v3.6.2 (2023-12-31)

Changes

• Added warnings about ignored PROPKA options (#365)

Fixes

• Fixed problem locating files with editable installations (#6)
• Fixed broken links in documentation (#363)

Known issues

• There is a confirmed issue with naming using the CHARMM force field for uncommon protonation states (#358)
• There is a potential problem adding hydrogens to non-experimental computer-generated structures (#365)

v3.6.1 (2023-03-12)

Fixes

• Fixed problems with documentation build (#348)

v3.6.0 (2023-03-11)

Fixes

• Fix problems with protonated terminal residue naming (#301)
• Fix problem with terminal histidine protonation (#301)

Changes

• Rename pdb2pqr30 to pdb2pqr. The old pdb2pqr30 executable is still available but will be deprecated in a future release.
• Update Python version support for compatibility with PROPKA (#342); minimal supported Python is 3.8, highest tested is 3.11
• Eliminate need for extra temporary file (#315)
• Add support for cyclic peptides (#307)

v3.5.2 (2022-01-23)

Fixes

• Fixes problems with XML parsing of large files (#293)

3.5.1 (2022-01-17)

Changes

• Add support for integer-only residue names (#291).
• Remove temporary files created by PDB2PQR (#286).

v3.5.0 (2022-01-01)

Fixes

• Addressed problem where critical failures are missed in testing (#262). This doesn't represent a change to the (documented) API but will change functionality for external code that isn't ready to handle the raised error.
• Fixed calculation of non-integer charge (#264).
• Fixed problem with missing RNA phosphate oxygens (#267).
• Fixed problem with non-optimal hydrogen bond orientation for non-bonded atoms; mainly affects water orientation. (#9).

Changes

• Supressed excessive "Tetrahedral hydrogen reconstruction not available for nucleic acids" warnings (#253).
• Increased verbosity of output (warnings and information) for missing and reconstructed atoms.
• Standardized testing and output for troubleshooting with non-integer residue charges.
• Added HG1 as alternate name for serine hydroxyl hydrogen (#214).
• Removed non-functional command line version of psize (#181).
• Provided clearer error messages for unsupported MOL2 bond types (#178).
• Added --run-long option to tests and cleaned up test warning messages.
• Updated list of visualization tools to include NGL Viewer (#38).
• Updated documentation to warn users against using more than one ligand in calculations (#23).

v3.4.1 (2021-12-18)

Fixes

• Fix bug for incorrect assignment of ASN HD21 and HD22 (#242)

v3.4.0 (2021-12-11)

Fixes

• Fix bug for wrong pKas assigned to terminal residues (#245).

v3.3.3 (2021-11-24)

Fixes

• Fix bug for calculating grid lengths (#254)

v3.3.2 (2021-11-21)

Fixes

Fix bug for application of pKa predictions to proteins with more than 999 residues (#250)