schrodinger.analysis.substructure module¶
Functionality for generating connected molecule substructures.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.analysis.substructure.
ConnectedMoleculeChain
(st1, atlist1, st2, atlist2)¶ Bases:
object
Superpose st2 and st1 by moving each molecule independently.
This is accomplished by fixing the first molecule of st1 (with atoms in the atom list), and aligning all molecules in st2 that contain atoms which map to the atoms in this molecule of st1. These atoms are now fixed and all molecules in st1 which contain atoms which map to the now-fixed atoms of st2 are aligned to the existing fixed st1/st2 molecules. This fixing and aligning is continued until all molecules in the ensemble connected to the first molecule in st1 is completed. If this did not include all molecules in the st1/st2 system, the next, non-fixed st1 molecule is used to start a new fixing/aligning chain. If there are still un-fixed molecules when all the st1 molecules are fixed, then these atoms only appear in st2 and so are fixed at the input st2 locations.
Parameters: Returns: rmsd, st2 and st1 rotated and translated to align
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__init__
(st1, atlist1, st2, atlist2)¶ Initialize self. See help(type(self)) for accurate signature.
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getConnectivityChain
()¶ Build a chain of which structure moves, which atoms are fixed, and the corresponding moving atoms.
Parameters: - return – The chain has the format (st_moving, fixed_list, moving_list) where st_moving is 0 for the first structure and 1 for the second, and the lists are lists of ints.
- type – 3-tuple of int, list of ints, list of ints
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__class__
¶ alias of
builtins.type
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__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.analysis.substructure', '__doc__': '\n Superpose st2 and st1 by moving each molecule independently.\n\n This is accomplished by fixing the first molecule of st1 (with atoms in the atom\n list), and aligning all molecules in st2 that contain atoms which map to the atoms\n in this molecule of st1. These atoms are now fixed and all molecules in st1 which\n contain atoms which map to the now-fixed atoms of st2 are aligned to the existing\n fixed st1/st2 molecules. This fixing and aligning is continued until all molecules\n in the ensemble connected to the first molecule in st1 is completed. If this did not\n include all molecules in the st1/st2 system, the next, non-fixed st1 molecule is\n used to start a new fixing/aligning chain. If there are still un-fixed molecules\n when all the st1 molecules are fixed, then these atoms only appear in st2 and so\n are fixed at the input st2 locations.\n\n :param st1: first structure\n :type st1: Structure\n\n :param atlist1: list of atom indexes for structure 1\n :type atlist1: list of ints\n\n :param st2: second structure\n :type st2: Structure\n\n :param atlist2: list of atom indexes for structure 2\n :type atlist2: list of ints\n\n :return: rmsd, st2 and st1 rotated and translated to align\n ', '__init__': <function ConnectedMoleculeChain.__init__>, '_initializeChain': <function ConnectedMoleculeChain._initializeChain>, '_setMovingParts': <function ConnectedMoleculeChain._setMovingParts>, '_getNewConnections': <function ConnectedMoleculeChain._getNewConnections>, 'getConnectivityChain': <function ConnectedMoleculeChain.getConnectivityChain>, '__dict__': <attribute '__dict__' of 'ConnectedMoleculeChain' objects>, '__weakref__': <attribute '__weakref__' of 'ConnectedMoleculeChain' objects>})¶
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__dir__
() → list¶ default dir() implementation
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__eq__
¶ Return self==value.
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__format__
()¶ default object formatter
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__ge__
¶ Return self>=value.
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__getattribute__
¶ Return getattr(self, name).
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__gt__
¶ Return self>value.
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__hash__
¶ Return hash(self).
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__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
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__le__
¶ Return self<=value.
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__lt__
¶ Return self<value.
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__module__
= 'schrodinger.analysis.substructure'¶
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__ne__
¶ Return self!=value.
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__new__
()¶ Create and return a new object. See help(type) for accurate signature.
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__reduce__
()¶ helper for pickle
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__reduce_ex__
()¶ helper for pickle
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__repr__
¶ Return repr(self).
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__setattr__
¶ Implement setattr(self, name, value).
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__sizeof__
() → int¶ size of object in memory, in bytes
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__str__
¶ Return str(self).
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__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).
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__weakref__
¶ list of weak references to the object (if defined)
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