Adding metadata

16 files changed, 604 insertions, 365 deletions

diff --git a/sci-chemistry/ParmEd/Manifest b/sci-chemistry/ParmEd/Manifest
index ec26f250d1a6..c2528ac7febf 100644
--- a/sci-chemistry/ParmEd/Manifest
+++ b/sci-chemistry/ParmEd/Manifest
@@ -1 +1,2 @@
 DIST ParmEd-4.3.0.tar.gz 70101920 BLAKE2B 66da35ece5f6c244b8205f3889bee3c86471b3d54814ba3dd6096ab5f057b1276d74b1fe4f37523a629ecb18412aafddc0ed13e68d24abe10dda40247d0b30e4 SHA512 44abe47e1a8c904d74c91fe5f1c30d52e8683f0bddc3abaaee51fa38075c1d6be7b5977bb72cb4f0d266aa157e39f6028e94d0240b8c63fa66f1a7ccd7c4b569
+DIST ParmEd-4.3.1.tar.gz 70098028 BLAKE2B 630879c9fc01b44c09b819b3132bf4091b2e506c6ef46d6037cf41f1956da2f63ebbdbec80f789a3e497fb047c56a832f4ca2adb649a4af7d0b57373543cca85 SHA512 5e6b6673533e61a65a26c4f1b305f0024f636b9cc77f9b4a0fc1395ffb23cf5f0d29b2d7f982322f28bf8348e569fd66181256cc30da0ab71a3b788aa8097ff7
diff --git a/sci-chemistry/ParmEd/ParmEd-4.3.1.ebuild b/sci-chemistry/ParmEd/ParmEd-4.3.1.ebuild
new file mode 100644
index 000000000000..2e55563e6acb
--- /dev/null
+++ b/sci-chemistry/ParmEd/ParmEd-4.3.1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 2022-2026 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="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 -> ${P}.tar.gz"
+
+LICENSE="LGPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+	# From Debian
+	"${FILESDIR}/${PN}-4.3.1-openmm-tests.patch"
+	"${FILESDIR}/${PN}-4.3.1-network-tests.patch"
+)
+
+distutils_enable_tests pytest
+
+python_test() {
+	# disable online tests and those needing rdkit
+	local -x CI=true
+	epytest -k 'not test_deserialize_integrator and not test_download and not test_optimized_reader and not test_delete_bond'
+}
diff --git a/sci-chemistry/ParmEd/files/ParmEd-4.3.1-network-tests.patch b/sci-chemistry/ParmEd/files/ParmEd-4.3.1-network-tests.patch
new file mode 100644
index 000000000000..684bf5f77a01
--- /dev/null
+++ b/sci-chemistry/ParmEd/files/ParmEd-4.3.1-network-tests.patch
@@ -0,0 +1,173 @@
+Description: Skip tests requiring network access.
