v1.6

This release significantly boosts PDBCor's performance thanks to profiling and provides a "fast mode" for analysis of large datasets. Output files are assigned clearer names to allow saving results from angle-based analysis and a new option is now available to use only angle- or distance-based features for analysis. Additionally, a number of internal improvements and bug fixes are newly implemented.

Patches 1.6.0 - 1.6.5 are combined together here, as they were not released publicly and only differ by minor fixes/updates.

New features

• "Fast mode" via --fast CLI option
• More output (including more angle-based analysis results by default)
• Option --features FEATURES to analyse only angles or only distances

Improvements

• Boost to performance outside of "fast mode"
• Enable plotting angle clustering without needing to disable standard PDBCor analysis
• Clearer output filenames
• I/O-related functions/classes moved to own file io.py
• Updated dependencies (& fixed import for newer matplotlib version)
• Improved compatibility with Python 3.7-3.9
• Minor bug fixes (.ent files detected as PDB format, skipped residue numbers taken into account for output, crash prevented if no valid residues in chain (e.g. for protein-RNA complexes))

Full Changelog

v1.5.2...v1.6.5

v1.5

This release changes the featurization method used to transform protein angles before clustering. Important: this changes PDBCor's behaviour without raising a warning at runtime. Instead of "shifting" all angles to place the largest difference on the -180 - 180 degree gap, the angles are now transformed into a tuple of their sine & cosine values.

Patches 1.5.0 - 1.5.2 are combined together here, as they were not released publicly and only differ by minor fixes/updates.

Improvements

• Updated dependencies
• Fixed MyPy path
• Fixed missing types/type errors

Full Changelog

v1.4.2...v1.5.2

v1.4

This release adds functionality to plot the results of angle clustering over all protein residues. Patches 1.4.0 - 1.4.2 are combined together here, as they were not released publicly and only differ by minor fixes/updates.

Improvements

• Updated dependencies
• Updated IDE config files

Full Changelog

v1.3.1...v1.4.2

v1.3.1

This release provides new options and optimisations for easier user interaction on the commandline.

Important: The package's Python version is now set to 3.9 and above in pyproject.toml. Therefore, a corresponding environment is required for installation from the wheel package. However, the base functionality should also work for lower python versions - if this is needed, one can use the source code directly by cloning locally and running python -m pdbcor from the repository's parent directory.

New features

• Option to choose output directory name (both using CLI and class-based API)
• PyMOL script output alongside Chimera executable for visualisation
• "Rich" library included for easier output formatting
• "Quiet mode" added, e.g. for batch scripts

Improvements

• State assignments added to results.json
• Abbreviated options added for most common CLI options
• Additional minor CLI changes

Previous releases

Previous releases were only packaged locally. Here is a short summary of each minor version's main changes:

v1.1

This release implements a Poetry script for direct CLI access via pdbcor <BUNDLE>. Additionally, PDBCor now supports the PDBx/mmCIF file format, and a few further optimisations have been made.

• Direct CLI entry point as Poetry script
• Implementation of PDBx/mmCIF format parser
• Restructured codebase for easier packaging
• Updated README.md

v1.2

This release contains structural changes in the codebase, as well as the addition of features to make future development easier.

• Ruff and MyPy added for development
• Docstrings added to all functions/classes
• Restructured codebase (separation into different files)
• Code reformatted, changes to class/function names
• Minor changes to list/loop implementations
• Updated dependencies

Full changelog

v1.0.0-post...v1.3.1

v1.0.0 (packaged)

This release contains the original implementation of PDBCor, reorganized for packaging with Poetry.

Due to missing metadata, the package is marked as a pre-release - please see later releases for further information and licensing details.

Changes during packaging: https://github.com/hfswetton/PDBCor/commits/v1.0.0-post

v1.0.0-pre

PDBCor prior to Poetry packaging.

Used to generate a tag for easy comparison to newer versions.