schrodinger.application.bioluminate.antibody.utils

Module utils

Useful classes and functions for working with Antibodies

Functions

[hide private]

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.

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.

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

Variables

[hide private]

maestro = None
hash(x)

preferences = prefs.Preferences(prefs.SCRIPTS)

GENERAL_PREF_GROUP = 'antibody_general'

PREF_ACTIVE_DATABASES = 'active_databases'

PREF_ALL_DATABASES = 'all_databases'

DATABASE_TOKEN = '|'

__package__ = 'schrodinger.application.bioluminate.antibody'

Function Details

[hide private]

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)

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.

Returns: list

List of results, each item is a FrameworkTemplate object