+Author: Andrius Merkys <merkys@debian.org>
+Forwarded: not-needed
+--- a/test/test_parmed_formats.py
++++ b/test/test_parmed_formats.py
+@@ -2206,6 +2206,7 @@
+     def setUp(self):
+         self.url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/'
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_off(self):
+         """ Tests automatic loading of downloaded OFF files """
+         self.assertTrue(amber.AmberOFFLibrary.id_format(self.url + 'amino12.lib'))
+@@ -2214,24 +2215,28 @@
+         for key, item in off.items():
+             self.assertIsInstance(item, ResidueTemplate)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_amber_prmtop(self):
+         """ Tests automatic loading of downloaded AmberParm object """
+         self.assertTrue(amber.AmberFormat.id_format(self.url + 'tip4p.parm7'))
+         parm = amber.AmberFormat.parse(self.url + 'tip4p.parm7')
+         self.assertIsInstance(parm, amber.AmberParm)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_amoeba_prmtop(self):
+         """ Tests automatic loading of downloaded AmoebaParm object """
+         self.assertTrue(amber.AmberFormat.id_format(self.url + 'nma.parm7'))
+         parm = amber.AmberFormat.parse(self.url + 'nma.parm7')
+         self.assertIsInstance(parm, amber.AmoebaParm)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_chamber_prmtop(self):
+         """ Tests automatic loading of downloaded ChamberParm object """
+         self.assertTrue(amber.AmberFormat.id_format(self.url + 'ala_ala_ala.parm7'))
+         parm = amber.AmberFormat.parse(self.url + 'ala_ala_ala.parm7')
+         self.assertIsInstance(parm, amber.ChamberParm)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_raw_amber_format(self):
+         """ Tests automatic loading of downloaded AmberFormat object """
+         self.assertTrue(amber.AmberFormat.id_format(self.url + 'cSPCE.mdl'))
+@@ -2239,36 +2244,42 @@
+         self.assertIsInstance(parm, amber.AmberFormat)
+         self.assertNotIsInstance(parm, amber.AmberParm)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_amber_restart_ascii(self):
+         """ Tests automatic loading of downloaded Amber ASCII restart file """
+         self.assertTrue(amber.AmberAsciiRestart.id_format(self.url + 'trx.inpcrd'))
+         parm = amber.AmberAsciiRestart(self.url + 'trx.inpcrd')
+         self.assertIsInstance(parm, amber.AmberAsciiRestart)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_amber_traj_ascii(self):
+         """ Tests automatic loading of downloaded Amber mdcrd file """
+         self.assertTrue(amber.AmberMdcrd.id_format(self.url + 'tz2.truncoct.crd'))
+         crd = amber.AmberMdcrd(self.url + 'tz2.truncoct.crd', natom=5827, hasbox=True)
+         self.assertIsInstance(crd, amber.AmberMdcrd)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_charmm_psf(self):
+         """ Tests automatic loading of downloaded CHARMM PSF file """
+         self.assertTrue(formats.PSFFile.id_format(self.url + 'ala_ala_ala.psf'))
+         parm = formats.PSFFile.parse(self.url + 'ala_ala_ala.psf')
+         self.assertIsInstance(parm, charmm.CharmmPsfFile)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_charmm_crd(self):
+         """ Tests automatic loading of downloaded CHARMM crd file """
+         self.assertTrue(charmm.CharmmCrdFile.id_format(self.url + 'dhfr_min_charmm.crd'))
+         crd = charmm.CharmmCrdFile(self.url + 'dhfr_min_charmm.crd')
+         self.assertIsInstance(crd, charmm.CharmmCrdFile)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_charmm_restart(self):
+         """ Tests automatic loading of downloaded CHARMM restart file """
+         self.assertTrue(charmm.CharmmRstFile.id_format(self.url + 'sample-charmm.rst'))
+         crd = charmm.CharmmRstFile(self.url + 'sample-charmm.rst')
+         self.assertIsInstance(crd, charmm.CharmmRstFile)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_pdb(self):
+         """ Tests automatic loading of downloaded PDB files """
+         self.assertTrue(formats.PDBFile.id_format(self.url + '4lzt.pdb'))
+@@ -2276,6 +2287,7 @@
+         self.assertIsInstance(pdb, Structure)
+         self.assertEqual(len(pdb.atoms), 1164)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_cif(self):
+         """ Tests automatic loading of downloaded PDBx/mmCIF files """
