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]

Added

  • LigNetwork: an interaction diagram with atomistic details for the ligand and residue-level details for the protein, fully interactive in a browser/notebook, inspired from LigPlot (PR #19)

  • fp.generate: a method to get the IFP between two prolif.Molecule objects (PR #19)

Changed

  • Default residue name and number: UNK and 0 are now the default values if None or '' is given

  • The Hydrophobic interaction now uses +0 (no charge) instead of !$([+{1-},-{1-}]) (not negatively or positively charged) for part of its SMARTS pattern (PR #19)

  • Moved the return_atoms parameter from the run methods to to_dataframe to avoid recalculating the IFP if one wants to display it with atomic details (PR #19)

  • Changed the values returned by fp.bitvector_atoms: the atom indices have been separated in two lists, one for the ligand and one for the protein (PR #19)

Deprecated

Removed

Fixed

  • Residues with a resnumber of 0 are not converted to None anymore (Issue #13)

[0.3.1] - 2021-02-02

Added

  • Integration with Zenodo to automatically generate a DOI for new releases

  • Citation page

  • Docking section in the Quickstart notebook (Issue #11)

  • PDBQT, MOL2 and SDF molecule suppliers to make it easier for users to use docking results as input (Issue #11)

  • Molecule.from_rdkit classmethod to easily prepare RDKit molecules for ProLIF

Changed

  • The visualisation notebook now displays the protein with py3Dmol. Some examples for creating and displaying a graph from the interaction dataframe have been added

  • Updated the installation instructions to show how to install a specific release

  • The previous repr method of ResidueId was easy to confuse with a string, especially when trying to access the Fingerprint.ifp results by string. The new repr method is now more explicit.

  • Added the Fingerprint.run_from_iterable method, which uses the new supplier functions to quickly generate a fingerprint.

  • Sorted the output of Fingerprint.list_available

Deprecated

Removed

Fixed

  • Fingerprint.to_dataframe is now much faster (Issue #7)

  • ResidueId.from_string method now supports 1-letter and 2-letter codes for RNA/DNA (Issue #8)

[0.3.0] - 2020-12-23

Added

  • Reading input directly from RDKit Mol as well as MDAnalysis AtomGroup objects

  • Proper documentation and tests

  • CI through GitHub Actions

  • Publishing to PyPI triggered by GitHub releases

Changed

  • All the API and the underlying code have been modified

  • Repository has been moved from GitHub user @cbouy to organisation @chemosim-lab

Deprecated

Removed

  • Custom MOL2 file reader

  • Command-line interface

Fixed

  • Interactions not detected properly

[0.2.1] - 2019-10-02

Base version for this changelog