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.