Pdb2pqr

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)

Fixes
=====

* Fixed problems with documentation build (348)

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)

Fixes
===

* Fixes problems with XML parsing of large files (293)

Changes
=======

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

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](http://nglviewer.org/ngl/) (#38).
* Updated documentation to warn users against using more than one ligand in calculations (23).