @@
- src/bin/ccenergy/get_params.cc   |    2 +-
- src/bin/cclambda/get_params.cc   |    2 +-
- src/bin/ccresponse/get_params.cc |    2 +-
- src/bin/ccsort/get_params.cc     |    2 +-
- 4 files changed, 4 insertions(+), 4 deletions(-)
-
-diff --git a/src/bin/ccenergy/get_params.cc b/src/bin/ccenergy/get_params.cc
-index 53f4c83..a2fa932 100644
---- a/src/bin/ccenergy/get_params.cc
-+++ b/src/bin/ccenergy/get_params.cc
-@@ -193,7 +193,7 @@ void get_params()
-     }
-   }
-   else if(params.local) {
--    local.weakp = (char *) malloc(4 * sizeof(char));
-+    local.weakp = (char *) malloc(5 * sizeof(char));
-     sprintf(local.weakp, "%s", "NONE");
-   }
- 
-diff --git a/src/bin/cclambda/get_params.cc b/src/bin/cclambda/get_params.cc
-index 4a9d2c8..8a2ae17 100644
---- a/src/bin/cclambda/get_params.cc
-+++ b/src/bin/cclambda/get_params.cc
-@@ -150,7 +150,7 @@ void get_params(void)
-     }
-   }
-   else if(params.local) {
--    local.weakp = (char *) malloc(4 * sizeof(char));
-+    local.weakp = (char *) malloc(5 * sizeof(char));
-     sprintf(local.weakp, "%s", "NONE");
-   }
-   
-diff --git a/src/bin/ccresponse/get_params.cc b/src/bin/ccresponse/get_params.cc
-index a96db13..5c40aa0 100644
---- a/src/bin/ccresponse/get_params.cc
-+++ b/src/bin/ccresponse/get_params.cc
-@@ -207,7 +207,7 @@ void get_params()
-     }
-   }
-   else if(params.local) {
--    local.weakp = (char *) malloc(4 * sizeof(char));
-+    local.weakp = (char *) malloc(5 * sizeof(char));
-     sprintf(local.weakp, "%s", "NONE");
-   }
- 
-diff --git a/src/bin/ccsort/get_params.cc b/src/bin/ccsort/get_params.cc
-index ad7f0c3..6ee1993 100644
---- a/src/bin/ccsort/get_params.cc
-+++ b/src/bin/ccsort/get_params.cc
-@@ -120,7 +120,7 @@ void get_params()
-     }
-   }
-   else if(params.local) {
--    local.weakp = (char *) malloc(4 * sizeof(char));
-+    local.weakp = (char *) malloc(5 * sizeof(char));
-     sprintf(local.weakp, "%s", "NONE");
-   }
- 
diff --git a/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch b/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch
deleted file mode 100644
index 8283e6d8d8ea..000000000000
--- a/sci-chemistry/psi/files/3.4.0-gcc-4.3.patch
+++ /dev/null
@@ -1,293 +0,0 @@
-diff --git a/src/bin/mcscf/block_matrix.cc b/src/bin/mcscf/block_matrix.cc
-index fe1e131..3ad0bcd 100644
---- a/src/bin/mcscf/block_matrix.cc
-+++ b/src/bin/mcscf/block_matrix.cc
-@@ -1,6 +1,7 @@
- #include "block_matrix.h"
- #include "matrix_base.h"
- #include "memory_manager.h"
-+#include <cstdio>
- 
- extern FILE* outfile;
- 
-diff --git a/src/bin/mcscf/block_vector.cc b/src/bin/mcscf/block_vector.cc
-index fb383c7..36f55d4 100644
---- a/src/bin/mcscf/block_vector.cc
-+++ b/src/bin/mcscf/block_vector.cc
-@@ -1,6 +1,7 @@
- #include "block_vector.h"
- #include "vector_base.h"
- #include "memory_manager.h"
-+#include <cstdio>
- 
- extern FILE* outfile;
- 
-diff --git a/src/bin/mcscf/sblock_matrix.cc b/src/bin/mcscf/sblock_matrix.cc
-index 61aa7cc..4da4263 100644
---- a/src/bin/mcscf/sblock_matrix.cc
-+++ b/src/bin/mcscf/sblock_matrix.cc
-@@ -1,4 +1,5 @@
- #include <cstdlib>
-+#include <cstdio>
- #include <psifiles.h>
- #include "sblock_matrix.h"
- 
-@@ -103,4 +104,4 @@ void SBlockMatrix::check(const char* cstr)
-   }
- }
- 
--}}
-\ No newline at end of file
-+}}
-diff --git a/src/bin/mcscf/sblock_vector.cc b/src/bin/mcscf/sblock_vector.cc
-index 63c3926..f24fc5b 100644
---- a/src/bin/mcscf/sblock_vector.cc
-+++ b/src/bin/mcscf/sblock_vector.cc
-@@ -1,4 +1,5 @@
- #include <cstdlib>
-+#include <cstdio>
- #include <psifiles.h>
- 
- #include "sblock_vector.h"
-@@ -58,4 +59,4 @@ void SBlockVector::check(const char* cstr)
-   }
- }
- 
--}}
-\ No newline at end of file
-+}}
-diff --git a/src/bin/mcscf/scf.cc b/src/bin/mcscf/scf.cc
-index 77318fd..7d1e17f 100644
---- a/src/bin/mcscf/scf.cc
-+++ b/src/bin/mcscf/scf.cc
-@@ -5,6 +5,7 @@
- 
- #include <iostream>
- #include <cmath>
-+#include <cstdio>
- 
- extern FILE* outfile;
- 
-diff --git a/src/bin/mcscf/scf_Feff.cc b/src/bin/mcscf/scf_Feff.cc
-index 584aa83..8a99c3b 100644
---- a/src/bin/mcscf/scf_Feff.cc
-+++ b/src/bin/mcscf/scf_Feff.cc
-@@ -1,4 +1,5 @@
- #include <liboptions/liboptions.h>
-+#include <cstdio>
- 
- #include "scf.h"
- 
-diff --git a/src/bin/mcscf/scf_canonicalize_MO.cc b/src/bin/mcscf/scf_canonicalize_MO.cc
-index a2b3915..96bb6cc 100644
---- a/src/bin/mcscf/scf_canonicalize_MO.cc
-+++ b/src/bin/mcscf/scf_canonicalize_MO.cc
-@@ -1,6 +1,7 @@
- #include "scf.h"
- 
- #include <liboptions/liboptions.h>
-+#include <cstdio>
- 
- namespace psi{ namespace mcscf{
- 
-diff --git a/src/bin/mcscf/scf_check_orthonormality.cc b/src/bin/mcscf/scf_check_orthonormality.cc
-index 63fbbbb..a13436c 100644
---- a/src/bin/mcscf/scf_check_orthonormality.cc
-+++ b/src/bin/mcscf/scf_check_orthonormality.cc
-@@ -1,5 +1,6 @@
- #include <iostream>
- #include <cmath>
-+#include <cstdio>
- 
- #include "scf.h"
- 
-diff --git a/src/bin/mcscf/scf_compute_energy.cc b/src/bin/mcscf/scf_compute_energy.cc
-index fe7ee6d..20194eb 100644
---- a/src/bin/mcscf/scf_compute_energy.cc
-+++ b/src/bin/mcscf/scf_compute_energy.cc
-@@ -1,4 +1,5 @@
- #include <iostream>
-+#include <cstdio>
- 
- #include "scf.h"
- 
-diff --git a/src/bin/mcscf/scf_diis.cc b/src/bin/mcscf/scf_diis.cc
-index 9bcde15..261492a 100644
---- a/src/bin/mcscf/scf_diis.cc
-+++ b/src/bin/mcscf/scf_diis.cc
-@@ -1,4 +1,5 @@
- #include <iostream>
-+#include <cstdio>
- 
- #include <liboptions/liboptions.h>
- 
-diff --git a/src/bin/mcscf/scf_iterate_scf_equations.cc b/src/bin/mcscf/scf_iterate_scf_equations.cc
-index 9e96360..3a3acc3 100644
---- a/src/bin/mcscf/scf_iterate_scf_equations.cc
-+++ b/src/bin/mcscf/scf_iterate_scf_equations.cc
-@@ -1,6 +1,7 @@
- #include <cstdlib>
- #include <iostream>
- #include <cmath>
-+#include <cstdio>
- 
- #include <liboptions/liboptions.h>
- 
-diff --git a/src/bin/mcscf/scf_pairs.cc b/src/bin/mcscf/scf_pairs.cc
-index b0a8c9d..af5fc35 100644
---- a/src/bin/mcscf/scf_pairs.cc
-+++ b/src/bin/mcscf/scf_pairs.cc
-@@ -1,4 +1,5 @@
- #include <iostream>
-+#include <cstdio>
- 
- #include <libmoinfo/libmoinfo.h>
- 
-diff --git a/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc b/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc
-index 3aac92a..e28e9e3 100644
---- a/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc
-+++ b/src/bin/mcscf/scf_print_eigenvectors_and_MO.cc
-@@ -3,6 +3,7 @@
- #include <string>
- #include <utility>
- #include <algorithm>
-+#include <cstdio>
- 
- #include <libmoinfo/libmoinfo.h>
- 
-diff --git a/src/bin/psimrcc/blas_algorithms.cc b/src/bin/psimrcc/blas_algorithms.cc
-index bb36025..0a5a3e2 100644
---- a/src/bin/psimrcc/blas_algorithms.cc
-+++ b/src/bin/psimrcc/blas_algorithms.cc
-@@ -1,5 +1,6 @@
- #include <libmoinfo/libmoinfo.h>
- #include <libutil/libutil.h>
-+#include <cstdio>
- 
- #include "blas.h"
- #include "memory_manager.h"
-diff --git a/src/bin/psimrcc/blas_compatibile.cc b/src/bin/psimrcc/blas_compatibile.cc
-index 8de6d73..7caf4f3 100644
---- a/src/bin/psimrcc/blas_compatibile.cc
-+++ b/src/bin/psimrcc/blas_compatibile.cc
-@@ -1,6 +1,7 @@
- #include "blas.h"
- #include <libutil/libutil.h>
- #include <cstdlib>
-+#include <cstdio>
- 
- extern FILE *infile, *outfile;
- 
-diff --git a/src/bin/psimrcc/blas_parser.cc b/src/bin/psimrcc/blas_parser.cc
-index d211a24..78fe60a 100644
---- a/src/bin/psimrcc/blas_parser.cc
-+++ b/src/bin/psimrcc/blas_parser.cc
-@@ -3,6 +3,7 @@
- #include "debugging.h"
- #include <libutil/libutil.h>
- #include <algorithm>
-+#include <cstdio>
- 
- namespace psi{ namespace psimrcc{
- 
-diff --git a/src/bin/psimrcc/blas_solve.cc b/src/bin/psimrcc/blas_solve.cc
-index b138a5b..f5dcdfc 100644
---- a/src/bin/psimrcc/blas_solve.cc
-+++ b/src/bin/psimrcc/blas_solve.cc
-@@ -1,6 +1,7 @@
- #include "blas.h"
- #include "debugging.h"
- #include <libmoinfo/libmoinfo.h>
-+#include <cstdio>
- 
- namespace psi{ namespace psimrcc{
- 
-diff --git a/src/bin/psimrcc/index.cc b/src/bin/psimrcc/index.cc
-index 3465d88..68c2b77 100644
---- a/src/bin/psimrcc/index.cc
-+++ b/src/bin/psimrcc/index.cc
-@@ -5,6 +5,7 @@
-  ***************************************************************************/
- #include <iostream>
- #include <algorithm>
-+#include <cstdio>
- 
- #include <libmoinfo/libmoinfo.h>
- 
-diff --git a/src/bin/psimrcc/operation.cc b/src/bin/psimrcc/operation.cc
-index edbaed5..f4e881f 100644
---- a/src/bin/psimrcc/operation.cc
-+++ b/src/bin/psimrcc/operation.cc
-@@ -7,6 +7,7 @@
- #include "debugging.h"
- #include "blas.h"
- #include <libutil/libutil.h>
-+#include <cstdio>
- 
- namespace psi{ namespace psimrcc{
- 
-diff --git a/src/bin/psimrcc/operation_compute.cc b/src/bin/psimrcc/operation_compute.cc
-index 7d2553c..72a1b39 100644
---- a/src/bin/psimrcc/operation_compute.cc
-+++ b/src/bin/psimrcc/operation_compute.cc
-@@ -11,6 +11,7 @@
- #include "algebra_interface.h"
- #include <libmoinfo/libmoinfo.h>
- #include <cstdlib>
-+#include <cstdio>
- 
- extern FILE *infile, *outfile;
- 
-diff --git a/src/bin/psimrcc/sort_out_of_core.cc b/src/bin/psimrcc/sort_out_of_core.cc
-index 3f255c9..8fa31a3 100644
---- a/src/bin/psimrcc/sort_out_of_core.cc
-+++ b/src/bin/psimrcc/sort_out_of_core.cc
-@@ -8,6 +8,7 @@
- #include "sort.h"
- #include "matrix.h"
- #include <libmoinfo/libmoinfo.h>
-+#include <cstdio>
- 
- extern FILE* outfile;
- 
-diff --git a/src/lib/libmoinfo/moinfo_model_space.cc b/src/lib/libmoinfo/moinfo_model_space.cc
-index 3bf2030..0a63cde 100644
---- a/src/lib/libmoinfo/moinfo_model_space.cc
-+++ b/src/lib/libmoinfo/moinfo_model_space.cc
-@@ -1,6 +1,7 @@
- #include <iostream>
- #include <cmath>
- #include <cstdlib>
-+#include <cstdio>
- 
- #include <psifiles.h>
- #include <liboptions/liboptions.h>
-@@ -322,4 +323,4 @@ vector<string> MOInfo::get_matrix_names(std::string str)
-   return(names);
- }
- 
--}
-\ No newline at end of file
-+}
-diff --git a/src/lib/libmoinfo/moinfo_slaterdeterminant.cc b/src/lib/libmoinfo/moinfo_slaterdeterminant.cc
-index 8831cd5..a046679 100644
---- a/src/lib/libmoinfo/moinfo_slaterdeterminant.cc
-+++ b/src/lib/libmoinfo/moinfo_slaterdeterminant.cc
-@@ -1,4 +1,5 @@
- #include <iostream>
-+#include <cstdio>
- #include "moinfo.h"
- 
- extern FILE *infile, *outfile;
-diff --git a/src/lib/libutil/stl_string.cc b/src/lib/libutil/stl_string.cc
-index 0ec247d..f719dcd 100644
---- a/src/lib/libutil/stl_string.cc
-+++ b/src/lib/libutil/stl_string.cc
-@@ -2,6 +2,7 @@
- #include <cmath>
- #include <iomanip>
- #include <algorithm>
-+#include <cstdio>
- 
- #include "libutil.h"
- 
diff --git a/sci-chemistry/psi/files/3.4.0-ldflags.patch b/sci-chemistry/psi/files/3.4.0-ldflags.patch
deleted file mode 100644
index 41f6bb651120..000000000000
--- a/sci-chemistry/psi/files/3.4.0-ldflags.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Respect LDFLAGS
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -288,15 +288,13 @@
- )
- AC_SUBST(LDLIBS)
- 
--LDFLAGS=
- LIBDIRS=
- AC_ARG_WITH(libdirs,
- [  --with-libdirs          Specifies library directories (-Ldir1 -Ldir2).],
- LIBDIRS=$withval
--LDFLAGS=$withval
- AC_MSG_RESULT([Using extra library directories: $withval])
- )
--AC_SUBST(LDFLAGS)
-+AC_SUBST(LIBDIRS)
- 
- AC_CHECK_PROGS(PERL,perl,perl) AC_SUBST(PERL)
- 
diff --git a/sci-chemistry/psi/files/3.4.0-man_paths.patch b/sci-chemistry/psi/files/3.4.0-man_paths.patch
deleted file mode 100644
index 51917c4decda..000000000000
--- a/sci-chemistry/psi/files/3.4.0-man_paths.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-Fix man paths
-
-http://bugs.gentoo.org/show_bug.cgi?id=326185
-
---- a/src/bin/nonbonded/Makefile.in
-+++ b/src/bin/nonbonded/Makefile.in
-@@ -19,5 +19,5 @@
- endif
- 
- install_man:: nonbonded.1
--	$(MKDIRS) $(mandir)/man1
--	$(INSTALL_INCLUDE) $^ $(mandir)/man1
-+	$(MKDIRS) $(DESTDIR)$(mandir)/man1
-+	$(INSTALL_INCLUDE) $^ $(DESTDIR)$(mandir)/man1
---- a/src/bin/intder/Makefile.in
-+++ b/src/bin/intder/Makefile.in
-@@ -21,6 +21,6 @@
- endif
- 
- install_man:: intder.1
--	$(MKDIRS) $(mandir)/man1
--	$(INSTALL_INCLUDE) $^ $(mandir)/man1
-+	$(MKDIRS) $(DESTDIR)$(mandir)/man1
-+	$(INSTALL_INCLUDE) $^ $(DESTDIR)$(mandir)/man1
- 
diff --git a/sci-chemistry/psi/files/3.4.0-parallel_fix.patch b/sci-chemistry/psi/files/3.4.0-parallel_fix.patch
