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

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

Bases: object

Supports alignment of molecular structures

__slots__ = ('_ptr', '_ids', '_seltext')

atom selection object

__init__(ptr, seltext)

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

__len__()

number of selected atoms

__str__()

Return str(self).

__repr__()

Return repr(self).

ids

ids of selected atoms in the parent system

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.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.packages.msys.atomsel'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.