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.
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.