schrodinger.application.bioluminate.antibody.utils module

Useful classes and functions for working with Antibodies

Copyright (c) Schrodinger, LLC. All rights reserved

schrodinger.application.bioluminate.antibody.utils.get_bio_database()

Gets the default antibody database in bioluminate-vxxx/data/antibody.

schrodinger.application.bioluminate.antibody.utils.set_active_databases(databases)

Set the database paths as the default databases to open on panel initialization.

schrodinger.application.bioluminate.antibody.utils.set_all_databases(databases)

Set the database paths for “all_databases” in the preferences.

schrodinger.application.bioluminate.antibody.utils.set_antibody_scheme(scheme)

Set antibody numbering scheme in the preferences.

Parameters:scheme (str) – numbering scheme
schrodinger.application.bioluminate.antibody.utils.get_all_databases(default=None)

Returns a list of all databases a user has imported from their preferences.

schrodinger.application.bioluminate.antibody.utils.get_active_databases(default=None)

Returns a list of all databases a user has selected as active.

schrodinger.application.bioluminate.antibody.utils.get_antibody_scheme(default='Chothia')

Returns default antibody numbering scheme.

Parameters:default (str) – default numbering scheme
Returns:AB numbering scheme
Return type:str
schrodinger.application.bioluminate.antibody.utils.make_scheme_cb(parent=None)

This function creates and returns antibody numbering scheme combo box with default item defined by preference settings.

schrodinger.application.bioluminate.antibody.utils.get_databases()

Returns a list of all databases and whether they are active from the preferences set by the user. If there are none set by the user the default bio database will be returned.

schrodinger.application.bioluminate.antibody.utils.open_databases(database_paths=None)

Returns a list of open databases. If database_paths is not supplied the list of databases to open will be pulled from active databases in the preferences.

schrodinger.application.bioluminate.antibody.utils.search_antibody(light_seq, heavy_seq, databases, criteria=None, viewer=None, scheme='Chothia')

Searches the database for a matching antibody to the sequence supplied.

Parameters:
  • light_seq (str) – The text representation of a sequence such as obtained from the schrodinger.ui.sequencealignment.sequence.Sequence.text method. This should be for the light variable region
  • heavy_seq (str) – The text representation of a sequence such as obtained from the schrodinger.ui.sequencealignment.sequence.Sequence.text method This should be for the heavy variable region
  • criteria (list) – list of String, Numerical and Boolean schrodinger.application.bioluminate.propfilter.Criterion objects obtained from the schrodinger.application.bioluminate.propfilter for limited the antibodies searched in the database
  • database (schrodinger.application.prime.packages.PrimeStructureDatabase.PrimeStructureDB) – The database to search
  • viewer (schrodinger.application.bioluminate.ssv.viewer.SimplifiedSequenceViewer) – The SimplifiedSequenceViewer viewer to place results in.
  • scheme (str) – db numbering scheme
Return type:

list

Returns:

List of results, each item is a FrameworkTemplate object

class schrodinger.application.bioluminate.antibody.utils.FrameworkTemplate(score, light_alignment, heavy_alignment)

Bases: object

__init__(score, light_alignment, heavy_alignment)
Parameters:
  • score (float) – Search score for these alignments against the query
  • light_alignment (schrodinger.application.prime.packages.antibody.AntibodyAlignment) – The alignment object describing the Light Variable region alignment
  • heavy_alignment (schrodinger.application.prime.packages.antibody.AntibodyAlignment) – The alignment object describing the Heavy Variable region alignment
__str__()

Return str(self).

createLabel(maxlen=15)
Parameters:maxlen (int) – The maximum length for the name of each region template
Return type:str
Returns:A label describing this FrameworkTemplate
createSequence(region)
Parameters:region (str) – One of - Light - Heavy
Return type:schrodinger.ui.sequencealignment.sequence.Sequence
Returns:The Sequence object for this region - suitable for import into the SSV.
getFilename(region)
Parameters:region (str) – One of - Light - Heavy
Return type:schrodinger.ui.sequencealignment.sequence.Sequence
Returns:The Sequence object for this region - suitable for import into the SSV.
importRegion(region)
Parameters:region (str) – One of - Light - Heavy
Return type:schrodinger.ui.sequencealignment.sequence.Sequence
Returns:The Sequence object for this region - suitable for import into the SSV.
__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.bioluminate.antibody.utils', '__init__': <function FrameworkTemplate.__init__>, '__str__': <function FrameworkTemplate.__str__>, 'createLabel': <function FrameworkTemplate.createLabel>, 'createSequence': <function FrameworkTemplate.createSequence>, 'getFilename': <function FrameworkTemplate.getFilename>, 'importRegion': <function FrameworkTemplate.importRegion>, '__dict__': <attribute '__dict__' of 'FrameworkTemplate' objects>, '__weakref__': <attribute '__weakref__' of 'FrameworkTemplate' objects>, '__doc__': None})
__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.bioluminate.antibody.utils'
__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

__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)