v1.1.0 - 2022-11-18

[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.