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#

v0.10.0 - 2026-04-14#

Added#

  • Geometric transformation methods to Atom, Molecule, TemplateAtom and Template.

  • Mat4 class to store a transformation matrix in homogeneous coordinates.

Changed#

  • Bump minimum supported Limited API to Python 3.11 to use typed memoryviews.

Fixed#

  • Line tracing being enabled by default in Cython extensions.

v0.9.1 - 2025-12-22#

Added#

  • Documentation page with a command line interface reference.

Fixed#

  • Correct error type when calling Hit.dump with a Molecule where id is None (#9, by @RayHackett).

  • Broken AUR PKGBUILD not working with Limited API wheels.

v0.9.0 - 2025-11-26#

Added#

  • Molecule.name and Molecule.date properties exposing the metadata usually found in a PDB HEADER line.

  • dump and dumps methods to Atom and Molecule (#8, by @RayHackett).

Changed#

  • breaking: Turn Hit.template into a function to support transforming template atoms into query reference frame (#7, by @RayHackett).

  • Make Hit.dump write the element column (by @RayHackett).

  • Move I/O logic and auxilliary classes to a dedicated pyjess._io module.

Fixed#

  • Incorrect formatting of chain_id written from an Atom instantiated with the API (by @RayHackett).

v0.8.0 - 2025-11-12#

Added#

  • Testing for Python 3.14.

  • ignore_endmdl parameter value in mmCIF parser to ignore models past the first one.

  • dump and dumps methods to Template and TemplateAtom (#5).

Fixed#

  • Parsing issues with CIF files (by @RayHackett).

  • Incorrect example use of the pyjess.API in README.md (#6).

  • Broken format detection for PDB or mmCIF files starting with comment lines (and fix handling of non-seekable files).

v0.7.0 - 2025-09-13#

Added#

  • Command Line Interface with the same features as the Jess CLI.

  • Molecule.from_biopython, Molecule.from_biotite and Molecule.from_gemmi to create a Molecule with objects from other libraries.

  • Hit.dump and Hit.dumps methods to write a hit to PDB format.

  • Molecule.load option to skip parsing of HETATM from PDB files.

  • Support for Selenocysteine and Pyrrolysine residues in TemplateAtom.

  • Support for parsing Molecule objects from CIF files using gemmi.

Fixed#

  • breaking: Incorrect handling of max_candidates in Jess.query, causing PyJess to erroneously ignore some templates.

  • Template.dimension reporting incorrect numbers for identical residues across different residues.

  • Issue with alignment of atom names in TemplateAtom.

  • Validate data in PDB parser to ensure it is not parsing a mmCIF file.

  • Parsing of mmCIF files with atoms missing occupancy values.

  • Incorrect alignment of TemplateAtom names for names of less than 4 characters.

  • max_candidates causing Query to stop before reaching the actual number of maximum candidates.

Changed#

  • breaking: Set the max_candidates default value to None in Jess.query, disabling max candidates filtering by default.

  • breaking: Use string variants instead of bool to control the behaviour of ignore_chain argument.

  • breaking: Make id and ignore_endmdl arguments of Molecule.load and Molecule.loads keyword-only.

  • Use unrolled string comparison to compare atom names instead of strcasecmp in Jess code.

  • Make altloc and insertion_code arguments of Atom optional.

  • Setup deployment of Limited API wheels for CPython 3.8 onwards.

  • Implement format detection between PDB and mmCIF in Molecule.load.

  • Implement Template.copy and TemplateAtom.copy using C-level API rather than Python copy.

v0.6.0 - 2025-09-01#

Added#

  • Several algorithmic optimizations to Jess, greatly improving runtime:

    • Use QuickSelect ($O(n)$) instead of QuickSort ($O(nlog(n))$) to select the medians used for space partitioning on k-d tree initialization.

    • Use approximate intersection on bounding boxes rather than exact code involving multiple annuli when querying the k-d tree for atoms.

    • breaking: Reorder the matching order of template atoms to reduce the amount of backtracking and k-d tree querying performed in the average and worst case.

  • reorder argument to Jess.query to support disabling template atom reordering if needed for Jess 1-to-1 consistency.

Changed#

  • Hardcode space dimensions to 3 to encourage compilers to unroll loops over dimensions.

  • Recycle memory between templates within a query to reduce total amount of allocation/deallocation in hot paths.

v0.5.2 - 2025-08-26#

Added#

  • pickle protocol support to Hit objects.

Fixed#

  • Improve performance of residue index using binary search on name queries.

  • Avoid copying atoms in Hit.atoms if no transformation is required.

v0.5.1 - 2025-08-20#

Fixed#

  • Typo in Hit.molecule returning incorrect coordinates when transformation is required.

Changed#

  • Implement an index to quickly access atoms by residue names in a Molecule, and accelerate initial candidate set creation for compatible match modes.

v0.5.0 - 2025-04-09#

Fixed#

  • Remove invalid platform key from pyproject.toml.

Changed#

  • Hit.molecule is now a method and can optionally rotate the hit molecule.

v0.4.1 - 2024-11-29#

Fixed#

  • TemplateAtom.__hash__ implementation.

Changed#

  • TemplateAtom.residue_names and TemplateAtom.atom_names are now tuples.

v0.4.0 - 2024-11-29#

Added#

  • __eq__, __hash__, __copy__, and __reduce__ to Molecule, Atom, Template, TemplateAtom and Jess.

Changed#

  • Move project development stage from Alpha to Beta.

  • List conda support in the Install page of the documentation.

v0.3.3 - 2024-11-05#

Fixed#

  • Tests crashing on missing importlib.resources.files function.

v0.3.2 - 2024-11-05#

Added#

  • Support for Python 3.13.

Changed#

  • Use scikit-build-core to build the project.

  • Use CMake to detect availability of qsort_r / qsort_s on the current platform.

  • Use thread-local storage to support parallelism on platforms without qsort_r.

Removed#

  • Support for Python 3.6.

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.