schrodinger.structutils.structalign module

A module for performing protein structure alignment. This requires Prime to be installed and licensed appropriately as the SKA program distributed with Prime is what is actually used to do the alignment.

The structural alignment is performed and the results are added as properties to the input CTs. For each template the alignment is returned along with the raw output from ska.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.structutils.structalign.StructAlign

Bases: object

This is the class used to perform the structural alignment. This class will check at initialization time if Prime is installed by trying to import schrodinger.applications.ska and will fail if it’s not installed as nothing more can be done.

There are a number of properties that can be set for instances of this class which are used to control how the alignment is done:

gap_penalty - default = 2.0 deletion_penalty = default = 1.0 use_scanning_alignment - default = False window_length - default = 5 minimum_similarity - default = 1.0 minimum_length - default = 2 use_automatic_settings - default = False use_standard_residues - default = False reorder_by_connectivity - default = False

__init__()

Construct an instance of a StructAlign object. This method will check that schrodinger.application.ska is available and fail with a RuntimeError if it’s not

gap_penalty

Access to the gap penalty for the alignment

deletion_penalty

Access to the deletion penalty for the alignment

use_scanning_alignment

Access to the use scanning alignment flag

window_length

Access to the window length for the aligment

minimum_similarity

Access to the minimum similarity used in the alignment

minimum_length

Access to the minimum length used in the alignment

align(ref_st, sts)

Perform a structural alignment on the Structure objects in the list ‘sts’ relative to the reference structure ‘ref_st’ Each structure in the list is aligned relative to the reference structure. The coordinates of the input structures are modified to give the best structural alignment.

alignStructure(ref_st, mob_st)

Perform a structural alignment on the mob_st structure relative to the ref_st structure. The coordinates of the input mob_st structure are modified to give the best structural alignment.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.structutils.structalign', '__doc__': "\n This is the class used to perform the structural alignment. This class\n will check at initialization time if Prime is installed by trying to\n import schrodinger.applications.ska and will fail if it's not installed\n as nothing more can be done.\n\n There are a number of properties that can be set for instances of this\n class which are used to control how the alignment is done:\n\n gap_penalty - default = 2.0\n deletion_penalty = default = 1.0\n use_scanning_alignment - default = False\n window_length - default = 5\n minimum_similarity - default = 1.0\n minimum_length - default = 2\n use_automatic_settings - default = False\n use_standard_residues - default = False\n reorder_by_connectivity - default = False\n\n ", '__init__': <function StructAlign.__init__>, '_setGapPenalty': <function StructAlign._setGapPenalty>, '_getGapPenalty': <function StructAlign._getGapPenalty>, 'gap_penalty': <property object>, '_setDeletionPenalty': <function StructAlign._setDeletionPenalty>, '_getDeletionPenalty': <function StructAlign._getDeletionPenalty>, 'deletion_penalty': <property object>, '_setUseScanningAlignment': <function StructAlign._setUseScanningAlignment>, '_getUseScanningAlignment': <function StructAlign._getUseScanningAlignment>, 'use_scanning_alignment': <property object>, '_setWindowLength': <function StructAlign._setWindowLength>, '_getWindowLength': <function StructAlign._getWindowLength>, 'window_length': <property object>, '_setMinimumSimilarity': <function StructAlign._setMinimumSimilarity>, '_getMinimumSimilarity': <function StructAlign._getMinimumSimilarity>, 'minimum_similarity': <property object>, '_setMinimumLength': <function StructAlign._setMinimumLength>, '_getMinimumLength': <function StructAlign._getMinimumLength>, 'minimum_length': <property object>, 'align': <function StructAlign.align>, 'alignStructure': <function StructAlign.alignStructure>, '__dict__': <attribute '__dict__' of 'StructAlign' objects>, '__weakref__': <attribute '__weakref__' of 'StructAlign' 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.structutils.structalign'

__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)