+         self.assertTrue(formats.CIFFile.id_format(self.url + '4LZT.cif'))
+@@ -2283,6 +2295,7 @@
+         self.assertIsInstance(cif, Structure)
+         self.assertEqual(len(cif.atoms), 1164)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_mol2(self):
+         """ Tests automatic loading of downloaded mol2 and mol3 files """
+         self.assertTrue(formats.Mol2File.id_format(self.url + 'test_multi.mol2'))
+@@ -2292,6 +2305,7 @@
+         mol3 = formats.Mol2File.parse(self.url + 'tripos9.mol2')
+         self.assertIsInstance(mol3, ResidueTemplate)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     @unittest.skipUnless(HAS_GROMACS, "Cannot run GROMACS tests without GROMACS")
+     def test_download_gromacs_topology(self):
+         """ Tests automatic loading of downloaded Gromacs topology file """
+@@ -2299,12 +2313,14 @@
+         top = gromacs.GromacsTopologyFile(self.url + '1aki.charmm27.top')
+         self.assertIsInstance(top, gromacs.GromacsTopologyFile)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_gromacs_gro(self):
+         """ Tests automatic loading of downloaded Gromacs GRO file """
+         self.assertTrue(gromacs.GromacsGroFile.id_format(self.url + '1aki.ff99sbildn.gro'))
+         gro = gromacs.GromacsGroFile.parse(self.url + '1aki.ff99sbildn.gro')
+         self.assertIsInstance(gro, Structure)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_download_netcdf(self):
+         """ Tests that NetCDF files always fail when trying to download them """
+         self.assertFalse(amber.NetCDFRestart.id_format(self.url + 'ncinpcrd.rst7'))
+--- a/test/test_parmed_genopen.py
++++ b/test/test_parmed_genopen.py
+@@ -53,18 +53,21 @@
+         text = bz2.BZ2File(self.get_fn('test.bz2', written=True), 'r').read()
+         self.assertEqual(text.decode('ascii'), ALPHABET)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_read_normal_URL(self):
+         """ Tests genopen reading a remote file """
+         url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/tripos1.mol2'
+         with closing(genopen(url, 'r')) as f:
+             self.assertEqual(f.read(), open(get_fn('tripos1.mol2')).read())
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_read_bzipped_URL(self):
+         """ Tests genopen reading a bzipped remote file """
+         url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/4lzt.pdb.bz2'
+         with closing(genopen(url, 'r')) as f:
+             self.assertEqual(f.read(), genopen(get_fn('4lzt.pdb.bz2')).read())
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_read_gzipped_URL(self):
+         """ Tests genopen reading a gzipped remote file """
+         url = 'https://github.com/ParmEd/ParmEd/raw/master/test/files/4lzt.pdb.gz'
+@@ -105,12 +108,14 @@
+         text = bz2.BZ2File(self.get_fn('test.txt.bz2', written=True)).read()
+         self.assertEqual(text.decode('ascii'), ALPHABET*2)
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_append_remote_file(self):
+         """ Tests that genopen appending a remote file fails """
+         url = 'http://q4md-forcefieldtools.org/REDDB/projects/W-73/tripos1.mol2'
+         self.assertRaises(ValueError, lambda: genopen(url, 'a'))
+         self.assertRaises(ValueError, lambda: genopen(url, 'w'))
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_read_bad_URL(self):
+         """ Tests proper exception handling of non-existent URL """
+         self.assertRaises(IOError, lambda: genopen('http://asdkfjasdf.lib'))
+--- a/test/test_parmed_structure.py
++++ b/test/test_parmed_structure.py
+@@ -1384,6 +1384,7 @@
+         self.assertEqual(len(self.sys2.cmaps), len(x2.cmaps))
+         self.assertEqual(len(self.sys3.cmaps), len(x3.cmaps))
+ 
++    @unittest.skip("Not running tests requiring network access")
+     def test_save_psf2(self):
+         """ Test saving PSF file for unparametrized system """
+         url = 'http://ambermd.org/tutorials/advanced/tutorial1/files/polyAT.pdb'
diff --git a/sci-chemistry/ParmEd/files/ParmEd-4.3.1-openmm-tests.patch b/sci-chemistry/ParmEd/files/ParmEd-4.3.1-openmm-tests.patch
new file mode 100644
index 000000000000..a16e57f5b58c
--- /dev/null
+++ b/sci-chemistry/ParmEd/files/ParmEd-4.3.1-openmm-tests.patch
@@ -0,0 +1,108 @@
+Description: Skip tests which fail due to a compatibility issue with OpenMM 7.7.0.