deleted file mode 100644
index 8c8d8c35121a..000000000000
--- a/sci-chemistry/psi/files/3.4.0-parallel_fix.patch
+++ /dev/null
@@ -1,400 +0,0 @@
---- a/Makefile.in
-+++ b/Makefile.in
-@@ -17,62 +17,19 @@
- INSTALL = @INSTALL@
- INSTALL_PROGRAM = @INSTALL_PROGRAM@
- 
--all:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making in $${dir} && $(MAKE) all) || exit 1; \
--          done
--
--install: install_host
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install) || exit 1; \
--          done
--
--install_inc:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_inc) || exit 1; \
--          done
--
--install_man:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_man) || exit 1; \
--          done
--
--depend:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making depend in $${dir} && $(MAKE) depend) || exit 1; \
--          done
--
--clean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making clean in $${dir} && $(MAKE) clean) || exit 1; \
--          done
--
--dclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making dclean in $${dir} && $(MAKE) dclean) || exit 1; \
--          done
--
--targetclean:
--	for dir in $(subdirs) tests doc; \
--          do \
--            (cd $${dir} && echo Making clean in $${dir} && $(MAKE) targetclean) || exit 1; \
--          done
-+all clean install install_inc install_man depend dclean targetclean:
-+	for dir in $(subdirs); do \
-+		$(MAKE) -C $$dir $@; \
-+	done
- 
- tests:
--	(cd tests && echo Running test suite... && $(MAKE)) || exit 1;
-+	$(MAKE) -C tests
- 
- testsclean:
--	(cd tests && echo Cleaning test suite... && $(MAKE) clean) || exit 1;
-+	$(MAKE) -C tests clean
- 
- doc:
--	(cd doc && echo Building documentation... && $(MAKE)) || exit 1;
-+	$(MAKE) -C doc
- 
- $(top_srcdir)/configure: $(top_srcdir)/configure.ac $(top_srcdir)/aclocal.m4
- 	cd $(top_srcdir) && autoconf
---- a/lib/Makefile.in
-+++ b/lib/Makefile.in
-@@ -31,7 +31,7 @@
- 	$(INSTALL_DATA) $(srcdir)/psi.dat $(DESTDIR)$(pkgdatadir)
- 	for dir in $(subdirs); \
-           do \
--            (cd $${dir}; echo Making in $${dir}; $(MAKE) install) || exit 1; \
-+            $(MAKE) -C $$dir install; \
-           done
- 
- install_man: macro.psi
---- a/src/Makefile.in
-+++ b/src/Makefile.in
-@@ -6,53 +6,10 @@
- 
- default: all
- 
--all:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making in $${dir} && $(MAKE) all) || exit 1; \
--          done
--
--install:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install) || exit 1; \
--          done
--
--install_inc:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_inc) || exit 1; \
--          done
--
--install_man:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making install in $${dir} && $(MAKE) install_man) || exit 1; \
--          done
--
--depend:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making depend in $${dir} && $(MAKE) depend) || exit 1; \
--          done
--
--clean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making clean in $${dir} && $(MAKE) clean) || exit 1; \
--          done
--
--dclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making dclean in $${dir} && $(MAKE) dclean) || exit 1; \
--          done
--
--targetclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo Making clean in $${dir} && $(MAKE) targetclean) || exit 1; \
--          done
-+all clean install depend dclean targetclean:
-+	for dir in $(subdirs); do \
-+		$(MAKE) -C $$dir $@; \
-+	done
- 
- top_srcdir = @top_srcdir@
- srcdir = @srcdir@
---- a/src/lib/Makefile.in
-+++ b/src/lib/Makefile.in
-@@ -4,56 +4,10 @@
- subdirs = libipv1 libciomr libchkpt libqt libpsio libiwl libdpd libutil \
-           liboptions libmoinfo libbasis libmints
- 
--all: default
--
--default:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \
--          done
--
--install:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \
--          done
--
--install_inc:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \
--          done
--
--install_man:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \
--          done
--
--depend:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \
--          done
--
--clean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \
--          done
--
--dclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \
--          done
--
--targetclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \
--          done
--
-+all clean install install_inc install_man depend dclean targetclean:
-+	for dir in $(subdirs); do \
-+		$(MAKE) -C $$dir $@; \
-+	done
- 
- #
- # keep the configuration information and makefile up-to-date
---- a/src/bin/Makefile.in
-+++ b/src/bin/Makefile.in
-@@ -13,55 +13,10 @@
- subdirs += psirb
- endif
- 
--all: default
--
--default:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \
--          done
--
--install:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \
--          done
--
--install_inc:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \
--          done
--
--install_man:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \
--          done
--
--depend:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \
--          done
--
--clean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \
--          done
--
--dclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \
--          done
--
--targetclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \
--          done
-+all install depend clean dclean targetclean:
-+	for dir in $(subdirs); do \
-+		$(MAKE) -C $$dir $@; \
-+	done
- 
- top_srcdir = @top_srcdir@
- srcdir = @srcdir@
---- a/src/samples/Makefile.in
-+++ b/src/samples/Makefile.in
-@@ -5,55 +5,10 @@
- 
- subdirs = mints
- 
--all: default
--
--default:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \
--          done
--
--install:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \
--          done
--
--install_inc:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \
--          done
--
--install_man:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \
--          done
--
--depend:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \
--          done
--
--clean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \
--          done
--
--dclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \
--          done
--
--targetclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \
--          done
-+all install depend clean dclean targetclean:
-+	for dir in $(subdirs); do \
-+		$(MAKE) -C $$dir $@; \
-+	done
- 
- top_srcdir = @top_srcdir@
- srcdir = @srcdir@
---- a/src/util/Makefile.in
-+++ b/src/util/Makefile.in
-@@ -3,55 +3,10 @@
- 
- subdirs = tocprint psi2molden
- 
--all: default
--
--default:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making in $${dir} ... && $(MAKE) default) || exit 1; \
--          done
--
--install:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install) || exit 1; \
--          done
--
--install_inc:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_inc) || exit 1; \
--          done
--
--install_man:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making install in $${dir} ... && $(MAKE) install_man) || exit 1; \
--          done
--
--depend:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making depend in $${dir} ... && $(MAKE) depend) || exit 1; \
--          done
--
--clean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) clean) || exit 1; \
--          done
--
--dclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making dclean in $${dir} ... && $(MAKE) dclean) || exit 1; \
--          done
--
--targetclean:
--	for dir in $(subdirs); \
--          do \
--            (cd $${dir} && echo ... Making clean in $${dir} ... && $(MAKE) targetclean) || exit 1; \
--          done
-+all install depend clean dclean targetclean:
-+	for dir in $(subdirs); do \
-+		$(MAKE) -C $$dir $@; \
-+	done
- 
- top_srcdir = @top_srcdir@
- srcdir = @srcdir@
---- a/src/lib/libipv1/Makefile.in
-+++ b/src/lib/libipv1/Makefile.in
-@@ -58,4 +58,4 @@
- # in case DODEPEND is no
- #
- 
--ip_read.o: y.tab.h
-+ip_read.o: y.tab.c y.tab.h
diff --git a/sci-chemistry/psi/files/psi-3.4.0-C99.patch b/sci-chemistry/psi/files/psi-3.4.0-C99.patch
deleted file mode 100644
index 798e29fadd96..000000000000
--- a/sci-chemistry/psi/files/psi-3.4.0-C99.patch
+++ /dev/null
@@ -1,22 +0,0 @@
-https://bugs.gentoo.org/886127
-
---- a/src/lib/libipv1/parse.y
-+++ b/src/lib/libipv1/parse.y
-@@ -1,6 +1,7 @@
- %{
- #include <stdio.h>
- #include <tmpl.h>
-+#include "ip_error.gbl"
- #include "ip_types.h"
- #include "ip_read.gbl"
- %}
---- a/src/lib/libipv1/scan.l
-+++ b/src/lib/libipv1/scan.l
-@@ -1,6 +1,7 @@
- %{
- #include <string.h>
- #include <tmpl.h>
-+#include "ip_error.gbl"
- #include "ip_types.h"
- #include "ip_global.h"
- #include "scan.gbl"
diff --git a/sci-chemistry/psi/files/psi-3.4.0-format-security.patch b/sci-chemistry/psi/files/psi-3.4.0-format-security.patch
deleted file mode 100644
index 10efa813ba3d..000000000000
--- a/sci-chemistry/psi/files/psi-3.4.0-format-security.patch
+++ /dev/null
@@ -1,33 +0,0 @@
- src/lib/libmints/matrix.cc | 12 +++++-------
- 1 file changed, 5 insertions(+), 7 deletions(-)
-
-diff --git a/src/lib/libmints/matrix.cc b/src/lib/libmints/matrix.cc
-index 2ce5ede..2c7b5de 100644
---- a/src/lib/libmints/matrix.cc
-+++ b/src/lib/libmints/matrix.cc
-@@ -549,10 +549,9 @@ void Matrix::save(const char *filename, bool append, bool saveLowerTriangle, boo
-     } else {
-         out = fopen(filename, "w");
-     }
--    
--    fprintf(out, name_.c_str());
--    fprintf(out, "\n");
--    
-+
-+    fprintf(out, "%s\n", name_.c_str());
-+
-     if (saveSubBlocks == false) {
-         // Convert the matrix to a full matrix
-         double **fullblock = to_block_matrix();
-@@ -1083,9 +1082,8 @@ void SimpleMatrix::save(const char *filename, bool append, bool saveLowerTriangl
-     } else {
-         out = fopen(filename, "w");
-     }
--    
--    fprintf(out, name_.c_str());
--    fprintf(out, "\n");
-+
-+    fprintf(out, "%s\n", name_.c_str());
- 
-     if (saveLowerTriangle) {
-         // Count the number of non-zero element
diff --git a/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch b/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch
deleted file mode 100644
index 2805cb195e24..000000000000
--- a/sci-chemistry/psi/files/psi-3.4.0-parallel-make.patch
+++ /dev/null
@@ -1,19 +0,0 @@
-diff --git a/src/lib/libipv1/Makefile.in b/src/lib/libipv1/Makefile.in
-index eafe8e2..141bf3b 100644
---- a/src/lib/libipv1/Makefile.in
-+++ b/src/lib/libipv1/Makefile.in
-@@ -33,10 +33,12 @@ LIBOBJ = $(ALLCSRC:%.c=%.o) $(ALLCXXSRC:%.cc=%.o)
- 
- include ../MakeRules
- 
--y.tab.c y.tab.h: parse.y
-+y.tab.h: y.tab.c
-+
-+y.tab.c: parse.y
- 	$(YACC) -v -d $<
- 
--scan.c: scan.l
-+scan.c: scan.l y.tab.h
- 	$(LEX) -t $^ > scan.c
- 
- install_inc:: $(ALLINCLUDE)
diff --git a/sci-chemistry/psi/files/psi-3.4.0-perl-File-Temp.patch b/sci-chemistry/psi/files/psi-3.4.0-perl-File-Temp.patch
deleted file mode 100644
index 691567ae0cc1..000000000000
--- a/sci-chemistry/psi/files/psi-3.4.0-perl-File-Temp.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- a/tests/psitest.pl
-+++ b/tests/psitest.pl
-@@ -2793,9 +2793,9 @@
- {
-   # It's better to use File::Temp but it doesn't seem to be installed by default
-   # use File::Temp;
--  use POSIX qw(tmpnam);
-+  use File::Temp ();
- 
--  my $tempfile = tmpnam();
-+  my $tempfile = File::Temp->new();
-   my $psicmd = build_psi_cmd("psi3 -c", 0, $SRC_PATH,  $PSITEST_EXEC_PATH, " 1>$tempfile 2>/dev/null");
-   my $psi_fail = system($psicmd);
-   open(RE, "$tempfile") || die "cannot open $tempfile $!";
diff --git a/sci-chemistry/psi/files/use-external-libint.patch b/sci-chemistry/psi/files/use-external-libint.patch
deleted file mode 100644
index 1d9ce91e3111..000000000000
--- a/sci-chemistry/psi/files/use-external-libint.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- psi3.orig/src/bin/cints/Makefile.in	2003-11-14 08:15:19.000000000 -0800
-+++ psi3/src/bin/cints/Makefile.in	2006-02-10 22:42:31.000000000 -0800
-@@ -51,25 +51,25 @@
- # and form the list of the libraries. Remember that libderiv and libr12
- # depend on libint, and hence need to come first for GNU ld to work.
