rdkit.Chem.rdMolAlign module

Module containing functions to align a molecule to a second molecule

class rdkit.Chem.rdMolAlign.BestAlignmentParams(self)

Bases: object

Parameters controlling RMSD alignment

property ignoreHs

if true, hydrogens will be ignored in the alignment

property map

the atom-atom mapping(s) used in the alignment

property maxMatches

maximum number of substructure matches to consider

property numThreads

number of threads to use

property symmetrizeConjugatedTerminalGroups

if true, conjugated terminal functional groups (like nitro or carboxylate) will be considered symmetrically.

property weights

the weights used in the alignment

class rdkit.Chem.rdMolAlign.O3A

Bases: object

Open3DALIGN object

Align(self) → float

aligns probe molecule onto reference molecule

Matches(self) → list

returns the AtomMap as found by Open3DALIGN

Score(self) → float

returns the O3AScore of the alignment

Trans(self) → object

returns the transformation which aligns probe molecule onto reference molecule

Weights(self) → list

returns the weight vector as found by Open3DALIGN