jade.RAbD_BM.tools_ab_db.get_all_clusters_for_length(db, cdr, length, limit_to_known=True, res_cutoff=2.8, rfac_cutoff=0.3)[source]

Get all unique clusters for a length and a cdr

jade.RAbD_BM.tools_ab_db.get_all_lengths(db, cdr, limit_to_known=True, res_cutoff=2.8, rfac_cutoff=0.3)[source]

Get all unique lengths for a CDR

jade.RAbD_BM.tools_ab_db.get_cdr_data_table_df(db_path)[source]

Get a dataframe with typical info from the cdr_data table in the PyIgClassify db. :param db_con: sqlite3.con :rtype: pandas.DataFrame

jade.RAbD_BM.tools_ab_db.get_cdr_rmsd_for_entry(db, pdb, original_chain, cdr, length, fullcluster)[source]
jade.RAbD_BM.tools_ab_db.get_center_dih_degrees_for_cluster_and_length(db, cdr, length, cluster)[source]

Returns a dictionary of center dihedral angles in positional order. Or returns False if not found. result[“phis’] = [phis as floats] result[“psis”] = [Psis as floats] result[“omegas”] = [Omegas as floats]

jade.RAbD_BM.tools_ab_db.get_center_for_cluster_and_length(db, cdr, length, cluster, data_names_array)[source]
jade.RAbD_BM.tools_ab_db.get_cluster_enrichment(df, gene, cdr, cluster)[source]

Get the number of matches in the df and pdbid to the cdr and cluster :param df: pandas.DataFrame :rtype: int

jade.RAbD_BM.tools_ab_db.get_cluster_matches(df, gene, cdr, cluster)[source]

Get a dataframe of the matching (“Recovered”) rows (DataFrame).

Parameters:df – pandas.DataFrame
Return type:pandas.DataFrame:
jade.RAbD_BM.tools_ab_db.get_data_for_cluster_and_length(db, cdr, length, cluster, data_names_array, limit_to_known=True, res_cutoff=2.8, rfac_cutoff=0.3)[source]

Get a set of data of a particular length, cdr, and cluster. data_names_array is a list of the types of data. Can include DISTINCT keyword

Example: data_names_array = [“PDB”, “original_chain”, “new_chain”, “sequence”]
jade.RAbD_BM.tools_ab_db.get_dihedral_string_for_centers(db, limit_to_known=True)[source]
jade.RAbD_BM.tools_ab_db.get_length_enrichment(df, gene, cdr, length)[source]

Get the number of matches in the df and pdbid to the cdr and length

Parameters:
  • df – pandas.DataFrame
  • length – int
Return type:

int
jade.RAbD_BM.tools_ab_db.get_length_matches(df, gene, cdr, length)[source]

Get a dataframe of the matching (“Recovered”) rows (DataFrame).

Parameters:
  • df – pandas.DataFrame
  • length – int
Return type:

pandas.DataFrame
jade.RAbD_BM.tools_ab_db.get_pdb_chain_subset(db, gene)[source]

Return a list of tuples of [pdb, chain] of the particular gene

jade.RAbD_BM.tools_ab_db.get_stem_rmsd_for_entry(db, pdb, original_chain, cdr, length, fullcluster)[source]
jade.RAbD_BM.tools_ab_db.get_total_entries(df, gene, cdr)[source]

Get a the total number of entries matching the gene and the cdr. Used for recovery. :param df: pandas.DataFrame :rtype: int

jade.RAbD_BM.tools_ab_db.get_unique_sequences_for_cluster(db, cluster, include_outliers, outlier_definition='conservative')[source]