schrodinger.application.bioluminate.antibody.utils module¶
Useful classes and functions for working with Antibodies
Copyright (c) Schrodinger, LLC. All rights reserved
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schrodinger.application.bioluminate.antibody.utils.
get_bio_database
()¶ Gets the default antibody database in bioluminate-vxxx/data/antibody.
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schrodinger.application.bioluminate.antibody.utils.
set_active_databases
(databases)¶ Set the database paths as the default databases to open on panel initialization.
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schrodinger.application.bioluminate.antibody.utils.
set_all_databases
(databases)¶ Set the database paths for “all_databases” in the preferences.
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schrodinger.application.bioluminate.antibody.utils.
set_antibody_scheme
(scheme)¶ Set antibody numbering scheme in the preferences.
Parameters: scheme (str) – numbering scheme
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schrodinger.application.bioluminate.antibody.utils.
get_all_databases
(default=None)¶ Returns a list of all databases a user has imported from their preferences.
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schrodinger.application.bioluminate.antibody.utils.
get_active_databases
(default=None)¶ Returns a list of all databases a user has selected as active.
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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
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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.
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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.
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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.
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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 theschrodinger.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- light_seq (str) – The text representation of a sequence such as obtained
from the
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class
schrodinger.application.bioluminate.antibody.utils.
FrameworkTemplate
(score, light_alignment, heavy_alignment)¶ Bases:
object
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__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
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__str__
()¶ Return str(self).
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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
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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.
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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.
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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.
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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.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})¶
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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.application.bioluminate.antibody.utils'¶
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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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__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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