+Bug: https://github.com/ParmEd/ParmEd/issues/1242
+Author: Andrius Merkys <merkys@debian.org>
+Forwarded: not-needed
+--- a/test/test_format_conversions.py
++++ b/test/test_format_conversions.py
+@@ -217,6 +217,7 @@
+         self.assertTrue(parm.has_NBFIX())
+         parm.createSystem()
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     @unittest.skipUnless(HAS_OPENMM, "Cannot test without OpenMM")
+     def test_energy_simple(self):
+         """ Check equal energies for Gromacs -> Amber conversion of Amber FF """
+@@ -237,6 +238,7 @@
+ 
+         self.check_energies(top, cong, parm, cona)
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     @unittest.skipUnless(HAS_OPENMM, "Cannot test without OpenMM")
+     def test_rb_torsion_conversion(self):
+         """ Check equal energies for Gromacs -> Amber conversion of Amber FF """
+@@ -263,6 +265,7 @@
+ 
+         self.check_energies(top, cong, parm, cona)
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     @unittest.skipUnless(HAS_OPENMM, "Cannot test without OpenMM")
+     def test_rb_torsion_conversion2(self):
+         """ Check equal energies for Gromacs -> Amber conversion of Amber FF """
+@@ -285,6 +288,7 @@
+ 
+         self.check_energies(top, cong, parm, cona)
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     @unittest.skipUnless(HAS_OPENMM, "Cannot test without OpenMM")
+     def test_rb_torsion_conversion3(self):
+         """ Check equal energies for Gromacs -> Amber conversion of Amber FF """
+@@ -307,6 +311,7 @@
+ 
+         self.check_energies(top, cong, parm, cona)
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     @unittest.skipUnless(HAS_OPENMM, "Cannot test without OpenMM")
+     def test_unconvertable_rb_torsion(self):
+         """ Check equal energies for Gromacs -> Amber conversion of Amber FF """
+--- a/test/test_openmm_amber_forces.py
++++ b/test/test_openmm_amber_forces.py
+@@ -33,6 +33,7 @@
+ @unittest.skipUnless(has_openmm, "Cannot test without OpenMM")
+ class TestAmberParm(TestCaseRelative, QuantityTestCase):
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     def test_gas_energy_conf_1(self):
+         """ Compare Amber and OpenMM gas phase energies and forces (topology 1) """
+         parm = AmberParm(
+@@ -73,6 +74,7 @@
+             for x1, x2 in zip(p, s):
+                 self.assertAlmostEqual(x1, x2, places=3)
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     def test_gas_energy_conf_2(self):
+         """ Compare Amber and OpenMM gas phase energies and forces (topology 2) """
+         parm = AmberParm(
+@@ -154,6 +156,7 @@
+                 self.assertAlmostEqual(x1, x2, places=3)
+ 
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     def test_gas_energy_conf_4(self):
+         """ Compare Amber and OpenMM gas phase energies and forces (topology 4) """
+         parm = AmberParm(get_fn('ethanol_T0.prmtop'), get_fn('ethanol_T0.rst7'))
+--- a/test/test_openmm_gromacs.py
++++ b/test/test_openmm_gromacs.py
+@@ -97,6 +97,7 @@
+         max_diff = get_max_diff(gmxfrc, ommfrc)
+         self.assertLess(max_diff, 0.05)
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     def test_small_peptide(self):
+         """ Test alanine dipeptide Gromacs system nrg and frc (no PBC) """
+         # Load the top and gro files
+@@ -123,6 +124,7 @@
+         max_diff = get_max_diff(gmxfrc, ommfrc)
+         self.assertLess(max_diff, 0.05)
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     def test_small_double_peptide(self):
+         """ Test interacting peptides Gromacs system nrg and frc (no PBC) """
