Package schrodinger :: Package application :: Package bioluminate :: Package antibody :: Module utils

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Module utils

Useful classes and functions for working with Antibodies

Copyright (c) Schrodinger, LLC. All rights reserved

Classes

FrameworkTemplate

Functions

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

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

set_all_databases(databases)
Set the database paths for "all_databases" in the preferences.

set_antibody_scheme(scheme)
Set antibody numbering scheme in the preferences.

get_all_databases(default=None)
Returns a list of all databases a user has imported from their preferences.

get_active_databases(default=None)
Returns a list of all databases a user has selected as active.

str

get_antibody_scheme(default=DEFAULT_SCHEME)
Returns default antibody numbering scheme.

make_scheme_cb(parent=None)
This function creates and returns antibody numbering scheme combo box with default item defined by preference settings.

get_databases()
Returns a list of all databases and whether they are active from the preferences set by the user.

open_databases(database_paths=None)
Returns a list of open databases.

list

search_antibody(light_seq, heavy_seq, databases, criteria=None, viewer=None, scheme=DEFAULT_SCHEME)
Searches the database for a matching antibody to the sequence supplied.

Variables

psd = None
hash(x)

psp_search = None
hash(x)

psp_antibody = None
hash(x)

maestro = None
hash(x)

GENERAL_PREF_GROUP = 'antibody_general'

PREF_ACTIVE_DATABASES = 'active_databases'

PREF_ALL_DATABASES = 'all_databases'

PREF_AB_SCHEME = 'antibody_scheme'

DEFAULT_SCHEME = 'Chothia'

preferences = prefs.Preferences(prefs.SCRIPTS)

DATABASE_TOKEN = '|'

Function Details

set_antibody_scheme(scheme)

Set antibody numbering scheme in the preferences.

Parameters:

scheme (str) - numbering scheme

get_antibody_scheme(default=DEFAULT_SCHEME)

Returns default antibody numbering scheme.

Parameters:

default (str) - default numbering scheme

Returns: str

AB numbering scheme

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.

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.

search_antibody(light_seq, heavy_seq, databases, criteria=None, viewer=None, scheme=DEFAULT_SCHEME)

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

Returns: list

List of results, each item is a FrameworkTemplate object