jade.antibody.cdr_data package

Submodules

jade.antibody.cdr_data.CDRData module

class jade.antibody.cdr_data.CDRData.CDRData(name, native_path, is_camelid=False)

Bases: object

Class holding cluster and length data from cluster or antibody features database.

add_data(strategy, con)

Function to add data to the class. Needs to be defined in subclass. :param strategy: Strategy for which we are adding data :param con: Sqlite3 Connection object

get_concatonated_map(cdr=None, decoy_list=None)

Returns a defaultDic: Default:

decoy: CDRDataInfo

If CDR != None:

[value, cdr] = CDRDataTriple

#->CDR to get back cdr_value, decoy for sorting on cdr_value

Return type:defaultdict

get_native_data()

get_pandas_dataframe(cdrs=None, drop_dir_prefix=False)

Gets all data as a pandas dataframe. Uses the set name as the score. You can then order, or select specific ones using the data frame. :rtype: pandas.DataFrame

get_strategy_data(strategy)

Get data for each decoy :param strategy: Strategy string :rtype: list of CDRDataInfo

get_strategy_data_for_decoy(strategy, decoy)

Get the data of the decoy :param strategy: Strategy string :param decoy: decoy including path and suffix :rtype: CDRDataInfo

set_native_data_input_tag(con, input_tag)

class jade.antibody.cdr_data.CDRData.CDRDataInfo(name, strategy, decoy)

Bases: object

Simple class for holding and accessing Cluster and Length data for a particular Decoy.

get_data()

get_value_for_cdr(cdr)

has_data(cdr)

is_camelid()

Return True if missing light chain data

set_data(data)

Dictionary for each CDR: L1, L2, L3, H1, H2, H3

set_value(cdr, value)

set_value_for_cdr(cdr, value)

jade.antibody.cdr_data.CDRDataTypes module

class jade.antibody.cdr_data.CDRDataTypes.CDRAlignedSequenceData(individual_clustal_outdir, combined_clustal_outdir, native_path, is_camelid=False)

Bases: jade.antibody.cdr_data.CDRDataTypes.CDRSequenceData

Uses Clustal Omega to align sequences from each database.

add_data(strategy, con)

Function to add data to the class. Needs to be defined in subclass. :param strategy: Strategy for which we are adding data :param con: Sqlite3 Connection object

get_concatonated_map(only_cdr=None, decoy_list=None, use_saved_data=True)

Returns a defaultDic: Default:

decoy: CDRDataInfo

If CDR != None:

[value, cdr] = CDRDataTriple

#->CDR to get back cdr_value, decoy for sorting on cdr_value

Return type:defaultdict

class jade.antibody.cdr_data.CDRDataTypes.CDRClusterData(native_path, is_camelid=False)

Bases: jade.antibody.cdr_data.CDRData.CDRData

add_data(strategy, con)

Function to add data to the class. Needs to be defined in subclass. :param strategy: Strategy for which we are adding data :param con: Sqlite3 Connection object

class jade.antibody.cdr_data.CDRDataTypes.CDRLengthData(native_path, is_camelid=False)

Bases: jade.antibody.cdr_data.CDRData.CDRData

add_data(strategy, con)

Function to add data to the class. Needs to be defined in subclass. :param strategy: Strategy for which we are adding data :param con: Sqlite3 Connection object

class jade.antibody.cdr_data.CDRDataTypes.CDRSequenceData(native_path, is_camelid=False)

Bases: jade.antibody.cdr_data.CDRData.CDRData

add_data(strategy, con)

Function to add data to the class. Needs to be defined in subclass. :param strategy: Strategy for which we are adding data :param con: Sqlite3 Connection object

class jade.antibody.cdr_data.CDRDataTypes.CDRdSASAData(native_path, is_camelid=False)

Bases: jade.antibody.cdr_data.CDRData.CDRData

add_data(strategy, con)

Function to add data to the class. Needs to be defined in subclass. :param strategy: Strategy for which we are adding data :param con: Sqlite3 Connection object