BioSimSpace.Align.rmsdAlign¶
-
BioSimSpace.Align.
rmsdAlign
(molecule0, molecule1, mapping=None, property_map0={}, property_map1={})¶ Align atoms in molecule0 to those in molecule1 using the mapping between matched atom indices. The molecule is aligned using rigid-body translation and rotations, with a root mean squared displacement (RMSD) fit to find the optimal translation vector (as opposed to merely taking the difference of centroids).
- Parameters
molecule0 (
Molecule
) – The molecule to align.molecule1 (
Molecule
) – The reference molecule.mapping (dict) – A dictionary mapping atoms in molecule0 to those in molecule1.
property_map0 (dict) – A dictionary that maps “properties” in molecule0 to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }
property_map1 (dict) – A dictionary that maps “properties” in molecule1 to their user defined values.
- Returns
molecule – The aligned molecule.
- Return type
Examples
Align molecule0 to molecule1 based on a precomputed mapping.
>>> import BioSimSpace as BSS >>> molecule0 = BSS.Align.rmsdAlign(molecule0, molecule1, mapping)
Align molecule0 to molecule1. Since no mapping is passed one will be autogenerated using
matchAtoms
with default options.>>> import BioSimSpace as BSS >>> molecule0 = BSS.Align.rmsdAlign(molecule0, molecule1)