- #
--INTLIBS := -lPSI_int
-+INTLIBS := -lint
- ifeq ($(findstring MP2R12,$(SUBDIRS)),MP2R12)
--  ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12)
--    INTLIBS := -lPSI_r12 $(INTLIBS)
-+  ifneq ($(findstring -lr12,$(INTLIBS)),-lr12)
-+    INTLIBS := -lr12 $(INTLIBS)
-   endif
- endif
- ifeq ($(findstring R12_Ints,$(SUBDIRS)),R12_Ints)
--  ifneq ($(findstring -lPSI_r12,$(INTLIBS)),-lPSI_r12)
--    INTLIBS := -lPSI_r12 $(INTLIBS)
-+  ifneq ($(findstring -lr12,$(INTLIBS)),-lr12)
-+    INTLIBS := -lr12 $(INTLIBS)
-   endif
- endif
- ifeq ($(findstring Default_Deriv1,$(SUBDIRS)),Default_Deriv1)
--  ifneq ($(findstring -lPSI_deriv,$(INTLIBS)),-lPSI_deriv)
--    INTLIBS := -lPSI_deriv $(INTLIBS)
-+  ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv)
-+    INTLIBS := -lderiv $(INTLIBS)
-   endif
- endif
- ifeq ($(findstring Default_Deriv2,$(SUBDIRS)),Default_Deriv2)
--  ifneq ($(findstring -lderiv,$(INTLIBS)),-lPSI_deriv)
--    INTLIBS := -lPSI_deriv $(INTLIBS)
-+  ifneq ($(findstring -lderiv,$(INTLIBS)),-lderiv)
-+    INTLIBS := -lderiv $(INTLIBS)
-   endif
- endif
- 
diff --git a/sci-chemistry/psi/metadata.xml b/sci-chemistry/psi/metadata.xml
deleted file mode 100644
index 34f6bdcc5379..000000000000
--- a/sci-chemistry/psi/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="sourceforge">psicode</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/psi/psi-3.4.0-r3.ebuild b/sci-chemistry/psi/psi-3.4.0-r3.ebuild
deleted file mode 100644
index aaeed8c8d19c..000000000000
--- a/sci-chemistry/psi/psi-3.4.0-r3.ebuild
+++ /dev/null
@@ -1,89 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit autotools fortran-2 toolchain-funcs
-
-DESCRIPTION="Suite for ab initio quantum chemistry computing various molecular properties"
-HOMEPAGE="http://www.psicode.org/"
-SRC_URI="https://downloads.sourceforge.net/psicode/${P}.tar.gz"
-S="${WORKDIR}/${PN}${PV:0:1}"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-IUSE="test"
-# psi3/psiclean segfault because tests were never run before
-RESTRICT="test"
-
-RDEPEND="
-	!sci-visualization/extrema
-	virtual/blas
-	virtual/lapack
-	>=sci-libs/libint-1.1.4:1"
-DEPEND="${RDEPEND}"
-BDEPEND="
-	dev-util/byacc
-	virtual/pkgconfig
-	test? ( dev-lang/perl )"
-
-PATCHES=(
-	"${FILESDIR}"/${PV}-dont-build-libint.patch
-	"${FILESDIR}"/use-external-libint.patch
-	"${FILESDIR}"/${PV}-gcc-4.3.patch
-	"${FILESDIR}"/${PV}-destdir.patch
-	"${FILESDIR}"/${P}-parallel-make.patch
-	"${FILESDIR}"/${PV}-man_paths.patch
-	"${FILESDIR}"/${PV}-ldflags.patch
-	"${FILESDIR}"/${PV}-parallel_fix.patch
-	"${FILESDIR}"/${PV}-fortify.patch
-	"${FILESDIR}"/${P}-format-security.patch
-	"${FILESDIR}"/${P}-perl-File-Temp.patch
-	"${FILESDIR}"/${P}-C99.patch
-)
-
-src_prepare() {
-	default
-
-	# Broken test
-	sed \
-		-e 's:scf-mvd-opt ::g' \
-		-e 's:scf-mvd-opt-puream ::g' \
-		-i tests/Makefile.in || die
-	sed \
-		-e "/LIBPATTERNS/d" \
-		-i src/{bin,util,samples}/MakeVars.in || die
-
-	eautoreconf
-}
-
-src_configure() {
-	# This variable gets set sometimes to /usr/lib/src and breaks stuff
-	unset CLIBS
-
-	econf \
-		--with-opt="${CXXFLAGS}" \
-		--datadir="${EPREFIX}"/usr/share/${PN} \
-		--with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \
-		--with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)"
-}
-
-src_compile() {
-	emake \
-		SCRATCH="${WORKDIR}/libint" \
-		DODEPEND="no" \
-		YACC=byacc
-}
-
-src_test() {
-	emake EXECDIR="${S}"/bin TESTFLAGS="" -j1 tests
-}
-
-src_install() {
-	emake DESTDIR="${D}" DODEPEND="no" install
-	einstalldocs
-
-	# convenience libraries
-	rm "${ED}"/usr/$(get_libdir)/*.a || die
-}
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
deleted file mode 100644
index c54a0cc1b0c4..000000000000
--- a/sci-chemistry/pymol/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pymol-3.1.0.tar.gz 29550866 BLAKE2B 0ad054407ac74bf2d088b1d4f7857bfd021ac283b05b95189aae7e9db2d6af8bf34d8b1ceb944af74d66a2d7b4481fa0b7dc42021d653d27d8661e00b1a44fbf SHA512 2eab9f12b0d716ae807659ebf4475f5a4748d4aa9db8266cea25059679898ce6f4c566d304ddaacf069b56baebc0f7c029c4bd1b2e983b8f7226c0d5cea5d097
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
deleted file mode 100644
index 8a087408c332..000000000000
--- a/sci-chemistry/pymol/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<use>
-		<flag name="web">Install Pymodule needed for web app support</flag>
-	</use>
-	<upstream>
-		<remote-id type="github">schrodinger/pymol-open-source</remote-id>
-		<remote-id type="sourceforge">pymol</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-3.1.0-r1.ebuild b/sci-chemistry/pymol/pymol-3.1.0-r1.ebuild
deleted file mode 100644
index 15b0b761c5e8..000000000000
--- a/sci-chemistry/pymol/pymol-3.1.0-r1.ebuild
+++ /dev/null
@@ -1,123 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-DISTUTILS_USE_PEP517="standalone"
-DISTUTILS_EXT=1
-
-inherit desktop xdg distutils-r1
-
-DESCRIPTION="Python-extensible molecular graphics system"
-HOMEPAGE="https://www.pymol.org/"
-SRC_URI="https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}"/${PN}-open-source-${PV}
-
-LICENSE="BitstreamVera BSD freedist HPND MIT-0 OFL-1.0 public-domain UoI-NCSA" #844991
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~x64-macos"
-IUSE="+netcdf web"
-
-DEPEND="
-	dev-cpp/msgpack-cxx
-	dev-libs/mmtf-cpp
-	dev-python/numpy[${PYTHON_USEDEP}]
-	>=dev-python/pillow-10.3.0[${PYTHON_USEDEP}]
-	virtual/zlib:=
-	media-libs/freetype:2
-	media-libs/glew:0=
-	media-libs/glm
-	media-libs/libpng:0=
-	netcdf? ( sci-libs/netcdf:0= )
-"
-RDEPEND="${DEPEND}
-	media-video/mpeg-tools
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	|| (
-		dev-python/pyqt6[opengl,${PYTHON_USEDEP}]
-		dev-python/pyside[opengl,${PYTHON_USEDEP}]
-	)
-	dev-python/pmw[${PYTHON_USEDEP}]
-	sci-chemistry/chemical-mime-data
-"
-BDEPEND="
-	test? ( >=dev-cpp/catch-2:0 )
-	dev-python/setuptools[${PYTHON_USEDEP}]
-	dev-python/wheel[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
-
-# FIXME: We need to still figure out about how to make all the tests pass
-# https://bugs.gentoo.org/932127
-RESTRICT="test"
-
-python_prepare_all() {
-	sed \
-		-e 's/no_launcher = False/no_launcher = True/' \
-		-i setup.py || die
-
-	if use !netcdf; then
-		sed -e 's/vmd_plugins = True/vmd_plugins = False/' \
-			-i setup.py || die
-	fi
-
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-		-i setup.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-	sed \
-		-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
-		-i setup.py || die
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install \
-		--pymol-path="${EPREFIX}/usr/share/pymol"
-
-	sed \
-		-e '1i#!/usr/bin/env python' \
-		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
-	python_doscript "${T}"/${PN}
-}
-
-python_test() {
-	"${EPYTHON}" -m pymol -ckqy testing/testing.py --offline --no-mmlibs --no-undo --run all || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	# Move data to correct location
-	dodir /usr/share/pymol
-	mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF || die
-		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${S}"/data/pymol/icons/icon2.svg ${PN}.svg
-	make_desktop_entry "${PN} %u"  PyMol ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/pdby;chemical/x-mdl-sdfile;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;chemical/x-macromodel-input;chemical/x-vmd;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
diff --git a/sci-chemistry/raster3d/Manifest b/sci-chemistry/raster3d/Manifest
deleted file mode 100644
index fe0765d711a9..000000000000
--- a/sci-chemistry/raster3d/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST Raster3D_3.0-6.tar 1729698 BLAKE2B d51b752c189ef720306e78a97e75a8b30c4286b1e75bfa20dd6d8c6e02e3a57d49508faaa1324d8b1f8311049ab3a9b18847bdcb73e7237e3bc91c34fb1ea55b SHA512 656bc19fdef882713c540598173e7f46246b4245f7983edc906fe9fdab7393c47c1687c6e9366987e8af7627d4bfe56a996ff0003aa19872d79724b3e555fdda
diff --git a/sci-chemistry/raster3d/files/3.0.2-as-needed.patch b/sci-chemistry/raster3d/files/3.0.2-as-needed.patch
deleted file mode 100644
index 9e0961952535..000000000000
--- a/sci-chemistry/raster3d/files/3.0.2-as-needed.patch
+++ /dev/null
@@ -1,50 +0,0 @@
-diff --git a/Makefile b/Makefile
-index 1a1c549..4d74dd0 100644
---- a/Makefile
-+++ b/Makefile
-@@ -58,7 +58,7 @@ linux:
- 	@echo OSDEFS =  -DLINUX -DNETWORKBYTEORDER       >> Makefile.incl
- 	@echo include Makefile.package        >> Makefile.incl
- 	@echo                                 >> Makefile.incl
--	@echo qinp.o: qinp.f                  >> Makefile.incl
-+	@echo qinp.o: qinp.f normal3d.o render.o >> Makefile.incl
- 	@echo "	\$$(FC) -g -O0 -Wall -Wtabs -c -o qinp.o qinp.f" >> Makefile.incl
- 	@echo                                 >> Makefile.incl
- 
-@@ -214,20 +214,20 @@ ribbon:	ribbon.f ribbon1.f modsubs.f
- 	ribbon.f ribbon1.f modsubs.f -o ribbon
- 
- rastep:	rastep.f quadric.o suv.o
--	$(FC) $(FFLAGS) \
--	rastep.f quadric.o suv.o $(LDFLAGS) \
-+	$(FC) $(FFLAGS) $(LDFLAGS) \
-+	rastep.f quadric.o suv.o \
- 	-o rastep 
- 
- render:	render.o local.o quadric.o parse.o r3dtogd.o ungz.o qinp.o
--	$(FC) $(FFLAGS) \
-+	$(FC) $(FFLAGS) $(LDFLAGS) \
- 	render.o local.o quadric.o parse.o r3dtogd.o ungz.o \
- 	qinp.o \
--	$(LIBS) $(LDFLAGS) \
--	-o render
-+	-o render \
-+	$(LIBS)
- 
- normal3d:	normal3d.o quadric.o qinp.o ungz.o parameters.incl
--	$(FC) $(FFLAGS) \
--	normal3d.o quadric.o ungz.o qinp.o $(LDFLAGS) \
-+	$(FC) $(FFLAGS) $(LDFLAGS) \
-+	normal3d.o quadric.o ungz.o qinp.o \
- 	-o normal3d
- 
- stereo3d:
-@@ -264,7 +264,7 @@ example1.png: render_small
- 	./render_small
- 
- render_small: render_small.o local.o quadric.o parse_small.o r3dtogd.o ungz.o qinp_small.o
--	$(FC) $(FFLAGS) $^ $(LIBS) $(LDFLAGS) -o $@
-+	$(FC) $(FFLAGS) $(LDFLAGS) -o $@ $^ $(LIBS)
- 
- .SUFFIXES: .incl
- SMALL=10
diff --git a/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch b/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch
deleted file mode 100644
index 19b6cac3a6fe..000000000000
--- a/sci-chemistry/raster3d/files/3.0.2-gentoo-prefix.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/Makefile.template b/Makefile.template
-index 59de553..0ed283d 100644
---- a/Makefile.template
-+++ b/Makefile.template
-@@ -8,15 +8,15 @@ include VERSION
- #
- # Where to install the program, data files, and manuals
- #
--prefix  = /usr/local
-+prefix  = @GENTOO_PORTAGE_EPREFIX@/usr/
- bindir  = $(prefix)/bin
- datadir = $(prefix)/share/Raster3D/materials
- mandir  = $(prefix)/man/manl
--htmldir = $(prefix)/share/Raster3D/html
-+htmldir = $(prefix)/share/doc/MYPF/html
- examdir = $(prefix)/share/Raster3D/examples
- 
--INCDIRS  =	-I/usr/include -I/usr/local/include
--LIBDIRS  =	-L/usr/local/lib
-+INCDIRS  =	-I@GENTOO_PORTAGE_EPREFIX@/usr/include
-+LIBDIRS  =	-L@GENTOO_PORTAGE_EPREFIX@/usr/MYLIB
- 
- #
- # TIFF support (enabled by default)
diff --git a/sci-chemistry/raster3d/metadata.xml b/sci-chemistry/raster3d/metadata.xml
deleted file mode 100644
index a1d690946ace..000000000000
--- a/sci-chemistry/raster3d/metadata.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <upstream>
-    <changelog>http://skuld.bmsc.washington.edu/raster3d/CHANGELOG</changelog>
-  </upstream>
-  <use>
-    <flag name="gd">libgd support for PNG and JPEG output</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-chemistry/raster3d/raster3d-3.0.6-r1.ebuild b/sci-chemistry/raster3d/raster3d-3.0.6-r1.ebuild
deleted file mode 100644
index 7cc100f6265f..000000000000
--- a/sci-chemistry/raster3d/raster3d-3.0.6-r1.ebuild
+++ /dev/null
@@ -1,107 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit fortran-2 flag-o-matic prefix toolchain-funcs
-
-MY_PN="Raster3D"
-MY_PV=$(ver_rs 2 -)
-MY_P="${MY_PN}_${MY_PV}"
-
-DESCRIPTION="Generation high quality raster images of proteins or other molecules"
-HOMEPAGE="http://www.bmsc.washington.edu/raster3d/raster3d.html"
-SRC_URI="http://www.bmsc.washington.edu/${PN}/${MY_P}.tar.gz -> ${MY_P}.tar"
-
-LICENSE="Artistic-2"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86"
-IUSE="gd tiff"
-
-RDEPEND="
-	gd? ( media-libs/gd[jpeg,png] )
-	tiff? ( media-libs/tiff:= )"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-	"${FILESDIR}"/3.0.2-as-needed.patch
-	"${FILESDIR}"/3.0.2-gentoo-prefix.patch
-)
-
-src_prepare() {
-	default
-
-	sed \
-		-e "s:MYPF:${PF}:" \
-		-e "s:MYLIB:$(get_libdir):g" \
-		-i Makefile.template || \
-		die "Failed to patch makefile.template"
-
-	if ! use gd; then
-		sed \
-			-e "/GDLIBS/s:^:#:g" \
-			-e "/GDDEFS/s:^:#:g" \
-			-i Makefile.template || die
-	fi
-
-	if ! use tiff; then
-		sed \
-			-e "/TLIBS/s:^:#:g" \
-			-e "/TDEFS/s:^:#:g" \
-			-i Makefile.template || die
-	fi
-
-	if [[ $(tc-getFC) =~ gfortran ]]; then
-		append-cflags -Dgfortran
-	fi
-
-	append-fflags -ffixed-line-length-132
-
-	eprefixify Makefile.template
-	cp Makefile.template Makefile.incl || die
-}
-
