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

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

Bases: object

Supports alignment of molecular structures

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.

alignedRMSD(other)

Return the aligned rmsd to other.

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)

getPositions()

ids

ids of selected atoms in the parent system

raw_alignment(other)

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

system

parent system