ProLIF

Published November 17, 2022 | Version v1.1.0

Software Open

[1.1.0] - 2022-11-18 Added

Fingerprint.run now has a converter_kwargs parameter that can pass kwargs to the underlying RDKitConverter from MDAnalysis (Issue #57).
Formatting with black.

Changed

The SMARTS for the following groups have been updated to a more accurate definition (Issue #68, PR #73 by @DrrDom, and PR #84):
- Hydrophobic: excluded F, Cl, tetracoordinated C and S, C connected to N, O or F.
- HBond donor: exclude charged O, S and charged aromatic N, only accept nitrogen that is in valence 3 or ammonium
- HBond acceptor: exclude amides and some amines, exclude biaryl ethers and alkoxy oxygen from esters, include some aromatic oxygen and nitrogen,
- Anion: include resonance forms of carboxylic, sulfonic and phosphorus acids,
- Cation: include amidine and guanidine,
- Metal ligand: exclude amides and some amines.
The Pi stacking interactions have been changed for a more accurate implementation (PR #97, PR #98).
The Van der Waals contact has been added to the default interactions, and the tolerance parameter has been set to 0.
The pdbqt_supplier will not add explicit hydrogen atoms anymore, to avoid detecting hydrogen bonds with "random" hydrogens that weren't in the PDBQT file (PR #99).
When using the pdbqt_supplier, irrelevant warnings and logs have been disabled (PR #99).
Updated the minimal RDKit version to 2021.03.1

Fixed

Dead link in the quickstart notebook for the MDAnalysis quickstart (PR #75, @radifar).
The pdbqt_supplier now correctly preserves hydrogens from the input PDBQT file (PR #99).
If no interaction was detected, to_dataframe would error without giving a helpful message. It now returns a dataframe with the correct number of frames in the index and no column.

Notes

If you use this software, please cite the corresponding article (see preferred-citation).

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chemosim-lab/ProLIF-v1.1.0.zip md5:d0e27608fcbe31e90196e42f832e2e70	5.2 MB	Preview Download