-src_compile() {
-	local target
-	if [[ $(tc-getFC) =~ gfortran ]]; then
-		target="linux"
-	else
-		target="linux-$(tc-getFC)"
-	fi
-
-	local i
-	for i in render.o ${target} all; do
-		emake \
-			CFLAGS="${CFLAGS}" \
-			LDFLAGS="${LDFLAGS}" \
-			FFLAGS="${FFLAGS}" \
-			CC="$(tc-getCC)"\
-			FC="$(tc-getFC)" \
-			INCDIRS="-I${EPREFIX}/usr/include" \
-			LIBDIRS="-L${EPREFIX}/usr/$(get_libdir)" \
-			${i}
-	done
-}
-
-src_install() {
-	emake prefix="${ED}"/usr \
-		bindir="${ED}"/usr/bin \
-		datadir="${ED}"/usr/share/Raster3D/materials \
-		mandir="${ED}"/usr/share/man/man1 \
-		htmldir="${ED}"/usr/share/doc/${PF}/html \
-		examdir="${ED}"/usr/share/Raster3D/examples \
-		install
-
-	newenvd - 10raster3d <<-EOF
-		R3D_LIB="${EPREFIX}/usr/share/${NAME}/materials"
-	EOF
-}
-
-pkg_postinst() {
-	elog "Add following line:"
-	elog "<delegate decode=\"r3d\" command='\"render\" < \"%i\" > \"%o\"' />"
-	elog "to ${EPREFIX}/usr/$(get_libdir)/ImageMagick-6.5.8/config/delegates.xml"
-	elog "to make imagemagick use raster3d for .r3d files"
-}
diff --git a/sci-chemistry/surf/Manifest b/sci-chemistry/surf/Manifest
deleted file mode 100644
index 1f44e53f3c4d..000000000000
--- a/sci-chemistry/surf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST surf-1.0.tar.Z 74347 BLAKE2B 543696838470f8b263d3841e177bb9054eb24a1ff0978fa09d9617e32a3a3e6b0662b37c1faa83fa449321276c8b3dd4aed80e978ea3c8315ed5b11f37196a73 SHA512 55b0e771f880931e43d677498ef4cdd92e5f57980d90b686b13c7ae612c8d695353a6f3b5ad0dab184d44e67d8cc5244e7b3f45b4f067c4174ed4399c184d435
diff --git a/sci-chemistry/surf/files/surf-1.0-Wreturn-type.patch b/sci-chemistry/surf/files/surf-1.0-Wreturn-type.patch
deleted file mode 100644
index 9ad6cf31593d..000000000000
--- a/sci-chemistry/surf/files/surf-1.0-Wreturn-type.patch
+++ /dev/null
@@ -1,108 +0,0 @@
---- a/compute.c
-+++ b/compute.c
-@@ -210,7 +210,7 @@
- 
-   Current_atom = atom_id;
- 
--  if (!compute_neighbors(atom_id, &num_constraints)) return;
-+  if (!compute_neighbors(atom_id, &num_constraints)) return -1;
- 
-   compute_planes(atom_id, num_constraints,constraints);
- 
-@@ -597,7 +597,7 @@
-   */
-   if (all_verts_in_sphere(rvertices, rvertices_count, sq_radius)) 
-   { /* printf("atom_id %d all_in = TRUE \n", atom_id); */
--    return;
-+    return -1;
-   }
- 
-   for(i = 0; i < rfaces_count; i++)	       /* for each face    */
-@@ -647,7 +647,7 @@
-   if (DOTPROD3(diff, diff) < 1e-10)
-   /* atom center lies in the feasible region, and so can be also
-      taken to be the tes_origin - no more computations required */
--    return;
-+    return -1;
- 
-   /* try computing the tes_origin as the average of all int_pts */
-   VEC3_ZERO(temp_origin); count = 0;
---- a/tessel_concave.c
-+++ b/tessel_concave.c
-@@ -178,7 +178,7 @@
-   if ((sq_side_len[0] < EPS) && 
-       (sq_side_len[1] < EPS) && 
-       (sq_side_len[2] < EPS)) 
--  { return;
-+  { return -1;
-   }
- 
-   /* evaluate which side of the plane the points lie wrt the probe center */
-@@ -195,14 +195,14 @@
-   max_len = FMAX((FMAX(sq_side_len[0], sq_side_len[1])), sq_side_len[2]);
-   max_side = (max_len==sq_side_len[0])?0:((max_len==sq_side_len[1])? 1 : 2);
- 
--  if (num_fine_points == 0) return;      /* all points are on the wrong side */
-+  if (num_fine_points == 0) return -1;      /* all points are on the wrong side */
- 
-   if (max_len <= Max_Tess_Len_Sq)
-   { /* sufficiently small so display but first check to see whether it
-        intersects the plane or not and if so, clip it accordingly */
-     if (num_fine_points == 3)
-     { gen_tris(points[0], points[1], points[2]);
--      return;
-+      return -1;
-     }
-     else if (num_fine_points == 1) /* two points are on the wrong side */
-       i = (itemp[0] == 1)? 0 : ((itemp[1] == 1)? 1: 2);
-@@ -305,7 +305,7 @@
-       (sq_side_len[1] < EPS) && 
-       (sq_side_len[2] < EPS)) 
-   { 
--    return;
-+    return -1;
-   }
- 
-   if (max_len > Max_Tess_Len_Sq)
---- a/tessel_convex.c
-+++ b/tessel_convex.c
-@@ -74,7 +74,7 @@
-      atoms[atom_id].center[Y], atoms[atom_id].center[Z], atoms[atom_id].radius);
-     fflush(stderr);
-     free(sph_side);
--    return;
-+    return -1;
-   }
- 
-   
---- a/tessel_torus.c
-+++ b/tessel_torus.c
-@@ -191,7 +191,7 @@
- 
-   if (j > n)
-   { printf("gen_torus(): Too many torus verts %d (limit %d)\n",j, n);
--    return ;
-+    return -1;
-   }
-   old_j = j;
- 
-@@ -202,7 +202,7 @@
-     gen_linear_recurse(tor_pts[0][i],tor_pts[1][i],r[k],&j,fcenter,fradius,0);
-     if (j > n)
-     { printf("gen_torus(): Too many torus verts %d (limit %d)\n",j, n);
--      return ;
-+      return -1;
-     }
- 
-     for(m = 0; m < j-1; m++)
---- a/utils.c
-+++ b/utils.c
-@@ -91,7 +91,7 @@
-   disc = radius*radius - DOTPROD3(EO, EO);
-   if (FP_EQ_EPS(disc, 0, GP_EPS*GP_EPS))
-   { VEC3_ASN_OP(int_point, =, ray_pt);
--    return;
-+    return -1;
-   }
- 
-   one_by_sq_dir_mag = 1.0/DOTPROD3(ray_dir, ray_dir);
diff --git a/sci-chemistry/surf/files/surf-1.0-makefile.patch b/sci-chemistry/surf/files/surf-1.0-makefile.patch
deleted file mode 100644
index ae5177ffb501..000000000000
--- a/sci-chemistry/surf/files/surf-1.0-makefile.patch
+++ /dev/null
@@ -1,112 +0,0 @@
---- a/Makefile
-+++ b/Makefile
-@@ -1,24 +1,19 @@
- # Compilation flags
- #CC	    = cc
--CC	    = cc
--INCLUDE     = -I. 
-+CPPFLAGS += -I.
- #LINCLUDE    = -lcurses -ltermcap -lm
--LINCLUDE    = -lm
--OPT_CFLAGS  = -O2 $(FLAGS) $(INCLUDE)
--#CFLAGS	    = -g $(FLAGS) $(INCLUDE)
--CFLAGS	    = -O2 $(FLAGS) $(INCLUDE)
-+LDLIBS      = -lm
- 
- # These are the user object files in the application
- SRCS        = surf.c io.c compute.c dual.c utils.c lp.c chull.c tessel_cases.c \
- 	      tessel_patches.c tessel_convex.c tessel_concave.c tessel_torus.c 
- 
- # obj files for sequential execution
--OBJS        = surf.o io.o compute.o dual.o utils.o lp.o chull.o tessel_cases.o \
-+OBJS        = io.o compute.o dual.o utils.o lp.o chull.o tessel_cases.o \
- 	      tessel_patches.o tessel_convex.o tessel_concave.o tessel_torus.o  
- 
- # make objects
--surf: $(OBJS) Makefile 
--	$(CC) $(CFLAGS) $(OBJS) -o surf $(LINCLUDE)
-+surf: $(OBJS)
- 
- lint:
- 	lint $(INCLUDE) $(SRCS)
-@@ -29,80 +24,3 @@
- release:
- 	tar -cvf surf.tar README *.[hc] Makefile
- 	compress surf.tar
--
--.c.o: 
--	$(CC) $(CFLAGS) -c $*.c
--
--
--# make depend makes the proper include file dependencies.  You _could_ run
--# it on a sun4, but there's a bug in the SunOS version of sed that causes
--# the all-important "cat makedep | sed -e 's/\.o/.d4o/p'" etc. line to
--# not print the results to the stdout (but to keep pumping it through the
--# edits.  The 'p' flag effectively does nothing). To avoid this I have
--# replaced the 'p' flag by the 'w file' flag in sed.
--
--DEPEND = $(SRCS)
--
--depend: $(DEPEND)
--	@ echo making dependencies...
--	@ echo ' ' > makedep
--	@ makedepend $(INCLUDE) -f makedep $(DEPEND)
--	@ echo '/^# DO NOT DELETE THIS LINE/+2,$$d' >eddep
--	@ echo '$$r makedep' >>eddep
--	@ echo 'w' >>eddep
--	@ cp Makefile Makefile.bak
--	@ ed - Makefile < eddep
--	@ rm eddep makedep 
--	@ echo '  ' >> Makefile
--	@ echo '# DEPENDENCIES MUST END AT END OF FILE' >> Makefile
--	@ echo '# IF YOU PUT STUFF HERE IT WILL GO AWAY' >> Makefile
--	@ echo '# see make depend above' >> Makefile
--	@ echo 'done.'
--	@ echo '  ' >> Makefile
--
--# DO NOT DELETE THIS LINE -- make depend depends on it.
--  
-- 
--# DO NOT DELETE THIS LINE -- make depend depends on it.
--
--surf.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
--surf.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
--surf.o: linalg.h
--io.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
--io.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
--io.o: linalg.h
--compute.o: surf.h /usr/include/stdio.h /usr/include/math.h
--compute.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
--compute.o: /usr/include/sys/time.h linalg.h chull.h dual.h
--dual.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
--dual.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
--dual.o: linalg.h dual.h chull.h
--utils.o: surf.h /usr/include/stdio.h /usr/include/math.h
--utils.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
--utils.o: /usr/include/sys/time.h linalg.h
--lp.o: surf.h /usr/include/stdio.h /usr/include/math.h /usr/include/stdlib.h
--lp.o: /usr/include/sgidefs.h /usr/include/string.h /usr/include/sys/time.h
--lp.o: linalg.h
--chull.o: surf.h /usr/include/stdio.h /usr/include/math.h
--chull.o: /usr/include/stdlib.h /usr/include/sgidefs.h /usr/include/string.h
--chull.o: /usr/include/sys/time.h linalg.h chull.h
--tessel_cases.o: surf.h /usr/include/stdio.h /usr/include/math.h
--tessel_cases.o: /usr/include/stdlib.h /usr/include/sgidefs.h
--tessel_cases.o: /usr/include/string.h /usr/include/sys/time.h linalg.h dual.h
--tessel_patches.o: surf.h /usr/include/stdio.h /usr/include/math.h
--tessel_patches.o: /usr/include/stdlib.h /usr/include/sgidefs.h
--tessel_patches.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
--tessel_convex.o: surf.h /usr/include/stdio.h /usr/include/math.h
--tessel_convex.o: /usr/include/stdlib.h /usr/include/sgidefs.h
--tessel_convex.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
--tessel_concave.o: surf.h /usr/include/stdio.h /usr/include/math.h
--tessel_concave.o: /usr/include/stdlib.h /usr/include/sgidefs.h
--tessel_concave.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
--tessel_torus.o: surf.h /usr/include/stdio.h /usr/include/math.h
--tessel_torus.o: /usr/include/stdlib.h /usr/include/sgidefs.h
--tessel_torus.o: /usr/include/string.h /usr/include/sys/time.h linalg.h
--  
--# DEPENDENCIES MUST END AT END OF FILE
--# IF YOU PUT STUFF HERE IT WILL GO AWAY
--# see make depend above
--  
diff --git a/sci-chemistry/surf/metadata.xml b/sci-chemistry/surf/metadata.xml
deleted file mode 100644
index b71795dbfba5..000000000000
--- a/sci-chemistry/surf/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<maintainer type="project">
-	<email>sci-chemistry@gentoo.org</email>
-	<name>Gentoo Chemistry Project</name>
-</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/surf/surf-1.0.ebuild b/sci-chemistry/surf/surf-1.0.ebuild
deleted file mode 100644
index 4113c7a1d0ed..000000000000
--- a/sci-chemistry/surf/surf-1.0.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Solvent accesible Surface calculator"
-HOMEPAGE="http://www.ks.uiuc.edu/"
-SRC_URI="http://www.ks.uiuc.edu/Research/vmd/extsrcs/surf.tar.Z -> ${P}.tar.Z"
-
-LICENSE="SURF"
-SLOT="0"
-KEYWORDS="amd64 ~x86"
-
-RDEPEND="!www-client/surf"
-
-S="${WORKDIR}"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-makefile.patch
-	"${FILESDIR}"/${P}-Wreturn-type.patch
-)
-
-src_configure() {
-	tc-export CC
-}
-
-src_install() {
-	dobin surf
-	einstalldocs
-}
diff --git a/sci-chemistry/theseus/Manifest b/sci-chemistry/theseus/Manifest
deleted file mode 100644
index e89bd4c6849f..000000000000
--- a/sci-chemistry/theseus/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST theseus_3.3.0.tar.gz 22548124 BLAKE2B 0ad49f768e1584bf40e90ff6fd0d884b6b27ee59ad31ce75050293b817a3747969ab0c4b4ff982aadbdc5301c1c56522540b78aab045e841c099a80dd546c8e9 SHA512 1fba3e8019a40214defdae13d4721d170ee698337d8efd4e872af22f8ab3cb1fdd52fa9f19a858ee51bc98150692af0c6016033feb0d76f29acaf7fffbb430e2
diff --git a/sci-chemistry/theseus/metadata.xml b/sci-chemistry/theseus/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/theseus/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild b/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild
deleted file mode 100644
index 4149ed4f3cba..000000000000
--- a/sci-chemistry/theseus/theseus-3.3.0-r1.ebuild
+++ /dev/null
@@ -1,71 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="Maximum likelihood superpositioning and analysis of macromolecular structures"
-HOMEPAGE="http://www.theseus3d.org/"
-SRC_URI="http://www.theseus3d.org/src/${PN}_${PV}.tar.gz"
-S="${WORKDIR}"/${PN}_src
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-RDEPEND="
-	sci-libs/gsl:=
-	|| (
-		sci-biology/clustalw:2
-		sci-biology/kalign
-		sci-biology/mafft
-		sci-biology/muscle
-		sci-biology/probcons
-		sci-biology/t-coffee
-	)
-"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-src_prepare() {
-	default
-
-	cat >> make.inc <<- EOF || die
-	ARCH = $(tc-getAR)
-	ARCHFLAGS = -rvs
-	RANLIB = $(tc-getRANLIB)
-	LOCALLIBDIR = "${EPREFIX}"/usr/$(get_libdir)
-	SYSLIBS = $($(tc-getPKG_CONFIG) --libs gsl) -lpthread
-	LIBS = -ldistfit -lmsa -ldssplite -ldltmath -lDLTutils -ltheseus
-	LIBDIR = -L./lib
-	INSTALLDIR = "${ED}"/usr/bin
-	OPT =
-	WARN =
-	CFLAGS = ${CFLAGS} -std=c11 \$(WARN)
-	CC = $(tc-getCC)
-	EOF
-
-	sed \
-		-e 's|theseus:|theseus: libs|g' \
-		-e '/-o theseus/s:$(CC):$(CC) ${LDFLAGS}:g' \
-		-i Makefile || die
-
-	sed \
-		-e 's:/usr/bin/sed:sed:g' \
-		-e "s:/usr/local/bin/:/usr/bin/:g" \
