2.0.0 - 2022.08.25

Added

• The functions duplicate_conformers, get_mcs, generate_conformers, constraintconf and constraintconf_cmd and the class ProteinLigandClashFilter. The code was borrowed from Pat Walters. It is used if constraint docking is needed.

• constraintconf can be called from the command line.

• moldrug.fitness.vinadock() a simple wrapper around vina. This function will be used for all the implemented cost functions inside of the module moldrug.fitness. It could be used for constraint docking.

• moldrug.data.constraintref. This module is used for testing in case constraint docking is needed. It has two MolBlock strings: r_6lu7 and r_x0161. That could be easily converted in RDKit molecules..

  from rdkit import Chem
  from moldrug.data import constraintref
  mol = Chem.MolFromMolBlock(constraintref.r_x0161)

  This molecule is needed for the keyword argument constraint_ref of the functions of the moldrug.fitness module in case of constraint docking is used.

• Constraint docking capability in all implemented cost functions of the module moldrug.fitness.

• moldrug.data.receptor_pdb. This module is similar to moldrug.data.receptor_pdbqt but in pdb format.

• Documentation and tutorials.

Changed

• moldrug.utils.make_sdf only will create the sdf file based on the pdbqt attribute. If pdbqt is a list, it will work as previous version works with pdbqts attribute.
• Name of the module moldrug.data.receptors to moldrug.data.receptor_pdbqt.
• Name of keyword argument receptor_path to receptor_pdbqt_path on the cost functions: moldrug.fitness.Cost and moldrug.fitness.CostOnlyVina.
• Name of keyword arguments receptor_path, vina_score_types, boxcenters and boxsizes to receptor_pdbqt_path, vina_score_type, boxcenter and boxsize respectively on the cost functions: moldrug.fitness.CostMultiReceptors and moldrug.fitness.CostMultiReceptorsOnlyVina.
• smiles attribute in moldrug.utils.Individual now it is always without explicit Hs, despite if the mol attribute has them.