jade.antibody.ab_db.get_all_clusters_for_length(db, cdr, length, limit_to_known=True, res_cutoff=2.8, rfac_cutoff=0.3)

Get all unique clusters for a length and a cdr

jade.antibody.ab_db.get_all_lengths(db, cdr, limit_to_known=True, res_cutoff=2.8, rfac_cutoff=0.3)

Get all unique lengths for a CDR

jade.antibody.ab_db.get_cdr_rmsd_for_entry(db, pdb, original_chain, cdr, length, fullcluster)

jade.antibody.ab_db.get_center_dih_degrees_for_cluster_and_length(db, cdr, length, cluster)

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.antibody.ab_db.get_center_for_cluster_and_length(db, cdr, length, cluster, data_names_array)

Get the center for a particular cluster and length

jade.antibody.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)

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.antibody.ab_db.get_dihedral_string_for_centers(db, limit_to_known=True)

Get a string of the dihedral angles for all centers

jade.antibody.ab_db.get_pdb_chain_subset(db, gene, use_cutoffs=False, res_cutoff=2.8, rfac_cutoff=0.3)

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

jade.antibody.ab_db.get_stem_rmsd_for_entry(db, pdb, original_chain, cdr, length, fullcluster)

jade.antibody.ab_db.get_unique_sequences_for_cluster(db, cluster, include_outliers, outlier_definition='conservative')