moleculekit.smallmol.tools.restrainedembed module

moleculekit.smallmol.tools.restrainedembed.restrainedEmbed(mol, atomPos={}, restraintStrengths=(100, 25), forceField=<Boost.Python.function object>, numMinim=40, **kwargs)

Restrained embedding of a molecule

Generates an embedding of a molecule where part of the molecule is restrained to specific coordinates. It works in an iterative manner minimizing with different restraint strength in each iteration.

Parameters
  • mol (rdkit.Chem.Mol) – The molecule to embed. This function will modify the molecule in place.

  • atomPos (dict) – A dictionary with key the index of the atom as an integer and value a list of the three xyz coordinates where the atom should be restrained to. For the atoms for which no keys are in the dictionary, they will be left unrestrained.

  • restraintStrengths (list) – A list of restraints strengths which will be applied in order.

  • forceField (rdkit ForceField) – The rdkit forcefield to use for the minimization.

  • numMinim (int) – The number of minimizations to perform at each iteration.