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233 Open 708 Closed
233 Open 708 Closed
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Issues list

Topology.remove_isomoprhic_molecule helper method
#2053 opened May 10, 2025 by IAlibay
Topology.from_pdb can't handle NH4+
#2051 opened Apr 30, 2025 by j-wags
1
@j-wags
"No module named constraint"
#2050 opened Apr 29, 2025 by nickjbrowning
2
FileNotFoundError: '[...]/data/defaults.txt/constants.txt'
#2044 opened Apr 10, 2025 by j-wags
2
Topology.identical_molecule_groups is too slow polymer-performance Runtime of loading and/or parametrizing (bio)polymers
#2035 opened Mar 18, 2025 by mattwthompson
@j-wags
Molecule de-duplication lost in Topology roundtrips polymer-performance Runtime of loading and/or parametrizing (bio)polymers
#2034 opened Mar 18, 2025 by mattwthompson
@j-wags
Roundtrip through SDF fails for molecules with an achiral center that appears chiral
#2022 opened Feb 13, 2025 by Yoshanuikabundi
ForceField sources allows strings but description doesn't seem mention it. documentation
#2021 opened Feb 12, 2025 by IAlibay
2
Remove setup.cfg in favor of pyproject.toml
#2019 opened Feb 11, 2025 by j-wags
Mid-chain neutral Arginine is missing from the substructure library
#2011 opened Feb 6, 2025 by Yoshanuikabundi
Molecule.from_polymer_pdb throws warning and error when multiple polymers are present reliability
#2010 opened Feb 4, 2025 by mattwthompson
Sage monatomics issues in PDB loading
#2005 opened Jan 31, 2025 by Yoshanuikabundi
Various package build issues
#2003 opened Jan 25, 2025 by yurivict
Run-time requirements aren't declared
#2002 opened Jan 24, 2025 by yurivict
4
Improve performance of Topology.from_pdb with long chains
#1995 opened Jan 13, 2025 by mattwthompson
RDKitToolkitWrapper, using rdkit=2024.09.3, writes some charged atoms to MOL/SDF without explicit charge
#1988 opened Dec 16, 2024 by j-wags
Failing to assign AM1 charges with ambertools on macOS-13
#1947 opened Oct 21, 2024 by lilyminium
2
Optionally preserve ambertools temporary directory
#1931 opened Aug 30, 2024 by stgeo
5
Confusing HierarchyElement.__str__() reliability
#1924 opened Aug 5, 2024 by mattwthompson
Atom-level and residue-level metadata easily fall out of sync bug documentation pdb reading reliability
#1921 opened Aug 2, 2024 by mattwthompson
@j-wags
5
Partial charge methods fail in clean environment
#1911 opened Jul 26, 2024 by slochower
27
Improve citation guidelines documentation
#1905 opened Jul 10, 2024 by mattwthompson
Openeye license check
#1896 opened Jun 19, 2024 by insukjoung
@j-wags
6
OpenEye license check in OpenEyeToolkitWrapper
#1895 opened Jun 18, 2024 by isty2e
2
Generating conformers with some single ions in OpenEye results in additional ghost atoms
#1892 opened Jun 14, 2024 by lilyminium
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