schrodinger.application.desmond.packages.msys.atomsel module

class schrodinger.application.desmond.packages.msys.atomsel.Atomsel(ptr, seltext)

Bases: object

Supports alignment of molecular structures

__init__(ptr, seltext)

don’t use directly - use System.atomsel()

__len__()

number of selected atoms

property ids

ids of selected atoms in the parent system

property system

parent system

getPositions()

raw_alignment(other)

Compute alignment to other object. Compute and return aligned rmsd, and rotational and translational transformations.

currentRMSD(other)

compute RMS distance to other object, which may be Atomsel or an array of positions. In either it must be the case that len(other) equals len(self) or len(self.system)

alignedRMSD(other)

Return the aligned rmsd to other.

alignCoordinates(other)

If other is an Atomsel instance, align the coordinates of other’s System with self. If other is a numpy array, align the array with self, using corresponding indices.

In either case, return the aligned RMSD.