+         # Load the top and gro files
+@@ -208,6 +210,7 @@
+         max_diff = get_max_diff(gmxfrc, ommfrc)
+         self.assertLess(max_diff, 5)
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     def test_pme_switch(self):
+         """ Tests the DHFR Gromacs system nrg and force (PME w/ switch) """
+         # Load the top and gro files
+--- a/test/test_openmm_reporters.py
++++ b/test/test_openmm_reporters.py
+@@ -246,6 +246,7 @@
+         rep.report(sim, frame=10)
+         rep.finalize()
+ 
++    @unittest.skip("See https://github.com/ParmEd/ParmEd/issues/1242")
+     @unittest.skipUnless(HAS_GROMACS, 'Cannot test without GROMACS')
+     def test_reporters_pbc(self):
+         """ Test NetCDF and ASCII restart and trajectory reporters (w/ PBC) """
diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest
index 6c773b88604d..4f4a3e63e643 100644
--- a/sci-chemistry/chemex/Manifest
+++ b/sci-chemistry/chemex/Manifest
@@ -1,2 +1,2 @@
-DIST chemex-2026.4.0.tar.gz 139333 BLAKE2B 7519aa31d34bef57abd928df751803222c92521b672451341daf0aefb0e28c55195ca640e7187c6cd4f66381eb7dda944a381b1efb6344a8fad7e852d0371dc9 SHA512 c9fa9d86128999823de3e9abb2dc0e518e7fceec0b30c361b96f7752dfcb7c8b18d8147ebf06e965c565faba384e07a9e92cb450120a7fa33689150233c3fc39
 DIST chemex-2026.5.0.tar.gz 139373 BLAKE2B 226e3e6119b7c81567ef949672371190b76e69d0551c75137cf95d0b16875f2dba83c3dd1be29def6fb9002d779422ef1f683603ef2eb1e398eb419edf508493 SHA512 831978bf149d841660e5ea98eab18a2d21b7969fbfc7f36cfcf74cada5d2fa19fdfc585d4aaffc85b3b0c1cb8124d327716ae23ffa63bf3ac485187fad5934ae
+DIST chemex-2026.6.0.tar.gz 155098 BLAKE2B 7930a4b59eea06d02059a09805c9812c3c04d1faecfb0718f866c0b79c53f7542988fa269908c7bf8ad81805265ac42012581e77442c49e832a9d7525abc58e5 SHA512 61d2a3ba9afd2a3e789a39057e49383147949bd538940d00bbe20367637ce8ddcaa15ab67b9c934a6e5ac59685106ed3238e5b7437a07167e1a95b2689d12307
diff --git a/sci-chemistry/chemex/chemex-2026.4.0.ebuild b/sci-chemistry/chemex/chemex-2026.6.0.ebuild
index ad9ff99811c4..ad9ff99811c4 100644
--- a/sci-chemistry/chemex/chemex-2026.4.0.ebuild
+++ b/sci-chemistry/chemex/chemex-2026.6.0.ebuild
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r11.ebuild
index 045af390992a..8864d50030f1 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r10.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r11.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2025 Gentoo Authors
+# Copyright 1999-2026 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -41,7 +41,7 @@ RDEPEND="
 	virtual/zlib:=
 	virtual/glu
 	x11-libs/libXpm
-	x11-libs/motif:0
+	x11-libs/motif:0=
 	x11-apps/xdpyinfo
 	media-fonts/font-adobe-100dpi
 "
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" "${PN}.png"
-
-	einstalldocs
-	dodoc HISTORY
-}
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 336f074b2917..ea27a18b1136 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1 +1,2 @@
 DIST openbabel-3.1.1_p20241221.tar.gz 36864825 BLAKE2B 55e6fbdd5c50a557c40fd5ffaca41753f73175b2b4eea22abe5c2b0031363e3c133acf9a8daf5b1cb362a3adb6398204497af036b9a7ba3630c1d8ccbce0f9d3 SHA512 44340c3d08b22783cf6a702c192480869b73fef21104641feaf5cbcd51f693fd17bb05ad31a3520f330aa57733d6f4be707b3c1243b3010d6ceccca8974e732f
+DIST openbabel-3.2.0.tar.gz 37815471 BLAKE2B b94e4de7a190c8e3b63adcb1f50ad114eb14c30809c2e85f297872b243c4fb6a6001b86d705dc5276d92b74a5122d31a04f26db48547d56e35a6bfacbefac6b1 SHA512 0def0b8c6185ec648c41b32c9c2963329f764b57105efe895fa435fd2ee4878b70141b0ac9e80dddbc82e2ca95281955f612a21ba0dd5c0e7ef715061acf8234
