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.

[1.0.0] - 2022-06-07

Support for multiprocessing, enabled by default (Issue #46). The number of processes can be controlled through n_jobs in fp.run and fp.run_from_iterable.
New interaction: van der Waals contact, based on the sum of vdW radii of two atoms.
Saving/loading the fingerprint object as a pickle with fp.to_pickle and Fingerprint.from_pickle (Issue #40).

Molecule suppliers can now be indexed, reused and can return their length, instead of being single-use generators.

ProLIF can now be installed through pip and conda (Issue #6).
If no interaction is detected in the first frame, to_dataframe will not complain about a KeyError anymore (Issue #44).
When creating a plf.Fingerprint, unknown interactions will no longer fail silently.

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

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

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

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

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

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)

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)

Residues with a resnumber of 0 are not converted to None anymore (Issue #13)
Fingerprint instantiated with an unknown interaction name will now raise a NameError

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

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

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)

Base version for this changelog