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Issues list

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.
#2021 opened Feb 12, 2025 by IAlibay
2
Charge assignment with ambertools failing on ubuntu with python 3.10 in examples CI
#2020 opened Feb 11, 2025 by j-wags
Remove setup.cfg in favor of pyproject.toml
#2019 opened Feb 11, 2025 by j-wags
Molecule.__repr__ effectively hangs for large molecules reliability
#2013 opened Feb 6, 2025 by mattwthompson
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
Topology.identical_molecule_groups scales poorly with many large molecules protein-performance Possibly related to speed of loading or parametrizing proteins
#2008 opened Feb 3, 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
Cannot create InChi of large molecule bug
#1977 opened Dec 9, 2024 by mattwthompson
Combine force fields in-memory reliability
#1948 opened Oct 21, 2024 by mattwthompson
1
@j-wags
3
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
5
Partial charge methods fail in clean environment
#1911 opened Jul 26, 2024 by slochower
24
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
how to describe a terminal atom type with openff
#1876 opened May 23, 2024 by Lili-Cao
7
ProTip! Updated in the last three days: updated:>2025-02-12.