diff --git a/sci-chemistry/openbabel/files/openbabel-3.2.0-cflags.patch b/sci-chemistry/openbabel/files/openbabel-3.2.0-cflags.patch
new file mode 100644
index 000000000000..099a01525fdd
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.2.0-cflags.patch
@@ -0,0 +1,11 @@
+# respect userflags
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -427,7 +427,6 @@ endif()
+ #define various build types
+ if(CMAKE_COMPILER_IS_GNUCXX)
+   set (CMAKE_CXX_FLAGS_RELEASE        "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG")
+-  set (CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -O2 -g")
+   set (CMAKE_CXX_FLAGS_DEBUG          "${CMAKE_CXX_FLAGS_DEBUG} -D_GLIBCXX_DEBUG -g3 -fno-inline")
+ endif()
+ 
diff --git a/sci-chemistry/openbabel/files/openbabel-3.2.0-system_inchi.patch b/sci-chemistry/openbabel/files/openbabel-3.2.0-system_inchi.patch
new file mode 100644
index 000000000000..1a2cdbc4dcfa
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.2.0-system_inchi.patch
@@ -0,0 +1,93 @@
+See PR pending https://github.com/openbabel/openbabel/pull/2969.patch
+fix headers with system InChI / various changes to handle InChI option
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -144,6 +144,7 @@ option(OPENBABEL_USE_SYSTEM_INCHI
+   "Use the system inchi library." OFF)
+ if(OPENBABEL_USE_SYSTEM_INCHI)
+   find_package(Inchi REQUIRED)
++  add_definitions(-DHAVE_SYSTEM_INCHI)
+   if (NOT INCHI_FOUND)
+     message(FATAL_ERROR "Inchi library not found.")
+   endif()
+--- a/include/openbabel/inchiformat.h
++++ b/include/openbabel/inchiformat.h
+@@ -21,8 +21,13 @@ GNU General Public License for more details.
+ #include <openbabel/obconversion.h>
+ #include <openbabel/obmolecformat.h>
+ 
++#ifdef HAVE_SYSTEM_INCHI
++#include <inchi_api.h>
++#define CURRENT_VER "unknown" // bcf_s.h is not packaged
++#else
+ #include "../inchi/inchi_api.h"
+ #include "../inchi/bcf_s.h"  // for CURRENT_VER
++#endif
+ #ifdef HAVE_SSTREAM
+ #include <sstream>
+ #else
+
+--- a/include/CMakeLists.txt
++++ b/include/CMakeLists.txt
+@@ -5,9 +5,13 @@ file(GLOB stereo_headers      openbabel/stereo/*.h)
+ file(GLOB depict_headers      openbabel/depict/*.h)
+ file(GLOB lbfgs_headers       LBFGS/*.h)
+ 
++if(WITH_INCHI)
+ if(NOT OPENBABEL_USE_SYSTEM_INCHI)
+ install(FILES inchi/inchi_api.h          DESTINATION include/inchi)
+ endif(NOT OPENBABEL_USE_SYSTEM_INCHI)
++else(WITH_INCHI)
++list(FILTER openbabel_headers      EXCLUDE REGEX ".*inchiformat\\.h$")
++endif(WITH_INCHI)
+ install(FILES chemdrawcdx.h        DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
+ install(FILES ${openbabel_headers} DESTINATION ${OB_INCLUDE_DIRS}/openbabel)
+ install(FILES ${math_headers}      DESTINATION ${OB_INCLUDE_DIRS}/openbabel/math)
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -34,10 +34,15 @@ set(descriptors
+   descriptors/cmpdfilter.cpp
+   descriptors/groupcontrib.cpp
+   descriptors/filters.cpp
+-  descriptors/inchidescriptor.cpp
+   descriptors/smartsdescriptors.cpp
+ )
+ 
++if(WITH_INCHI)
++  set(descriptors ${descriptors}
++    descriptors/inchidescriptor.cpp
++  )
++endif()
++
+ set(fingerprints
+   fingerprints/finger2.cpp
+   fingerprints/finger3.cpp
+
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -142,15 +142,17 @@ endif()
+ option(WITH_INCHI   "Build inchi support" ON)
+ option(OPENBABEL_USE_SYSTEM_INCHI
+   "Use the system inchi library." OFF)
+-if(OPENBABEL_USE_SYSTEM_INCHI)
+-  find_package(Inchi REQUIRED)
+-  add_definitions(-DHAVE_SYSTEM_INCHI)
+-  if (NOT INCHI_FOUND)
+-    message(FATAL_ERROR "Inchi library not found.")
