schrodinger.application.desmond.packages.msys.atomsel module¶
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class
schrodinger.application.desmond.packages.msys.atomsel.
Atomsel
(ptr, seltext)¶ Bases:
object
Supports alignment of molecular structures
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__init__
(ptr, seltext)¶ don’t use directly - use System.atomsel()
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__len__
()¶ number of selected atoms
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ids
¶ ids of selected atoms in the parent system
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system
¶ parent system
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getPositions
()¶
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raw_alignment
(other)¶ Compute alignment to other object. Compute and return aligned rmsd, and rotational and translational transformations.
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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)
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alignedRMSD
(other)¶ Return the aligned rmsd to other.
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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.
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