Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

v0.3.1 - 2024-07-18

Changed

• Migrate documentation to pydata-sphinx-theme.

• Make Hit.evalue and Hit.log_evalue release the GIL when possible.

Fixed

• Signatures of __init__ methods missing from all Cython types after the v3.0 update.

v0.3.0 - 2024-06-11

Added

• Slicing for Template, Molecule and Jess objects.

Fixed

• Typing for chain_id property of TemplateAtom.

• Query.__next__ ignores and raises a warning on NaN matrices caused by planar molecule coordinates.

Changed

• Make Jess generic over the internal template class to allow Template subclasses as inputs and Hit outputs attribute.

• Make Molecule.conserved return an instance of the caller class rather than a Molecule object.

v0.2.1 - 2024-05-30

Fixed

• Type hints for Molecule.load and Template.load not marked as accepting paths.

• Thread-unsafe use of qsort in Jess code, replaced with qsort_r or qsort_s to allow multithreading.

v0.2.0 - 2024-05-24

Added

• best_match argument to Jess.query to only return the best match to each template for a query molecule.

• id argument to Molecule.load and Molecule.loads to allow overriding the PDB ID stored in the file.

• ignore_endmdl argument to Molecule.load and Molecule.loads to control whether the parser should stop at the first model in a file.

Changed

• Make Molecule.load stop at the first model when parsing a PDB file.

Fixed

• Invalid pointer assignments in TessAtom.c causing compilation errors on stricter compilers.

v0.1.1 - 2024-04-18

Added

• Support for passing filenames to Template.load and Molecule.load directly.

• Default initialization of empty Jess objects from an empty iterable.

• Make Jess implement the Sized abstract base class interface.

Changed

• Skip displaying default attribute values in repr implementation of Atom and TemplateAtom.

• Make Jess.query optional parameters keyword-only.

v0.1.0 - 2024-04-18

Initial release.