-		-e "s:/usr/bin/:${EPREFIX}/usr/bin/:g" \
-		-i theseus_align || die
-}
-
-src_compile() {
-	emake ltheseus
-	default
-}
-
-src_install() {
-	dobin theseus theseus_align
-	dodoc theseus_man.pdf README AUTHORS
-	use examples && insinto /usr/share/${PN} && doins -r examples
-}
diff --git a/sci-chemistry/threeV/Manifest b/sci-chemistry/threeV/Manifest
deleted file mode 100644
index d6c802a230d4..000000000000
--- a/sci-chemistry/threeV/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST 3v-1.2.tgz 599194 BLAKE2B cc5f14cfe4d9adca54925ee9edea2616019c9780878e2a300dcdd9492b331fa9f186473548b4a38b2f006380440b6d53c52cf567f02dc1fb6342706fb21ecbb8 SHA512 063747e46be1ab8af585909185b735edbbb760945f9d4d345d478a264e3d90c551d72f578239e7eff7768482d18b34d2b00831f87e109ec87cb36b0fd4e6a757
diff --git a/sci-chemistry/threeV/files/threeV-1.2-format-security.patch b/sci-chemistry/threeV/files/threeV-1.2-format-security.patch
deleted file mode 100644
index b693559900ad..000000000000
--- a/sci-chemistry/threeV/files/threeV-1.2-format-security.patch
+++ /dev/null
@@ -1,198 +0,0 @@
- cavities.cpp |  8 ++++----
- channel.cpp  | 10 +++++-----
- fsv_calc.cpp |  8 ++++----
- solvent.cpp  |  8 ++++----
- tunnel.cpp   |  8 ++++----
- vdw.cpp      |  8 ++++----
- volume.cpp   |  8 ++++----
- 7 files changed, 29 insertions(+), 29 deletions(-)
-
-diff --git a/cavities.cpp b/cavities.cpp
-index 418a1a7..96b6a15 100644
---- a/cavities.cpp
-+++ b/cavities.cpp
-@@ -35,7 +35,7 @@ int main(int argc, char *argv[]) {
- 
-   while(argc > 1 && argv[1][0] == '-') {
-     if(argv[1][1] == 'i') {
--      sprintf(file,&argv[2][0]);
-+      sprintf(file,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'g') {
-       GRID = atof(&argv[2][0]);
-     } else if(argv[1][1] == 's') {
-@@ -45,11 +45,11 @@ int main(int argc, char *argv[]) {
-     } else if(argv[1][1] == 't') {
-       trim_rad = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'e') {
--      sprintf(ezdfile,&argv[2][0]);
-+      sprintf(ezdfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'm') {
--      sprintf(mrcfile,&argv[2][0]);
-+      sprintf(mrcfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'o') {
--      sprintf(pdbfile,&argv[2][0]);
-+      sprintf(pdbfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'h') {
-       cerr << "./Cavities.exe -i <file> -g <grid spacing> -s <shell radius> " << endl
-         << "\t-p <probe radius> -t <trim_probe_rad>  " << endl
-diff --git a/channel.cpp b/channel.cpp
-index c5acd20..9040631 100644
---- a/channel.cpp
-+++ b/channel.cpp
-@@ -35,7 +35,7 @@ int main(int argc, char *argv[]) {
- 
-   while(argc > 1 && argv[1][0] == '-') {
-     if(argv[1][1] == 'i') {
--      sprintf(file,&argv[2][0]);
-+      sprintf(file,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'b') {
-       BIGPROBE = atof(&argv[2][0]);
-     } else if(argv[1][1] == 's') {
-@@ -49,13 +49,13 @@ int main(int argc, char *argv[]) {
-     } else if(argv[1][1] == 'z') {
-       z = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'i') {
--      sprintf(file,&argv[2][0]);
-+      sprintf(file,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'o') {
--      sprintf(pdbfile,&argv[2][0]);
-+      sprintf(pdbfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'e') {
--      sprintf(ezdfile,&argv[2][0]);
-+      sprintf(ezdfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'm') {
--      sprintf(mrcfile,&argv[2][0]);
-+      sprintf(mrcfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'g') {
-       GRID = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'h') {
-diff --git a/fsv_calc.cpp b/fsv_calc.cpp
-index 9f81347..ef765b8 100644
---- a/fsv_calc.cpp
-+++ b/fsv_calc.cpp
-@@ -34,7 +34,7 @@ int main(int argc, char *argv[]) {
- 
-   while(argc > 1 && argv[1][0] == '-') {
-     if(argv[1][1] == 'i') {
--      sprintf(file,&argv[2][0]);
-+      sprintf(file,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 's') {
-       SMPROBE = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'b') {
-@@ -44,11 +44,11 @@ int main(int argc, char *argv[]) {
-     } else if(argv[1][1] == 'g') {
-       GRID = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'o') {
--      sprintf(pdbfile,&argv[2][0]);
-+      sprintf(pdbfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'e') {
--      sprintf(ezdfile,&argv[2][0]);
-+      sprintf(ezdfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'm') {
--      sprintf(mrcfile,&argv[2][0]);
-+      sprintf(mrcfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'h') {
-       cerr << "./FsvCalc.exe -i <file> -b <big_probe> -s <small_probe> " << endl
-         << "\t-t <trim probe> -g <gridspace> " << endl
-diff --git a/solvent.cpp b/solvent.cpp
-index d857696..bc9d67f 100644
---- a/solvent.cpp
-+++ b/solvent.cpp
-@@ -34,7 +34,7 @@ int main(int argc, char *argv[]) {
-  
-   while(argc > 1 && argv[1][0] == '-') {
-     if(argv[1][1] == 'i') {
--      sprintf(file,&argv[2][0]);   
-+      sprintf(file,"%s",&argv[2][0]);   
-     } else if(argv[1][1] == 's') {
-       SMPROBE = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'b') {
-@@ -42,11 +42,11 @@ int main(int argc, char *argv[]) {
-     } else if(argv[1][1] == 't') {
-       TRIMPROBE = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'e') {
--      sprintf(ezdfile,&argv[2][0]);
-+      sprintf(ezdfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'm') {
--      sprintf(mrcfile,&argv[2][0]);
-+      sprintf(mrcfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'o') {
--      sprintf(pdbfile,&argv[2][0]);
-+      sprintf(pdbfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'g') {
-       GRID = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'h') {
-diff --git a/tunnel.cpp b/tunnel.cpp
-index 0094d05..7472aaa 100644
---- a/tunnel.cpp
-+++ b/tunnel.cpp
-@@ -40,7 +40,7 @@ int main(int argc, char *argv[]) {
- 
-   while(argc > 1 && argv[1][0] == '-') {
-     if(argv[1][1] == 'i') {
--      sprintf(file,&argv[2][0]);
-+      sprintf(file,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'g') {
-       GRID = atof(&argv[2][0]);
-     } else if(argv[1][1] == 's') {
-@@ -50,11 +50,11 @@ int main(int argc, char *argv[]) {
-     } else if(argv[1][1] == 't') {
-       trim_prb = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'e') {
--      sprintf(ezdfile,&argv[2][0]);
-+      sprintf(ezdfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'm') {
--      sprintf(mrcfile,&argv[2][0]);
-+      sprintf(mrcfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'o') {
--      sprintf(pdbfile,&argv[2][0]);
-+      sprintf(pdbfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'h') {
-       cerr << "./Tunnel.exe -i <file> -g <grid spacing> -p <tunnel probe radius>" << endl
-         << "\t-e <EZD outfile> -o <PDB outfile> -m <MRC outfile>" << endl
-diff --git a/vdw.cpp b/vdw.cpp
-index 4df73f5..0e26edc 100644
---- a/vdw.cpp
-+++ b/vdw.cpp
-@@ -32,13 +32,13 @@ int main(int argc, char *argv[]) {
- 
-   while(argc > 1 && argv[1][0] == '-') {
-     if(argv[1][1] == 'i') {
--      sprintf(file,&argv[2][0]);
-+      sprintf(file,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'o') {
--      sprintf(pdbfile,&argv[2][0]);
-+      sprintf(pdbfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'e') {
--      sprintf(ezdfile,&argv[2][0]);
-+      sprintf(ezdfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'm') {
--      sprintf(mrcfile,&argv[2][0]);
-+      sprintf(mrcfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'g') {
-       GRID = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'h') {
-diff --git a/volume.cpp b/volume.cpp
-index a2ca9ad..c304b94 100644
---- a/volume.cpp
-+++ b/volume.cpp
-@@ -32,15 +32,15 @@ int main(int argc, char *argv[]) {
- 
-   while(argc > 1 && argv[1][0] == '-') {
-     if(argv[1][1] == 'i') {
--      sprintf(file,&argv[2][0]);
-+      sprintf(file,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'p') {
-       PROBE = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'o') {
--      sprintf(pdbfile,&argv[2][0]);
-+      sprintf(pdbfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'e') {
--      sprintf(ezdfile,&argv[2][0]);
-+      sprintf(ezdfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'm') {
--      sprintf(mrcfile,&argv[2][0]);
-+      sprintf(mrcfile,"%s",&argv[2][0]);
-     } else if(argv[1][1] == 'g') {
-       GRID = atof(&argv[2][0]);
-     } else if(argv[1][1] == 'h') {
diff --git a/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch b/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch
deleted file mode 100644
index 556e928d5818..000000000000
--- a/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch
+++ /dev/null
@@ -1,107 +0,0 @@
-diff --git a/Makefile b/Makefile
-index a58462c..616f51a 100644
---- a/Makefile
-+++ b/Makefile
-@@ -1,7 +1,7 @@
--CC = g++
--EXT=$(shell ./cpuflags.pl --opt )
--FLAGS = -Wall $(EXT)
--#FLAGS = -O3 -Wall -ffast-math
-+CXX ?= g++
-+#EXT=$(shell ./cpuCXXFLAGS.pl --opt )
-+#CXXFLAGS = -Wall $(EXT)
-+#CXXFLAGS = -O3 -Wall -ffast-math
- OBJS = utils-main.o utils-output.o utils-mrc.o
- 
- all:	cav chan fsv sol tun vdw vol
-@@ -17,54 +17,65 @@ volume:	vol
- objects:	utils-main.o utils-output.o utils-mrc.o
- 
- cav:	objects cavities.cpp
--	$(CC) $(FLAGS) -o Cavities.exe $(OBJS) cavities.cpp
--	chmod 777 Cavities.exe
--	mv Cavities.exe ../bin
-+	$(CXX) $(CXXFLAGS) -c -o cavities.o cavities.cpp
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Cavities $(OBJS) cavities.o
-+	chmod 755 Cavities
-+	mv Cavities ../bin
- 
- chan:	objects channel.cpp
--	$(CC) $(FLAGS) -o Channel.exe $(OBJS) channel.cpp
--	chmod 777 Channel.exe
--	mv Channel.exe ../bin
-+	$(CXX) $(CXXFLAGS) -c -o channel.o channel.cpp
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Channel $(OBJS) channel.o
-+	chmod 755 Channel
-+	mv Channel ../bin
- 
- fsv:	objects fsv_calc.cpp
--	$(CC) $(FLAGS) -o FsvCalc.exe $(OBJS) fsv_calc.cpp
--	chmod 777 FsvCalc.exe
--	mv FsvCalc.exe ../bin
-+	$(CXX) $(CXXFLAGS) -c -o fsv_calc.o fsv_calc.cpp
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o FsvCalc $(OBJS) fsv_calc.o
-+	chmod 755 FsvCalc
-+	mv FsvCalc ../bin
- 
- sol:	objects solvent.cpp
--	$(CC) $(FLAGS) -o Solvent.exe $(OBJS) solvent.cpp
--	chmod 777 Solvent.exe
--	mv Solvent.exe ../bin
-+	$(CXX) $(CXXFLAGS) -c -o solvent.o solvent.cpp
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Solvent $(OBJS) solvent.o
-+	chmod 755 Solvent
-+	mv Solvent ../bin
- 
- tun:	objects tunnel.cpp
--	$(CC) $(FLAGS) -o Tunnel.exe $(OBJS) tunnel.cpp
--	chmod 777 Tunnel.exe
--	mv Tunnel.exe ../bin
-+	$(CXX) $(CXXFLAGS) -c -o tunnel.o tunnel.cpp
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Tunnel $(OBJS) tunnel.o
-+	chmod 755 Tunnel
-+	mv Tunnel ../bin
- 
- vdw:	objects vdw.cpp
--	$(CC) $(FLAGS) -o VDW.exe $(OBJS) vdw.cpp
--	chmod 777 VDW.exe
--	mv VDW.exe ../bin
-+	$(CXX) $(CXXFLAGS) -c -o vdw.o vdw.cpp
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o VDW $(OBJS) vdw.o
-+	chmod 755 VDW
-+	mv VDW ../bin
- 
- vol:	objects volume.cpp
--	$(CC) $(FLAGS) -o Volume.exe $(OBJS) volume.cpp
--	chmod 777 Volume.exe
--	mv Volume.exe ../bin
-+	$(CXX) $(CXXFLAGS) -c -o volume.o volume.cpp
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Volume $(OBJS) volume.o
-+	chmod 755 Volume
-+	mv Volume ../bin
- 
- utils-main.o:	utils-main.cpp
--	$(CC) $(FLAGS) -c -o utils-main.o utils-main.cpp
-+	$(CXX) $(CXXFLAGS) -c -o utils-main.o utils-main.cpp
- 
- utils-output.o:	utils-main.o utils-output.cpp
--	$(CC) $(FLAGS) -c -o utils-output.o utils-output.cpp
-+	$(CXX) $(CXXFLAGS) -c -o utils-output.o utils-output.cpp
- 
- utils-mrc.o:	utils-mrc.cpp
--	$(CC) $(FLAGS) -c -o utils-mrc.o utils-mrc.cpp
-+	$(CXX) $(CXXFLAGS) -c -o utils-mrc.o utils-mrc.cpp
-+
-+install:
-+	install -d $(DESTDIR)/usr/bin
-+	install ../bin/* $(DESTDIR)/usr/bin/
- 
- clean:
- 	rm -fv *.o  *~
- 
- distclean:
--	rm -fv *.o ../bin/*.exe *~
-+	rm -fv *.o ../bin/* *~
- 
- none:	
- 	echo "Please type make xxx, where xxx = cav, cha, fsv, sol, tun, vdw, or vol"
diff --git a/sci-chemistry/threeV/metadata.xml b/sci-chemistry/threeV/metadata.xml
deleted file mode 100644
index d4ff1000a775..000000000000
--- a/sci-chemistry/threeV/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/threeV/threeV-1.2-r2.ebuild b/sci-chemistry/threeV/threeV-1.2-r2.ebuild
deleted file mode 100644
index 084ddb5ad0ad..000000000000
--- a/sci-chemistry/threeV/threeV-1.2-r2.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit toolchain-funcs
-
-DESCRIPTION="3V: Voss Volume Voxelator"
-HOMEPAGE="http://geometry.molmovdb.org/3v/"
-SRC_URI="http://geometry.molmovdb.org/3v/3v-${PV}.tgz"
-S=${WORKDIR}/3v-${PV}/src
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-PDEPEND="sci-chemistry/msms-bin"
-#	sci-chemistry/usf-rave"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-gentoo.patch
-	"${FILESDIR}"/${P}-format-security.patch
