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 twoprolif.Molecule
objects (PR #19)
Changed
Default residue name and number:
UNK
and0
are now the default values ifNone
or''
is givenThe 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 therun
methods toto_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 toNone
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 theFingerprint.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