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
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.