Changelog

Upcoming release (TBD)

Changes

• Removed the following unused command line options: -t, --thermophile, -a, --alignment, -m, --mutation, --mutator, --mutator-option

• Removed several unused API functions

Current

Fixes

• Address Sphinx search issue (#184)

3.5.1 (2023-12-31)

Changes

• Add more static typing and associated tests (#177 and #172)

• Refactor deprecated pkg_resources usage (#176)

• Increase number of valence electrons for ligand atoms (#169 and #170)

Fixes

• Fix topping up from all conformations, not just first (#167)

3.5.0 (2023-02-13)

Changes

• Remove support for Python 3.6 and 3.7; add support for up to Python 3.11 (#154 and #150)

• Add context manager for open_file_for_reading (#133)

Fixes

• Fix precision of MolecularContainer.get_pi() (#148)

• Rename vanadium from Va to V (#141)

• Fix rounding issues in folding profile reporting (#124)

• Fix malfunctioning -g -w command line options (#124)

v3.4.0 (2020-12-19)

Changes

• Removed PROPKA input support and argument --generate-propka-input (#99)

• Add Python 3.9 support to continuous integration. (#101)

• Removed logging abstraction from code to facilitate debugging and reduce code bloat. (#108)

Fixes

• Fixed bug that raised exception when missing amide nitrogen or oxygen. (#17)

• propka --version now shows the program version and exits. Previously this option took a version argument to specify the sub-version of propka. However, this was non-functional at least since 2012. (#89)

• Fix pI reporting in last line of .pka file. (https://github.com/jensengroup/propka/pull/91)

• Report correct version in .pka file header. (https://github.com/jensengroup/propka/pull/92)

• Fix handling of multi-model PDB without MODEL 1 entry. (https://github.com/jensengroup/propka/issues/96)

• Fixed bug and sped up algorithm for identifying bonds via bounding boxes. (#97, #110)

• Fixed bug in propka --display-coupled-residues that crashed the program. (#105)

v3.3.0 (2020-07-18)

Additions

• Add Sphinx documentation on readthedocs.io (#69, #76, #79)

Changes

• Updated read_molecule_file() to accept file-like objects. (#83)

• Use versioneer for version management. (#87)

• Add code coverage to continuous integration pipeline. (#62, #71, #76)

Fixes

• Bundle required JSON files with package. (#48)

• Fixed KeyError bug in read_parameter_file(). (#65)

• Update links to web server. (#80)

• Fixed PDB reading for PROPKA “single” runs. (#82)

v3.2.0 (2020-06-19)

Additions

• Significantly expanded testing framework. (#30, #36, #37)

Changes

• Improved ability to use PROPKA as a module in other Python scripts. (#8)

• Improved output via logging. (#11, #12)

• Replaced data/parameter pickle file with human-readable JSON. (#29)

• Significant delinting and formatting standardization against PEP8. (#33, #40)

• Improved package documentation. (#41, #61)

• Significant package refactoring. (#46, #47, #59)

• Simplify module import structure. (#49, #61)

• Improved tempfile handling. (#61)

v3.1.0

Archaeologists wanted to help us document the history of the code in versions 3.1.0 and earlier.