-)
-
-DOCS=( ../AUTHORS ../ChangeLog ../QUICKSTART ../README ../TODO ../VERSION )
-
-src_prepare() {
-	default
-	tc-export CXX
-	emake distclean
-
-	export MAKEOPTS+=" V=1"
-}
diff --git a/sci-chemistry/tinker/Manifest b/sci-chemistry/tinker/Manifest
deleted file mode 100644
index 78b83206c8b5..000000000000
--- a/sci-chemistry/tinker/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST tinker-8.2.1.tar.gz 33015410 BLAKE2B 0b7c94662248761459cf9d681056f5cf9c4d669a790a522f23f800bf355235f6a9f392e008b13d14cf1e17d9725abb6512077c24ff7772108d69c9cf35b43e6e SHA512 5039078781d1ce226456882dd95ad15715f1e91829d26efcdb29ceedc213973883699eb6710b0a162a74208809305b7fee734b175139e6df63d0460fe5751ae7
diff --git a/sci-chemistry/tinker/files/8.2.1-openmp.patch b/sci-chemistry/tinker/files/8.2.1-openmp.patch
deleted file mode 100644
index 17199f9d4cfa..000000000000
--- a/sci-chemistry/tinker/files/8.2.1-openmp.patch
+++ /dev/null
@@ -1,18 +0,0 @@
- source/initial.f | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/source/initial.f b/source/initial.f
-index ff6ed54..9769a81 100644
---- a/initial.f
-+++ b/initial.f
-@@ -85,8 +85,8 @@ c
- c     Intel compiler extensions to OpenMP standard, 268435456 bytes is
- c     2**28 bytes, or 256 MB; comment these lines for other compilers
- c
--c!$   call kmp_set_stacksize_s (268435456)
--c!$   call kmp_set_blocktime (0)
-+!$   call kmp_set_stacksize_s (268435456)
-+!$   call kmp_set_blocktime (0)
- c
- c     values of machine precision constants
- c
diff --git a/sci-chemistry/tinker/metadata.xml b/sci-chemistry/tinker/metadata.xml
deleted file mode 100644
index 9bfb6f28bafc..000000000000
--- a/sci-chemistry/tinker/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">TinkerTools/tinker</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild b/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild
deleted file mode 100644
index feb65912d0bf..000000000000
--- a/sci-chemistry/tinker/tinker-8.2.1-r1.ebuild
+++ /dev/null
@@ -1,120 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit flag-o-matic fortran-2 java-pkg-2 toolchain-funcs
-
-DESCRIPTION="Molecular modeling package that includes force fields, such as AMBER and CHARMM"
-HOMEPAGE="https://dasher.wustl.edu/tinker/"
-SRC_URI="https://dasher.wustl.edu/${PN}/downloads/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="Tinker"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-RESTRICT="mirror"
-
-COMMON_DEPEND="
-	>=sci-libs/fftw-3.2.2-r1[fortran,threads]
-	dev-libs/maloc
-	!sys-apps/bar
-	!dev-util/diffuse
-"
-RDEPEND="${COMMON_DEPEND}
-	>=virtual/jre-1.8:*
-"
-DEPEND="
-	${COMMON_DEPEND}
-	>=virtual/jdk-1.8:*
-"
-BDEPEND="virtual/pkgconfig"
-
-S="${WORKDIR}"/${PN}/source
-
-pkg_pretend() {
-	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-}
-
-pkg_setup() {
-	[[ ${MERGE_TYPE} != binary ]] && tc-check-openmp
-
-	fortran-2_pkg_setup
-}
-
-src_prepare() {
-	sed 's:strip:true:g' -i ../make/Makefile || die
-	[[ $(tc-getFC) =~ "ifort" ]] && eapply "${FILESDIR}"/${PV}-openmp.patch
-	default
-	java-pkg-2_src_prepare
-}
-
-src_compile() {
-	# tests fail with weird results under LTO
-	# https://bugs.gentoo.org/878059
-	# https://github.com/TinkerTools/tinker/issues/159
-	filter-lto
-
-	local javalib= _omplib _fftwlib
-	for i in $(java-config -g LDPATH | sed 's|:| |g'); do
-		[[ -f ${i}/libjvm.so ]] && javalib=${i}
-	done
-
-	# use dummy routines in pmpb.f instead of apbs calls
-	rm pmpb.c || die
-
-	if [[ $(tc-getFC) =~ "gfortran" ]]; then
-		append-flags -fopenmp
-		_omplib="-lgomp"
-	else
-		append-flags -openmp
-		_omplib="-liomp5"
-	fi
-
-	_fftwlib="$($(tc-getPKG_CONFIG) --libs fftw3 fftw3_threads)"
-
-	emake \
-		-f ../make/Makefile \
-		F77="$(tc-getFC)" \
-		CC="$(tc-getCC) -c" \
-		F77FLAGS=-c \
-		OPTFLAGS="${FFLAGS}" \
-		LINKFLAGS="${LDFLAGS} -Wl,-rpath ${javalib}" \
-		INCLUDEDIR="$(java-pkg_get-jni-cflags) -I${EPREFIX}/usr/include" \
-		LIBS="-lmaloc -L${javalib} -ljvm ${_omplib} ${_fftwlib}" \
-		all
-
-	mkdir "${S}"/../bin || die
-
-	emake \
-		-f ../make/Makefile \
-		BINDIR="${S}"/../bin \
-		rename_bin
-}
-
-src_test() {
-	local test
-	cd "${WORKDIR}"/${PN}/test/
-	for test in *.run; do
-		einfo "Testing ${test} ..."
-		bash ${test} || die
-	done
-}
-
-src_install() {
-	dobin "${WORKDIR}"/${PN}/perl/mdavg "${WORKDIR}"/${PN}/bin/*
-
-	insinto /usr/share/${PN}/
-	doins -r "${WORKDIR}"/${PN}/params
-
-	dodoc \
-		"${WORKDIR}"/${PN}/doc/{*.txt,*.pdf,0README}
-
-	if use examples; then
-		insinto /usr/share/${P}
-		doins -r "${WORKDIR}"/${PN}/example
-
-		doins -r "${WORKDIR}"/${PN}/test
-	fi
-
-}
diff --git a/sci-chemistry/tm-align/Manifest b/sci-chemistry/tm-align/Manifest
deleted file mode 100644
index b5d84e11a3fd..000000000000
--- a/sci-chemistry/tm-align/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST TMtools20150914.tar.gz 982948 BLAKE2B 788f43040c1262c7e9eae2b47b0035d320a30fe7194e340d682b78e5961b82e46eef2b0a43d1ae458b9d5da6570f9c0ec0aca51b6ec3e25f0447fd43d629f592 SHA512 5fda29f6437ac9b0216a037496a01502de07e5a36736815833cb09217158a959370e750b75c55a54a49c733e4bd28be53b2dcbb25d71e2897273a4280ed3b530
diff --git a/sci-chemistry/tm-align/files/CMakeLists.txt b/sci-chemistry/tm-align/files/CMakeLists.txt
deleted file mode 100644
index 64507389838b..000000000000
--- a/sci-chemistry/tm-align/files/CMakeLists.txt
+++ /dev/null
@@ -1,9 +0,0 @@
-cmake_minimum_required (VERSION 3.28)
-project (TMTools Fortran)
-
-include(GNUInstallDirs)
-
-add_executable(TMalign TMalign.f)
-add_executable(TMscore TMscore.f)
-
-install (TARGETS TMalign TMscore DESTINATION ${CMAKE_INSTALL_BINDIR})
diff --git a/sci-chemistry/tm-align/metadata.xml b/sci-chemistry/tm-align/metadata.xml
deleted file mode 100644
index c3d1b975b668..000000000000
--- a/sci-chemistry/tm-align/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-  TM-align is a computer algorithm for protein structure alignment using dynamic
-  programming and TM-score rotation matrix. An optimal alignment between two
-  proteins, as well as the TM-score, will be reported for each comparison. The
-  value of TM-score lies in (0,1]. In general, a comparison of TM-score smaller
-  0.2 indicates that there is no similarity between two structures; a TM-score
-  greater 0.5 means the structures share the same fold.
-
-  What is the difference between TM-score and TM-align? The TM-score program
-  is to compare two models based on their given and known residue equivalency.
-  It is usually NOT applied to compare two proteins of different sequences. The
-  TM-align is a structural alignment program for comparing two proteins whose
-  sequences can be different. The TM-align will first find the best equivalent
-  residues of two proteins based on the structure similarity and then output a
-  TM-score. The TM-score values in both programs have the same definition.
-  </longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild b/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild
deleted file mode 100644
index 3c1703b2e69d..000000000000
--- a/sci-chemistry/tm-align/tm-align-20150914-r1.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit cmake flag-o-matic fortran-2
-
-DESCRIPTION="Quick & Accurate Structural Alignment"
-HOMEPAGE="https://zhanggroup.org/TM-align/"
-SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz"
-
-LICENSE="tm-align"
-SLOT="0"
-KEYWORDS="amd64 ~ppc ppc64 ~x86"
-IUSE="custom-cflags"
-
-BDEPEND=">=dev-build/cmake-3.28"
-
-src_unpack() {
-	# S=${WORKDIR} is deprecated in cmake eclass
-	mkdir "${P}" || die
-	pushd "${P}" || die
-		unpack ${A}
-	popd || die
-}
-
-src_prepare() {
-	cp "${FILESDIR}"/CMakeLists.txt . || die
-	cmake_src_prepare
-
-	# Recommended by upstream
-	use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math
-}
diff --git a/sci-chemistry/vesta-bin/Manifest b/sci-chemistry/vesta-bin/Manifest
deleted file mode 100644
index eddda12fca79..000000000000
--- a/sci-chemistry/vesta-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST VESTA-gtk3.tar.bz2 24963082 BLAKE2B e3f32358c841ba3dadcb95df68385ef7bd3d004abdd4aad67ad170b04c252318bf49c8bf52eed505277342df22d59d80a1e68440d248c52d08fb12c870c519a2 SHA512 d6ec6ed11a173b899b8d29da0b727f454272e5b3127544c1992a0a8a5a9d4318b0e021230beddd0b43b92cdd5a077a1394dc987dd9dae1b40f00e8ebddef9843
diff --git a/sci-chemistry/vesta-bin/files/VESTA.desktop b/sci-chemistry/vesta-bin/files/VESTA.desktop
deleted file mode 100644
index 8741428db052..000000000000
--- a/sci-chemistry/vesta-bin/files/VESTA.desktop
+++ /dev/null
@@ -1,8 +0,0 @@
-[Desktop Entry]
-Name=VESTA
-Type=Application
-Comment=For the visualisation of molecular and crystal structures.
-Exec=/opt/VESTA/VESTA
-TryExec=/opt/VESTA/VESTA
-Icon=/usr/share/icons/hicolor/128x128/apps/VESTA.png
-Categories=Science;
diff --git a/sci-chemistry/vesta-bin/metadata.xml b/sci-chemistry/vesta-bin/metadata.xml
deleted file mode 100644
index 50dcf2837ce6..000000000000
--- a/sci-chemistry/vesta-bin/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM 'https://www.gentoo.org/dtd/metadata.dtd'>
-<pkgmetadata>
-	<maintainer type="person">
-		<email>patrick.joseph.taylor@gmail.com</email>
-		<name>Patrick J Taylor</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/vesta-bin/vesta-bin-3.5.8.ebuild b/sci-chemistry/vesta-bin/vesta-bin-3.5.8.ebuild
deleted file mode 100644
index e52f9072f0ab..000000000000
--- a/sci-chemistry/vesta-bin/vesta-bin-3.5.8.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit desktop xdg
-
-DESCRIPTION="Visualisation for Electronic and STructural Analysis."
-
-HOMEPAGE="https://jp-minerals.org/vesta/en/"
-
-SRC_URI="https://jp-minerals.org/vesta/archives/${PV}/VESTA-gtk3.tar.bz2"
-
-S="${WORKDIR}/VESTA-gtk3"
-
-LICENSE="VESTA"
-
-SLOT="0"
-
-KEYWORDS="~amd64"
-
-# As of 3.5.6, wayland support required for gtk even when running on xorg.
-RDEPEND="x11-libs/gtk+:3[wayland]
-	x11-libs/gtk+:2
-	>=virtual/glu-9.0-r2
-	>=virtual/jdk-17"
-
-RESTRICT="strip"
-
-QA_PREBUILT="opt/VESTA/*"
-
-src_install() {
-	insinto /opt/VESTA
-	doins -r "${S}"/*
-	fperms +x /opt/VESTA/VESTA
-	fperms +x /opt/VESTA/VESTA-gui
-
-	domenu "${FILESDIR}"/VESTA.desktop
-	newicon -s 128x128 "${D}"/opt/VESTA/img/logo.png VESTA.png
-
-	dosym -r /opt/VESTA/libVESTA.so /usr/lib64/libVESTA.so
-}
diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
deleted file mode 100644
index a736ed9ed3ca..000000000000
--- a/sci-chemistry/vmd/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST vmd-1.9.4_alpha57-gentoo-patches.tar.xz 14612 BLAKE2B e50a2fc734038207174dd5cc525f01824ce324a65b8ce604f83862ce50be6b1950d199188a717e2368b2b050256a4705662009e3530d621b19c52bb109b6a844 SHA512 6283076e47dfcd780bbc94f9ca2b044a028a472c09d78616d373813d81ec764bf1697e56a8f487f9f0999cf409c0f141bf248156f60851073347d1b640a6953c
-DIST vmd-1.9.4a57.src.tar.gz 43155120 BLAKE2B de0da96f6681c24e7b1d38890f109088187198cbdddb3d86d783322e837b7a71224085699f3addf2833cf293ab2689f06ab47df284b8fbe080162740094ae844 SHA512 0a3726d8fa279ac62c368cd18724cd09535618454ff6e299d147291ef5d4198ad9d58a94f0b05699ec8a23128753c55e7397c95a5ce194e36d3fabef1bcf454c
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-fltk-null.patch b/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-fltk-null.patch
deleted file mode 100644
index 9207af9b2dee..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-fltk-null.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/SelectionBuilder.C	2022-04-27 15:21:15.000000000 +0900
-+++ b/src/SelectionBuilder.C	2025-03-20 15:02:33.086330280 +0900
-@@ -182,7 +182,7 @@
- 
-   int line = self->macrobrowser->value();
-   if (!line) {
--    self->macrooutput->value(NULL);
-+    self->macrooutput->value("");
-     return;
-   }
-   const char *name = self->macrobrowser->text(line);
diff --git a/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-py3.13.patch b/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-py3.13.patch
deleted file mode 100644
index 33f3f9ccb498..000000000000
--- a/sci-chemistry/vmd/files/vmd-1.9.4_alpha57-py3.13.patch
+++ /dev/null
@@ -1,25 +0,0 @@
---- a/src/PythonTextInterp.C.old	2025-05-06 14:01:49.042312947 +0200
-+++ b/src/PythonTextInterp.C	2025-05-06 14:13:55.323651236 +0200
-@@ -102,7 +102,7 @@
- 
-   for (int i=0; i<PyList_GET_SIZE(cblist); i++) {
-     PyObject *obj = PyList_GET_ITEM(cblist, i);
--    PyObject *result = PyEval_CallObject(obj, arglist);
-+    PyObject *result = PyObject_CallObject(obj, arglist);
-     if (result == NULL) {
-       PyErr_Print();
-       PySequence_DelItem(cblist, i);
-@@ -172,13 +172,6 @@
-   PyImport_AppendInittab("vmd", PyInit_vmd);
- #endif
- 
--  // Do emit DeprecationWarnings
--#if PY_MAJOR_VERSION >= 3
--  PySys_AddWarnOption(L"default");
--#else
--  PySys_AddWarnOption((char*) "default");
--#endif
--
- #if 0 && PY_MAJOR_VERSION >= 3
-   // Set program name used to find library path etc. Defaults to 'python',
-   // must occur before initialization.
diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
deleted file mode 100644
index 76e9449169aa..000000000000
--- a/sci-chemistry/vmd/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="person">
-    <email>alexxy@gentoo.org</email>
-    <name>Alexey Shvetsov</name>
-  </maintainer>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <use>
-    <flag name="gromacs">Add support for TNG file format</flag>
-    <flag name="msms">Add support for MSMS SES calcualtion tool</flag>
-    <flag name="povray">Add support for povray raytracer for HQ images</flag>
-    <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag>
-  </use>
-</pkgmetadata>
diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r4.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r4.ebuild
deleted file mode 100644
index 93fcae6969a5..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r4.ebuild
+++ /dev/null
@@ -1,278 +0,0 @@
-# Copyright 1999-2026 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-PYTHON_COMPAT=( python3_{13..14} )
-
-inherit cuda desktop prefix python-single-r1 toolchain-funcs xdg
-
-DESCRIPTION="Visual Molecular Dynamics"
-HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
-
-MY_PV="${PV/_alpha/a}"
-MY_P="${PN}-${MY_PV}"
-SRC_URI="
-	${MY_P}.src.tar.gz
-	fetch+https://dev.gentoo.org/~pacho/${PN}/${PN}-1.9.4_alpha57-gentoo-patches.tar.xz
-"
-S="${WORKDIR}/${MY_P}"
-LICENSE="vmd"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RESTRICT="fetch"
-
-CDEPEND="${PYTHON_DEPS}
-	$(python_gen_cond_dep '
-		>=dev-python/numpy-2[${PYTHON_USEDEP}]
-	')
-	>=dev-lang/tk-8.6.1:0=
-	dev-lang/perl
-	dev-libs/expat
-	sci-libs/netcdf:0=
-	virtual/opengl
-	x11-libs/fltk:1=
-	x11-libs/libXft
-	x11-libs/libXi
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] )
-	sqlite? ( dev-db/sqlite:3= )
-	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
-	xinerama? ( x11-libs/libXinerama )
-"
-DEPEND="${CDEPEND}"
-BDEPEND="
-	virtual/pkgconfig
-	dev-lang/swig
-"
-RDEPEND="${CDEPEND}
-	sci-biology/stride
-	sci-chemistry/chemical-mime-data
-	sci-chemistry/surf
-	x11-misc/xdg-utils
-	x11-terms/xterm
-	msms? ( sci-chemistry/msms-bin )
-	povray? ( media-gfx/povray )
-"
-VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
-
-# Binary only plugin
-QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so"
-QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil"
-QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil"
-
-pkg_nofetch() {
-	elog "Please download ${MY_P}.src.tar.gz from"
-	elog "${VMD_DOWNLOAD}"
-	elog "after agreeing to the license."
-	elog "Place it into your DISTDIR directory."
-}
-
-src_prepare() {
-	# Apply user patches from ${WORKDIR} to allow patching on patches
-	# subdir too
-	cd "${WORKDIR}"
-	default
-
-	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html
-	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html
-	eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-plugins.patch
-
-	use cuda && cuda_sanitize
-
-	# Prepare plugins
-	cd plugins || die
-
-	sed '/^.SILENT/d' -i $(find -name Makefile)
-
-	sed \
-		-e "s:CC = gcc:CC = $(tc-getCC):" \
-		-e "s:CXX = g++:CXX = $(tc-getCXX):" \
-		-e "s:COPTO =.*\":COPTO = -fPIC -o \":" \
-		-e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \
-		-e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \
-		-e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \
-		-e "s:SHLD = gcc:SHLD = $(tc-getCC):" \
-		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX):" \
-		-e "s:-ltcl8.5:-ltcl:" \
-		-i Make-arch || die "Failed to set up plugins Makefile"
-
-	sed \
-		-e '/^AR /s:=:?=:g' \
-		-e '/^RANLIB /s:=:?=:g' \
-		-i ../plugins/*/Makefile || die
-
-	tc-export AR RANLIB
-
-	sed \
-		-e "s:\$(CXXFLAGS)::g" \
-		-i hesstrans/Makefile || die
-
-	# hack for some very old code with recent compilers
-	# stamp uses old syntax so we need to add -std=gnu89
-	sed \
-		-e "s: -c: -std=gnu89 -c:g" \
-		-i stamp/Makefile \
-		-i rnaview/Makefile \
-		-i clustalw/Makefile || die
-
-	# prepare vmd itself
-	cd "${S}" || die
-
-	eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-paths.patch
-
-	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html
-	eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4-tmpdir.patch
-
-	# https://bugs.gentoo.org/947213
-	eapply "${FILESDIR}"/${P}-fltk-null.patch
-
-	# https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/34831.html
-	# https://bugs.gentoo.org/952657
-	eapply "${FILESDIR}"/${P}-py3.13.patch
-
-	# PREFIX
-	sed \
-		-e "s:/usr/include/:${EPREFIX}/usr/include:g" \
-		-i configure || die
-
-	sed \
-		-e "s:gentoo-bindir:${ED}/usr/bin:g" \
-		-e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \
-		-e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \
-		-e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-gcc:$(tc-getCC):g" \
-		-e "s:gentoo-g++:$(tc-getCXX):g" \
-		-e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \
-		-e "s:gentoo-cflags:${CFLAGS}:g" \
-		-e "s:gentoo-cxxflags:${CXXFLAGS}:g" \
-		-e "s:gentoo-nvflags::g" \
-		-e "s:gentoo-ldflags:${LDFLAGS}:g" \
-		-e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \
-		-e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \
-		-e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \
-		-e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \
-		-e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \
-		-e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \
-		-i configure || die
-
-	if use cuda; then
-		sed \
-			-e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \
-			-e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \
-			-i configure src/Makefile || die
-		sed \
-			-e '/compute_/d' \
-			-i configure || die
-		sed \
-			-e 's:-gencode .*code=sm_..::' \
-			-i src/Makefile || die
-	fi
-
-	sed \
-		-e "s:LINUXPPC:LINUX:g" \
-		-e "s:LINUXALPHA:LINUX:g" \
-		-e "s:LINUXAMD64:LINUX:g" \
-		-e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \
-		-e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \
-		-e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \
-		-i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script"
-
-	EMAKEOPTS=(
-		TCLINC="-I${EPREFIX}/usr/include"
-		TCLLIB="-L${EPREFIX}/usr/$(get_libdir)"
-		NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so"
-		NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include"
-		NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)"
-		NETCDFDYNAMIC=1
-		EXPATINC="-I${EPREFIX}/usr/include"
-		EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)"
-		EXPATDYNAMIC=1
-	)
-	if use gromacs; then
-		EMAKEOPTS+=(
-			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
-			TNGINC="-I${EPREFIX}/usr/include"
-			TNGDYNAMIC=1
-		)
-	fi
-	if use sqlite; then
-		EMAKEOPTS+=(
-			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
-			SQLITEINC="-I${EPREFIX}/usr/include"
-			SQLITEDYNAMIC=1
-		)
-	fi
-}
-
-src_configure() {
-	local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT"
-	rm -f configure.options && echo $myconf >> configure.options
-
-	use cuda && myconf+=" CUDA"
-#	use mpi && myconf+=" MPI"
-	use tachyon && myconf+=" LIBTACHYON"
-	use xinerama && myconf+=" XINERAMA"
-
-	export \
-		PYTHON_INCLUDE_DIR="$(python_get_includedir)" \
-		PYTHON_LIBRARY_DIR="$(python_get_library_path)" \
-		PYTHON_LIBRARY="$(python_get_LIBS)" \
-		NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/_core/include" \
-		NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/_core/include"
-
-	perl ./configure LINUX \
-		${myconf} || die
-}
-
-src_compile() {
-	# build plugins
-	cd "${WORKDIR}"/plugins || die
-
-	emake \
-		${EMAKEOPTS[@]} \
-		LINUX
-
-	# build vmd
-	cd "${S}"/src || die
-	emake
-}
-
-src_install() {
-	# install plugins
-	cd "${WORKDIR}"/plugins || die
-	emake \
-			PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \
-			distrib
-
-	# install vmd
-	cd "${S}"/src || die
-	emake install
-
-	# install docs
-	cd "${S}" || die
-	dodoc Announcement README doc/ig.pdf doc/ug.pdf
-
-	# remove some of the things we don't want and need in
-	# /usr/lib
-	cd "${ED}"/usr/$(get_libdir)/vmd || die
-	rm -fr doc README Announcement LICENSE || \
-		die "failed to clean up /usr/lib/vmd directory"
-
-	# adjust path in vmd wrapper
-	sed \
-		-e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \
-		-e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \
-		|| die "failed to set up vmd wrapper script"
-
-	# install icon and generate desktop entry
-	insinto /usr/share/pixmaps
-	doins "${WORKDIR}"/vmd-patches/vmd.png
-	eprefixify "${WORKDIR}"/vmd-patches/vmd.desktop
-	domenu "${WORKDIR}"/vmd-patches/vmd.desktop
-}
diff --git a/sci-chemistry/xcrysden/Manifest b/sci-chemistry/xcrysden/Manifest
deleted file mode 100644
index a5d3d65323b0..000000000000
--- a/sci-chemistry/xcrysden/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST xcrysden-1.6.2.tar.gz 2460277 BLAKE2B f0b7c2c5aeff51db97b29c8052273ed44bb9c183e0df62c406eee327c4c5d86d141d8adfd05df70b97661a8cbddbf052c233c288f1f30b308e4c877539c06a84 SHA512 9ed1b7fc11674509a3f2bf6604aa11e087fd77a971afb93039ca542cb9abb62b2553c7f386b845f004df5d3d340bdf1fe673552319788f006fd031efb6a4ad67
diff --git a/sci-chemistry/xcrysden/files/icons/xcrysden.png b/sci-chemistry/xcrysden/files/icons/xcrysden.png
deleted file mode 100644
index f41eddceb9ef..000000000000
--- a/sci-chemistry/xcrysden/files/icons/xcrysden.png
+++ /dev/null
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-LDFLAGS.patch b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-LDFLAGS.patch
deleted file mode 100644
index 1ae39ae5ecf7..000000000000
--- a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-LDFLAGS.patch
+++ /dev/null
@@ -1,171 +0,0 @@
-diff --git a/C/Makefile b/C/Makefile
-index 2aa0307..452e0f1 100644
---- a/C/Makefile
-+++ b/C/Makefile
-@@ -12,7 +12,7 @@ include make-objects
- 
- .SUFFIXES: .o .c
- .c.o:
--	$(CC) $(CFLAGS) $(CPPFLAGS) $(INCS) -c $<
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) $(INCS) -c $<
- 
- objects = $(XC_OBJS) $(EXTERNAL_OBJS)
- 
-@@ -24,18 +24,18 @@ compile:
- #objects: $(objects)
- #
- #$(objects): %.o: %.c
--#	$(CC) $(CFLAGS) $(CPPFLAGS) $(INCS) -c $<
-+#	$(CC) $(LDFLAGS) $(CFLAGS) $(CPPFLAGS) $(INCS) -c $<
- 
- xcrys: $(XC_OBJS) $(EXTERNAL_OBJS)
--	$(CC)  $(CFLAGS) $(XC_OBJS) $(EXTERNAL_OBJS) \
-+	$(CC) $(LDFLAGS)  $(CFLAGS) $(XC_OBJS) $(EXTERNAL_OBJS) \
- 	-o xcrys $(FFTW3_LIB) $(MESCHACH_LIB) $(TK_LIB) $(TCL_LIB) $(TOGL_LIB) $(GLU_LIB) $(GL_LIB) $(X_LIB) $(MATH) $(LDLIB) $(EXT_LIB)
- 
- xctclsh: xcTclsh.o
--	$(CC) $(CFLAGS) xcTclsh.o -o xctclsh $(TCL_LIB) $(MATH) $(LDLIB)
-+	$(CC) $(LDFLAGS) $(CFLAGS) xcTclsh.o -o xctclsh $(TCL_LIB) $(MATH) $(LDLIB)
- 
- XFS_OBJS = xsf2xsf.o
- xsf2xsf: $(XFS_OBJS) 
--	$(CC) $(CFLAGS) $(XFS_OBJS) -o xsf2xsf $(MATH) $(LDLIB)
-+	$(CC) $(LDFLAGS) $(CFLAGS) $(XFS_OBJS) -o xsf2xsf $(MATH) $(LDLIB)
- 
- 
- install:
-diff --git a/F/Makefile b/F/Makefile
-index 3f8270e..92f17d1 100644
---- a/F/Makefile
-+++ b/F/Makefile
-@@ -4,10 +4,10 @@ include ../Make.sys
- .SUFFIXES : .o .f .f90
- 
- .f90.o:
--	$(FC) $(FFLAGS) -c $<
-+	$(FC) $(LDFLAGS) $(FFLAGS) -c $<
- 
- .f.o:
--	$(FC) $(FFLAGS) -c $<
-+	$(FC) $(LDFLAGS) $(FFLAGS) -c $<
- 
- OBJ =   gengeom.o \
- 	multhexa.o \
-@@ -73,70 +73,70 @@ spaghetti:
- 	cd SRC_spaghetti; $(MAKE)
- 
- gengeom: $(OBJ)
--	$(FC) $(FFLAGS) -o gengeom $(OBJ)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o gengeom $(OBJ)
- 
- calplane: $(OBJ2)
--	$(FC) $(FFLAGS) -o calplane $(OBJ2)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o calplane $(OBJ2)
- 
- atomlab: $(OBJ3)
--	$(FC) $(FFLAGS) -o atomlab $(OBJ3)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o atomlab $(OBJ3)
- 
- recvec: recvec.o auxil.o
--	$(FC) $(FFLAGS) -o recvec recvec.o auxil.o 
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o recvec recvec.o auxil.o 
- 
- str2xcr: $(OBJ5)
--	$(FC) $(FFLAGS) -o str2xcr $(OBJ5)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o str2xcr $(OBJ5)
- 
- fracCoor: fracCoor.o auxil.o  readf1.o
--	$(FC) $(FFLAGS) -o fracCoor fracCoor.o auxil.o  readf1.o
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o fracCoor fracCoor.o auxil.o  readf1.o
- 
- multislab: $(OBJ6)
--	$(FC) $(FFLAGS) -o multislab $(OBJ6)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o multislab $(OBJ6)
- 
- savestruct: $(OBJ7)
--	$(FC) $(FFLAGS) -o savestruct $(OBJ7)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o savestruct $(OBJ7)
- 
- ftnunit: ftnunit.o
--	$(FC) $(FFLAGS) -o ftnunit ftnunit.o
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o ftnunit ftnunit.o
- 
- kPath: $(OBJ8)
--	$(FC) $(FFLAGS) -o kPath $(OBJ8)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o kPath $(OBJ8)
- 
- pwKPath: $(OBJ88)
--	$(FC) $(FFLAGS) -o pwKPath $(OBJ88)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o pwKPath $(OBJ88)
- 
- fhi_inpini2ftn34: fhi_inpini2ftn34.o
--	$(FC) $(FFLAGS) -o fhi_inpini2ftn34 fhi_inpini2ftn34.o
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o fhi_inpini2ftn34 fhi_inpini2ftn34.o
- 
- fhi_coord2xcr: fhi_coord2xcr.o
--	$(FC) $(FFLAGS) -o fhi_coord2xcr fhi_coord2xcr.o
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o fhi_coord2xcr fhi_coord2xcr.o
- 
- wn_readbands: $(OBJ9)
--	$(FC) $(FFLAGS) -o wn_readbands $(OBJ9)  $(OBJ10)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o wn_readbands $(OBJ9)  $(OBJ10)
- 
- wn_readbakgen: wn_readbakgen.o
--	$(FC) $(FFLAGS) -o wn_readbakgen wn_readbakgen.o
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o wn_readbakgen wn_readbakgen.o
- 
- pw: pwi2xsf pwi2xsf_old pwo_xsf2xsf
- 
- 
- pwi2xsf_old: $(OBJ11) 
--	$(FC) $(FFLAGS) -o pwi2xsf_old $(OBJ11)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o pwi2xsf_old $(OBJ11)
- 
- pwi2xsf: $(OBJ111)
--	$(FC) $(FFLAGS) -o pwi2xsf $(OBJ111)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o pwi2xsf $(OBJ111)
- 
- pwo_xsf2xsf: $(OBJ13)
--	$(FC) $(FFLAGS) -o pwo_xsf2xsf $(OBJ13)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o pwo_xsf2xsf $(OBJ13)
- 
- fsReadBXSF: $(OBJ12)
--	$(FC) $(FFLAGS) -o fsReadBXSF $(OBJ12)
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o fsReadBXSF $(OBJ12)
- 
- cube2xsf: cube2xsf.o
--	$(FC) $(FFLAGS) -o cube2xsf cube2xsf.o
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o cube2xsf cube2xsf.o
- 
- xsf2cube: xsf2cube.o
--	$(FC) $(FFLAGS) -o xsf2cube xsf2cube.o
-+	$(FC) $(LDFLAGS) $(FFLAGS) -o xsf2cube xsf2cube.o
- 
- PROGRAMS = \
- 	gengeom calplane atomlab recvec str2xcr fracCoor \
-diff --git a/F/SRC_nn/Makefile b/F/SRC_nn/Makefile
-index 2e44de1..06ae768 100644
---- a/F/SRC_nn/Makefile
-+++ b/F/SRC_nn/Makefile
-@@ -7,7 +7,7 @@ OBJ =   nn.o \
- all: nn install
- 
- nn:     $(OBJ)
--	$(FC) $(FFLAGS) $(OBJ) -o nn 
-+	$(FC) $(LDFLAGS) $(FFLAGS) $(OBJ) -o nn 
- 
- install:
- 	if test -f nn.exe ; then cp nn.exe ../../bin ; \
-diff --git a/Makefile b/Makefile
-index cfdc14a..f40c8c1 100644
---- a/Makefile
-+++ b/Makefile
-@@ -4,6 +4,8 @@
- #
- #------------------------------------------------------------------------
- 
-+export LDFLAGS
-+
- SHELL     = /bin/sh
- TOPDIR    = $(CURDIR)
- TCL_INDEX = $(TOPDIR)/util/tcl_index
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl-lib.patch b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl-lib.patch
deleted file mode 100644
index 533c506500da..000000000000
--- a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl-lib.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Ensures that Togl is linked properly.
