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