ProLIF Versions Save

[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

Deprecated

Removed

• Custom MOL2 file reader
• Command-line interface

Fixed

• Interactions not detected properly