++if(WITH_INCHI)
++  if(OPENBABEL_USE_SYSTEM_INCHI)
++    find_package(Inchi REQUIRED)
++    add_definitions(-DHAVE_SYSTEM_INCHI)
++    if (NOT INCHI_FOUND)
++      message(FATAL_ERROR "Inchi library not found.")
++    endif()
++  else()
++    message(STATUS "Using included inchi library.")
++    set(INCHI_LIBRARY inchi)
+   endif()
+-else()
+-  message(STATUS "Using included inchi library.")
+-  set(INCHI_LIBRARY inchi)
+ endif()
+ 
+ if(WIN32)
diff --git a/sci-chemistry/openbabel/files/openbabel-python-3.2.cmake b/sci-chemistry/openbabel/files/openbabel-python-3.2.cmake
new file mode 100644
index 000000000000..5b1b275ec67c
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-python-3.2.cmake
@@ -0,0 +1,105 @@
+# The following is a cmake fragment taken from scripts/CMakeLists.txt and
+# and test/CMakeLists.txt edited for Gentoo python multibuild compatibility.
+# PYTHON_GENTOO_BINDINGS must be set instead of PYTHON_BINDINGS
+
+if (PYTHON_GENTOO_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
+			ketformat
+			cdjsonformat
+			pcjsonformat
+			#roundtrip #really long and heavy, could be >1500s
+			)
+		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 ${pybindtests})
+	endif (ENABLE_TESTS)
+endif(PYTHON_GENTOO_BINDINGS)
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild
deleted file mode 100644
index 1cc66e2c7a02..000000000000
--- a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221-r2.ebuild
+++ /dev/null
@@ -1,238 +0,0 @@
-# Copyright 1999-2025 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{13..14} )
-WX_GTK_VER=3.2-gtk3
-
-inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
-
-if [[ "${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-9999.ebuild b/sci-chemistry/openbabel/openbabel-3.2.0.ebuild
index 780e60991924..0df337b4de62 100644
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ b/sci-chemistry/openbabel/openbabel-3.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2025 Gentoo Authors
+# Copyright 1999-2026 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -16,9 +16,9 @@ if [[ "${PV}" == *9999* ]]; then
 	inherit git-r3
 	EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
 else
-	if [[ "${PV}" == *_p* ]]; then	# eg., openbabel-3.1.1_p20210325
+	if [[ "${PV}" == *_p* ]]; then
 		# Set to commit hash
-		OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
+		OPENBABEL_COMMIT=""
 		SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
 		S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
 	else
@@ -31,7 +31,7 @@ fi
 
 LICENSE="GPL-2"
 # See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/7.0.0"
+SLOT="0/8.0.0"
 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="
@@ -68,10 +68,12 @@ BDEPEND="
 "
 
 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
+	# fix headers for InChi
+	"${FILESDIR}"/${PN}-3.2.0-system_inchi.patch
+	# filter -O2
+	"${FILESDIR}"/${PN}-3.2.0-cflags.patch
 )
 
 pkg_pretend() {
@@ -86,7 +88,7 @@ gen_python_bindings() {
 	mkdir -p scripts/${EPYTHON} || die
 	# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
 	# each valid python implementation,
-	cat "${FILESDIR}"/${PN}-python-r2.cmake | \
+	cat "${FILESDIR}"/${PN}-python-3.2.cmake | \
 		sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
 			-e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
 			-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
@@ -134,7 +136,7 @@ src_configure() {
 		-DWITH_INCHI=$(usex inchi)
 		-DOPTIMIZE_NATIVE=OFF
 		-DPERL_BINDINGS=$(usex perl)
-		-DPYTHON_BINDINGS=$(usex python)
+		-DPYTHON_BINDINGS=OFF
 		-DRUN_SWIG=$(use_bindings)
 		-DWITH_COORDGEN=false
 		-DWITH_JSON=$(usex json)
@@ -150,12 +152,17 @@ src_configure() {
 		)
 	fi
 
+	if use python; then
+		mycmakeargs+=(
+			-DPYTHON_GENTOO_BINDINGS=ON
+		)
+	fi
+
 	if use test; then
-		# Help cmake find the python interpreter when dev-lang/python-exec is built
-		# without native-symlinks support.
