https://github.com/althonos/pyjess - v0.5.2

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.

- Cython
Published by github-actions[bot] 9 months ago

https://github.com/althonos/pyjess - v0.5.1

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.

- Cython
Published by github-actions[bot] 10 months ago

https://github.com/althonos/pyjess - v0.5.0

Fixed

• Remove invalid platform key from pyproject.toml.

Changed

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

- Cython
Published by github-actions[bot] about 1 year ago

https://github.com/althonos/pyjess - v0.4.1

Fixed

• TemplateAtom.__hash__ implementation.

Changed

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

- Cython
Published by github-actions[bot] over 1 year ago

https://github.com/althonos/pyjess - v0.4.0

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.

- Cython
Published by github-actions[bot] over 1 year ago

https://github.com/althonos/pyjess - v0.3.3

Fixed

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

- Cython
Published by github-actions[bot] over 1 year ago

https://github.com/althonos/pyjess - v0.3.2

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.

- Cython
Published by github-actions[bot] over 1 year ago

https://github.com/althonos/pyjess - v0.3.1

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.

- Cython
Published by github-actions[bot] almost 2 years ago

https://github.com/althonos/pyjess - v0.3.0

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.

- Cython
Published by github-actions[bot] almost 2 years ago

https://github.com/althonos/pyjess - v0.2.1

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.

- Cython
Published by github-actions[bot] about 2 years ago

https://github.com/althonos/pyjess - v0.2.0

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.

- Cython
Published by github-actions[bot] about 2 years ago

https://github.com/althonos/pyjess - v0.1.1

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.

- Cython
Published by github-actions[bot] about 2 years ago

https://github.com/althonos/pyjess - v0.1.0

Initial release.

- Cython
Published by github-actions[bot] about 2 years ago