schrodinger.application.bioluminate.antibody.utils module¶

Useful classes and functions for working with Antibodies

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

schrodinger.application.bioluminate.antibody.utils.calc_cdr_shifts(cdr_regions, scheme)¶

Convert a dict of CDR region boundraies to a parameter dict of shifts.

Parameters:: cdr_regions (dict) – Custom CDR region numbering (if any)
Return type:: dict
Returns:: Dictionary of parameters to pass to write_bld_input().

schrodinger.application.bioluminate.antibody.utils.get_align_ct(align)¶

Returns structure from a given alignment object.

Parameters:: align (schrodinger.application.prime.packages.antibody.AntibodyAlignment) – antibody alignment object
Returns:: structure
Return type:: structure.Structure

schrodinger.application.bioluminate.antibody.utils.get_align_data(align, name, default_value=None)¶

Returns data from a given alignment object.

Parameters:

align (schrodinger.application.prime.packages.antibody.AntibodyAlignment) – antibody alignment object
name (str) – name of property that we are retrieving data from.
default_value (str or float or int or bool or None) – optional default value with type appropriate for the given data name type

Returns:

data value

Return type:

str or int or float or bool

schrodinger.application.bioluminate.antibody.utils.get_align_seq_data(align, name, default_value=None)¶

Returns sequence data from a given alignment object. This data is precompiled, so a different call is made compared to get_align_data

Parameters:

align (schrodinger.application.prime.packages.antibody.AntibodyAlignment) – antibody alignment object
name (str) – name of property that we are retrieving data from.
default_value (str or float or int or bool or None) – optional default value with type appropriate for the given data name type

Returns:

data value

Return type:

str or int or float or bool

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.