-diff --git a/system/Make.sys-shared b/system/Make.sys-shared
-index 51891e7..ba478fa 100644
---- a/system/Make.sys-shared
-+++ b/system/Make.sys-shared
-@@ -48,7 +48,7 @@ X_INCDIR  =
- 
- TCL_LIB      = -ltcl$(TCL_VER2)
- TK_LIB       = -ltk$(TCL_VER2)
--TOGL_LIB     = -lTogl
-+TOGL_LIB     = -Wl,-rpath,"/usr/lib64/Togl2.0" -L/usr/lib64/Togl2.0 -lTogl2.0
- GLU_LIB      = -lGLU
- GL_LIB       = -lGL
- FFTW3_LIB    = -lfftw3
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-c23.patch b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-c23.patch
deleted file mode 100644
index 19924b4f09c8..000000000000
--- a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-c23.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-https://bugs.gentoo.org/945707
-Fix conflicting types for fabs.
---- a/C/xcBz.c
-+++ b/C/xcBz.c
-@@ -1397,7 +1397,6 @@ static int
- BzGetISS( int typ )
- {
-   int imen[3 * BZ_MAXPOINTS], imin = 0;
--  double fabs();
-   register int iss;
-   register double f, point;
-   register double tol = (double)(BZ_ISS - 1)/(double)BZ_ISS - (double)(BZ_ISS - 2)/(double)(BZ_ISS - 1);
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-ext-bwidget.patch b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-ext-bwidget.patch
deleted file mode 100644
index 0ca1f69b6005..000000000000
--- a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-ext-bwidget.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-Prevents bwidget from being automatically downloaded when it is already required as a build/run-time dependency.
-diff --git a/Makefile b/Makefile
-index cfdc14a..d0f7e6c 100644
---- a/Makefile
-+++ b/Makefile
-@@ -18,7 +18,7 @@ what:
- 
- all: tcl tk mesa togl fftw xcrysden
- #  meschach 
--xcrysden: usage bwidget bindir src-C src-F src-Tcl
-+xcrysden: usage bindir src-C src-F src-Tcl
- 
- usage: $(TOPDIR)/docs/xcrysden.1
- 	man $(TOPDIR)/docs/xcrysden.1 | awk 'BEGIN {lprint=0; print "## do not edit changes will be lost (file automatically generated)\n"; } /SYNOPSIS/ { lprint=1; } /SEE ALSO/ { lprint=0; } /a*/ { if (lprint) print; }' > usage
diff --git a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper-paths.patch b/sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper-paths.patch
deleted file mode 100644
index 8cc8b247a61c..000000000000
--- a/sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper-paths.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Ensures that wrapper scripts account for live filesystem merge.
-diff --git a/sys_utils/wrappers.sh b/sys_utils/wrappers.sh
-index 1fa3cc6..e078b22 100755
---- a/sys_utils/wrappers.sh
-+++ b/sys_utils/wrappers.sh
-@@ -5,8 +5,8 @@ do
- #!/bin/sh -f
- 
- # simple wrapper to run $cmd
--XCRYSDEN_TOPDIR="$prefix/share/$xcrysden"
--XCRYSDEN_LIB_BINDIR="$prefix/lib/$xcrysden"
-+XCRYSDEN_TOPDIR="/usr/share/$xcrysden"
-+XCRYSDEN_LIB_BINDIR="/usr/lib/$xcrysden"
- export XCRYSDEN_TOPDIR
- export XCRYSDEN_LIB_BINDIR
- 
diff --git a/sci-chemistry/xcrysden/files/xcrysden.desktop b/sci-chemistry/xcrysden/files/xcrysden.desktop
deleted file mode 100644
index 6880af1431e7..000000000000
--- a/sci-chemistry/xcrysden/files/xcrysden.desktop
+++ /dev/null
@@ -1,8 +0,0 @@
-[Desktop Entry]
-Name=XCrySDen
-Type=Application
-Comment=For the visualisation of molecular and crystal structures.
-Exec=xcrysden
-TryExec=xcrysden
-Icon=/usr/share/icons/hicolor/32x32/apps/xcrysden.png
-Categories=Science;
diff --git a/sci-chemistry/xcrysden/metadata.xml b/sci-chemistry/xcrysden/metadata.xml
deleted file mode 100644
index 50dcf2837ce6..000000000000
--- a/sci-chemistry/xcrysden/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM 'https://www.gentoo.org/dtd/metadata.dtd'>
-<pkgmetadata>
-	<maintainer type="person">
-		<email>patrick.joseph.taylor@gmail.com</email>
-		<name>Patrick J Taylor</name>
-	</maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/xcrysden/xcrysden-1.6.2-r2.ebuild b/sci-chemistry/xcrysden/xcrysden-1.6.2-r2.ebuild
deleted file mode 100644
index 8b5b27fb89a8..000000000000
--- a/sci-chemistry/xcrysden/xcrysden-1.6.2-r2.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-inherit desktop flag-o-matic toolchain-funcs xdg
-
-DESCRIPTION="For the visualisation of molecular and crystal structures."
-
-HOMEPAGE="http://www.xcrysden.org/"
-
-SRC_URI="http://www.xcrysden.org/download/${P}.tar.gz"
-
-LICENSE="GPL-2+"
-
-SLOT="0"
-
-KEYWORDS="~amd64"
-
-RDEPEND="
-	>=x11-base/xorg-server-21.1.4
-	>=virtual/glu-9.0-r2
-	>=dev-lang/tcl-8.6.12:=
-	>=dev-lang/tk-8.6.12:=
-	>=dev-tcltk/togl-2.0-r3
-	>=dev-tcltk/bwidget-1.9.14
-	media-libs/libglvnd[X]
-	sci-libs/fftw:3.0=
-	x11-libs/libX11
-"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}/${P}-ext-bwidget.patch"
-	"${FILESDIR}/${P}-LDFLAGS.patch"
-	"${FILESDIR}/${P}-Togl-lib.patch"
-	"${FILESDIR}/${P}-wrapper-paths.patch"
-	"${FILESDIR}/${P}-c23.patch"
-)
-
-src_prepare() {
-	default
-	cp "${S}/system/Make.sys-shared" "${S}/Make.sys" || die 'Copying Make.sys to build dir failed.'
-
-	# fix doc install path
-	sed -e "s|share/doc/\$(xcrysden)|share/doc/${PF}|" \
-		-e "/ln -sf .*doc/d" \
-		-e "/gzip/d" \
-		-i Makefile || die
-}
-
-src_compile() {
-	append-cflags "-fcommon"
-	emake xcrysden \
-		CC="$(tc-getBUILD_CC)" \
-		FC="$(tc-getFC)"
-}
-
-src_install() {
-	emake \
-		prefix="${ED}"/usr \
-		install
-
-	domenu "${FILESDIR}/${PN}.desktop"
-	doicon -s 32x32 "${FILESDIR}/icons/${PN}.png"
-	docompress -x /usr/share/doc/${PF}/examples
-}
diff --git a/sci-chemistry/xds-bin/Manifest b/sci-chemistry/xds-bin/Manifest
deleted file mode 100644
index 880c0c05bfa0..000000000000
--- a/sci-chemistry/xds-bin/Manifest
+++ /dev/null
@@ -1,2 +0,0 @@
-DIST XDS-INTEL64_Linux_x86_64-20240831.tar.gz 11067644 BLAKE2B d8687af54aad5694937cc633f511766147bb52616a388f03d0d052239a0f81b6e3692be0f234ea012905c89e13f2ef45e0254babe1e23598d954b2e65ed93d20 SHA512 773f074237311c8ea2d6dda974250cf906f84db02589bb40b646ff77afac2ee7d978d272993ab5f9b9f55c9dde7965b8e4fba7222349bf3665679f90ec6ef658
-DIST XDS_html_doc-20240831.tar.gz 151503 BLAKE2B c559d1a7b4ca75b00d5d37d2c9248fea177cca6a2dac5a9b42443430477337f8bc99add4f89f9eac2d57592b6b5843e167d4e86c6c3ce0ccbb5ba91234d534d8 SHA512 5d3a20dd0b6458c5bfd8ed46f4963fd53f59208fff72278acac19237c988537bae9d7b3c993342c8a9abc03e2ab5aed98a002caeb853fb87c19ae19a32f05faa
diff --git a/sci-chemistry/xds-bin/metadata.xml b/sci-chemistry/xds-bin/metadata.xml
deleted file mode 100644
index e490bcb8aa87..000000000000
--- a/sci-chemistry/xds-bin/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-chemistry/xds-bin/xds-bin-20240831.ebuild b/sci-chemistry/xds-bin/xds-bin-20240831.ebuild
deleted file mode 100644
index 4fcd833d3071..000000000000
--- a/sci-chemistry/xds-bin/xds-bin-20240831.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2024 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-DESCRIPTION="Software for processing single-crystal X-ray monochromatic diffraction data"
-HOMEPAGE="https://xds.mr.mpg.de"
-SRC_URI="
-	https://xds.mr.mpg.de/XDS-INTEL64_Linux_x86_64.tar.gz -> XDS-INTEL64_Linux_x86_64-${PVR}.tar.gz
-	https://xds.mr.mpg.de/XDS_html_doc.tar.gz -> XDS_html_doc-${PVR}.tar.gz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="-* ~amd64"
-IUSE="smp"
-RESTRICT="fetch"
-
-QA_PREBUILT="opt/xds-bin/*"
-
-# The web site uses a certificate that is not in the system certificate store.
-# Use a web browser to download, instead.
-pkg_nofetch() {
-	elog "Please visit"
-	elog "https://xds.mr.mpg.de/html_doc/downloading.html"
-	elog "and download XDS-INTEL64_Linux_x86_64.tar.gz and XDS_html_doc.tar.gz."
-	elog "Please save them as: ${A}. in your \${DISTDIR}"
-}
-
-src_unpack() {
-	default
-	mv XDS-* "${S}" || die
-}
-
-src_install() {
-	local HTML_DOCS=( "${WORKDIR}"/XDS_html_doc/. )
-	einstalldocs
-
-	local i suffix=$(usex smp '_par' '')
-	exeinto /opt/${PN}
-	doexe *
-
-	for i in xds mintegrate mcolspot xscale; do
-		dosym ../${PN}/${i}${suffix} /opt/bin/${i}
-	done
-
-	for i in 2cbf cellparm forkxds merge2cbf pix2lab xdsconv; do
-		dosym ../${PN}/${i} /opt/bin/${i}
-	done
-
-	insinto /usr/share/${PN}/INPUT_templates
-	doins -r "${WORKDIR}"/XDS_html_doc/html_doc/INPUT_templates/.
-}
-
-pkg_postinst() {
-	elog "This package will expire on August 31, 2024"
-}
author	root <root@alpha.trunkmasters.com>	2026-06-04 05:35:26 -0500
committer	root <root@alpha.trunkmasters.com>	2026-06-04 05:35:26 -0500
commit	f716a9fe6455d39eef01e718aae68dae61c19704 (patch)
tree	0c52bbae1c242fbc296bd650fcd1167685f81492 /sci-chemistry
parent	3f9cf298e89cd5037b982abba06091224ee76daf (diff)
download	baldeagleos-repo-f716a9fe6455d39eef01e718aae68dae61c19704.tar.gz baldeagleos-repo-f716a9fe6455d39eef01e718aae68dae61c19704.tar.xz baldeagleos-repo-f716a9fe6455d39eef01e718aae68dae61c19704.zip