+		# used for unittest
 		python_setup
 		mycmakeargs+=(
-			-DPYTHON_EXECUTABLE="${PYTHON}"
+			-DPython_EXECUTABLE="${PYTHON}"
 		)
 	fi
 
@@ -168,9 +175,9 @@ src_compile() {
 }
 
 src_test() {
-	local CMAKE_SKIP_TESTS=(
-		# https://github.com/openbabel/openbabel/issues/2766
-		test_align_{4,5}
+	local CMAKE_SKIP_TESTS=()
+	! use json && CMAKE_SKIP_TESTS+=(
+		test_ketformat*
 	)
 	! use wxwidgets && CMAKE_SKIP_TESTS+=(
 		test_tautomer_{22,27}
@@ -239,7 +246,7 @@ src_install() {
 	fi
 
 	if use wxwidgets; then
-		make_desktop_entry obgui "Open Babel" ${PN}
+		make_desktop_entry --eapi9 obgui -n "Open Babel" -i ${PN}
 		newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
 	fi
 }
diff --git a/sci-chemistry/propka/files/propka-3.5.1-python3.14.patch b/sci-chemistry/propka/files/propka-3.5.1-python3.14.patch
new file mode 100644
index 000000000000..383c20e039f3
--- /dev/null
+++ b/sci-chemistry/propka/files/propka-3.5.1-python3.14.patch
@@ -0,0 +1,15 @@
+Description: Fix FTBFS due to the change in annotation handling in Python 3.14.
+Author: Matthew Burn
+Forwarded: https://github.com/jensengroup/propka/pull/199
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1123164
+--- a/propka/parameters.py
++++ b/propka/parameters.py
+@@ -145,7 +145,7 @@
+         if len(words) == 0:
+             return
+         # parse the words
+-        typeannotation = self.__annotations__.get(words[0])
++        typeannotation = type(self).__annotations__.get(words[0])
+         if typeannotation is _T_NUMBER_DICTIONARY:
+             self.parse_to_number_dictionary(words)
+         elif typeannotation is _T_STRING_LIST:
diff --git a/sci-chemistry/propka/propka-3.5.1-r1.ebuild b/sci-chemistry/propka/propka-3.5.1-r1.ebuild
new file mode 100644
index 000000000000..5b6774b751df
--- /dev/null
+++ b/sci-chemistry/propka/propka-3.5.1-r1.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2026 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{13..14} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="pKa-value prediction of ionizable groups in protein and protein-ligand complexes"
+HOMEPAGE="https://github.com/jensengroup/propka"
+SRC_URI="https://github.com/jensengroup/propka/archive/refs/tags/v${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
+
+PATCHES=(
+	"${FILESDIR}/${PN}-3.5.1-python3.14.patch"
+)
+
+python_prepare_all() {
+	# Do not install the tests
+	sed -e "/exclude/s:scripts:\', \'tests:g" \
+		-i setup.py || die
+	distutils-r1_python_prepare_all
+}
+
+python_test() {
+	epytest -k 'not test_molecular_container'
+}