Skip to content

Latest commit

 

History

History
87 lines (79 loc) · 3.93 KB

CHANGELOG.md

File metadata and controls

87 lines (79 loc) · 3.93 KB

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.

[0.3.4] - 2021-09-28

Added

  • Added our J. Cheminformatics article to the citation page of the documentation and the CITATION.cff file.

Changed

  • Improved the documentation on how to properly restrict interactions to ignore the protein backbone (Issue #22), how to fix the empty dataframe issue when no bond information is present in the PDB file (Issue #15), how to save the LigNetwork diagram (Issue #21), and some clarifications on using fp.generate

Fixed

  • Mixing residue type with interaction type in the interactive legend of the LigNetwork would incorrectly display/hide some residues on the canvas (#PR 23)
  • MOL2 files starting with a comment (#) would lead to an error

[0.3.3] - 2021-06-11

Changed

  • Custom interactions must return three values: a boolean for the interaction, and the indices of residue atoms responsible for the interaction

Fixed

  • Custom interactions that only returned a single value instead of three would raise an uninformative error message

[0.3.2] - 2021-06-11

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)

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

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

Removed

  • Custom MOL2 file reader
  • Command-line interface

Fixed

  • Interactions not detected properly

[0.2.1] - 2019-10-02

Base version for this changelog