Issues

• Custom ResidueDefinition fails to match when crosslink atom has same name as linking bond atom

  openforcefield/openff-pablo#158 · Filter by author chapincavender opened on Oct 23, 2026
  1

  

• NH2 cap missing from STD_CCD_CACHE

  openforcefield/openff-pablo#156 · Filter by author chapincavender opened on Oct 9, 2026
  1

  

• Infer elements from atom names when element column is missing

  openforcefield/openff-pablo#149 · Filter by author Yoshanuikabundi opened on Feb 3, 2026

• Infer bonds from distances

  openforcefield/openff-pablo#148 · Filter by author Yoshanuikabundi opened on Feb 3, 2026

• Could disulfide bonds be inferred automatically?

  openforcefield/openff-pablo#146 · Filter by author jgreener64 opened on Feb 2, 2026
  2

  

• Fix 8ovp.pdb test

  bug
  openforcefield/openff-pablo#143 · Filter by author Yoshanuikabundi opened on Jan 16, 2026

• Support PDB files that are out-of-order

  feature
  openforcefield/openff-pablo#142 · Filter by author Yoshanuikabundi opened on Jan 16, 2026
  1

• Confusing error message about turning on CCD download

  openforcefield/openff-pablo#140 · Filter by author mattwthompson opened on Dec 16, 2025
  

• Document how to point to a local copy of components.cif

  feature
  openforcefield/openff-pablo#136 · Filter by author j-wags opened on Dec 1, 2025
  

• Refactor matching code

  openforcefield/openff-pablo#132 · Filter by author j-wags opened on Nov 6, 2025
  1

• Allow an arbitrary number of crosslinks/linking bonds

  featureneeds design
  openforcefield/openff-pablo#130 · Filter by author j-wags opened on Nov 3, 2025

• Pablo stage 3

  openforcefield/openff-pablo#128 · Filter by author j-wags opened on Oct 29, 2025

• rdkit.Chem.GetMolFrags(mol, asMols=True) is very slow for large systems

  openforcefield/openff-pablo#127 · Filter by author j-wags opened on Oct 15, 2025
  

• Investigate mmCIF files produced by OpenFold3

  openforcefield/openff-pablo#120 · Filter by author Yoshanuikabundi opened on Sep 18, 2025
  

• Improve residue match error messages

  openforcefield/openff-pablo#109 · Filter by author Yoshanuikabundi opened on Jul 31, 2025
  

• Recognize monoatomic ions when given element info but incorrect residue name

  openforcefield/openff-pablo#105 · Filter by author j-wags opened on Jul 23, 2025
  1

  

• CcdCache simplifications and refactor

  needs design
  openforcefield/openff-pablo#101 · Filter by author Yoshanuikabundi opened on Jun 26, 2025
  1

• Implement PDBx/mmCIF loading

  openforcefield/openff-pablo#91 · Filter by author j-wags opened on Jun 1, 2025

• Pablo stage 2

  openforcefield/openff-pablo#89 · Filter by author j-wags opened on Jun 1, 2025

• Make PTM test set

  openforcefield/openff-pablo#87 · Filter by author j-wags opened on Jun 1, 2025

• Consider interaction with Self Contained Sequence Representation (SCSR)

  openforcefield/openff-pablo#83 · Filter by author j-wags opened on Apr 10, 2025

• Disambiguate multiple matches with connectivity and formal charge

  feature
  openforcefield/openff-pablo#67 · Filter by author Yoshanuikabundi opened on Feb 18, 2025
  1

  

• Support resonance forms of residue definitions

  featureneeds design
  openforcefield/openff-pablo#62 · Filter by author Yoshanuikabundi opened on Feb 12, 2025
  1

  

• Add test of protein with disulfide bonds specified by SSBOND

  tests
  openforcefield/openff-pablo#50 · Filter by author j-wags opened on Jan 29, 2025
  

• Add tests of PDB files from common software packages

  tests
  openforcefield/openff-pablo#47 · Filter by author Yoshanuikabundi opened on Jan 29, 2025