schrodinger.protein.rotamers module

A rotamer library which can be applied to protein sidechains.

A Rotamers object is initialized with an atom from a Structure object. Exceptions will be generated if there is no rotamer information for the residue correspoding to that atom or if the residue is incomplete. Once the Rotamers object is created it’s possible to iterate through the rotamers, to apply any of them or to restore the original geometry.

Copyright Schrodinger LLC. All rights reserved.

class schrodinger.protein.rotamers.Rotamers(st, atom)

Bases: object

Manages a rotamer library for a given residue type.

__init__(st, atom)

Initialize the Rotamer Library with respect to a given atom in the input structure ‘st’.

findChiAtoms(res, chi_index)

Return a list of atom numbers for the given Chi dihedral of the residue.

restore()

Restore the sidechain back to the original coordinates

rotamers

A list of all the rotamers available for the current residue.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.protein.rotamers', '__doc__': '\n Manages a rotamer library for a given residue type.\n\n ', '__init__': <function Rotamers.__init__>, 'findChiAtoms': <function Rotamers.findChiAtoms>, '_apply': <function Rotamers._apply>, 'restore': <function Rotamers.restore>, '_getRotamerIterator': <function Rotamers._getRotamerIterator>, '_doc': '\n A list of all the rotamers available for the current residue.\n ', 'rotamers': <property object>, '__dict__': <attribute '__dict__' of 'Rotamers' objects>, '__weakref__': <attribute '__weakref__' of 'Rotamers' objects>})

__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.protein.rotamers'

__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

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__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).

__weakref__

list of weak references to the object (if defined)