jade.antibody package

Subpackages

• jade.antibody.decoy_data package
  • jade.antibody.decoy_data.DecoyData module
  • jade.antibody.decoy_data.DecoyDataTypes module

jade.antibody.CDRClusterer module

class jade.antibody.CDRClusterer.CDRClusterer(bio_pose)

A simple class for calculating a CDRs cluster from dihedrals or a renumbered pose.

get_fullcluster(cdr_name, chain=None, region=None)

IF DIHEDRALS is SET - AKA from before using the same class - WILL USE THE SAME DIHEDRALS AS BEFORE Rewritten from C++ code. Identifies the cluster of a known cdr type given either custom dihedrals or dihedrals calculated from a pose. Returns a pair or [cdr_cluster, distance] region is [int start, int end, chain] - This way you can cluster without renumbering if you want.

Return type:list[str, float]

get_length(cdr_name)

set_custom_dihedrals(dihedrals)

Dihedrals is a dict: [‘phi’]=[x, y, z]; [‘psi’] = [x, y, z]; [‘omega’] = [x, y, z (degrees)]

set_dihedrals_from_bio_pose(start, end, chain)

Set dihedrals from a BioPose :param start: int :param end: int :param chain: str

set_dihedrals_from_cdr(cdr_name, chain)

jade.antibody.ClusterData module

class jade.antibody.ClusterData.CDRClusterData(ab_db, cdr_dir, limit_to_known=True)

Bases: jade.antibody.ClusterData.Data

get_cdr_names()

get_cdr_paths()

Get the CDR path using the cdr directory

get_center_data()

get_center_name()

get_center_path()

get_data()

get_extra_data()

get_infos()

get_original_chain()

get_pdb()

has_center_data()

Returns:boolean

load_data(cdr, length, cluster, extra_sele=[])

class jade.antibody.ClusterData.CDRClusters(ab_db, cdr_dir, limit_to_known=True)

Bases: jade.antibody.ClusterData.Data

get_cluster_data(cluster)

Parameters:cluster – string Returns:CDRClusterData

get_clusters()

load_data(cdr, length, extra_sele=[])

class jade.antibody.ClusterData.CDRData(ab_db, cdr_dir, limit_to_known=True)

Bases: jade.antibody.ClusterData.Data

get_all_data()

get_cluster_data(cdr_name, length, cluster)

Parameters:

• cdr_name – string
• length – int
• cluster – string

Returns:

CDRClusterData

get_clusters(cdr_name, length)

get_clusters_data(cdr_name, length)

Parameters:

• cdr_name – string
• length – int

Returns:

CDRClusters

get_lengths(cdr_name)

Parameters:cdr_name – string Returns:list

get_lengths_data(cdr_name)

Parameters:cdr_name – string Returns:CDRLengths

load_data(extra_sele=[])

class jade.antibody.ClusterData.CDRLengths(ab_db, cdr_dir, limit_to_known=True)

Bases: jade.antibody.ClusterData.Data

get_clusters_data(length)

Parameters:length – int Returns:CDRCLusters

get_lengths()

load_data(cdr, extra_sele=[])

class jade.antibody.ClusterData.Data(ab_db, cdr_dir, limit_to_known=True)

load_data(extra_sele='')

set_res_cutoff(res_cutoff)

set_rfac_cutoff(rfac_cutoff)

class jade.antibody.ClusterData.Info(path, name, PDB, original_chain, cluster, dihedral_distance)

jade.antibody.ab_db module

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')

jade.antibody.outliers module

jade.antibody.outliers.get_outlier_definition_string(outlier_definition, rmsd_cutoff=1.5, dihdist_cutoff=40)

Returns a string for adding to a database query which removes outliers. Need to add AND manually to the string.

jade.antibody.outliers.get_outlier_string(include_outliers, outlier_definition, add_AND=True)

jade.antibody.split_structure module

jade.antibody.split_structure.has_Fc(parent_PDB)

jade.antibody.split_structure.has_chain(pdb_map, chain)

jade.antibody.split_structure.message(pdb_name, type)

jade.antibody.split_structure.run_main(ab_dir, output_dir, only_dimer=True)

jade.antibody.split_structure.run_split_proto_CDR4(ab_dir, output_dir, overhang=0, skip_present=False)

jade.antibody.split_structure.run_split_proto_CDR4_by_gene(db, ab_dir, output_dir, overhang=0, skip_present=False, res_cutoff=2.8, rfac_cutoff=0.3)

jade.antibody.split_structure.separate_pdb(pdb_path, output_dir, only_dimer=True)

Determine if we have Fv or FAB. If FAB, split into parts: Fc, Fv, linker.

jade.antibody.split_structure.separate_proto_CDR4(pdb_path, output_dir, chain, overhang=0, skip_present=True)

jade.antibody.split_structure.split_CDR4(parent_PDB, chain, overhang=0)

jade.antibody.split_structure.split_Fc(parent_PDB)

Split Fc from FAB. Return new pdb_map to save

jade.antibody.split_structure.split_Fv(parent_PDB)

Split Fv from FAB. Return new pdb_map to save

jade.antibody.split_structure.split_linker(parent_PDB)

Split 4 Residue linker from FAB. Linker may be longer than this, but I think this is about it.

jade.antibody.split_structure.split_linker_H(parent_PDB)

Split 4 Residue linker from FAB. Linker may be longer than this, but I think this is about it.

jade.antibody.split_structure.split_linker_L(parent_PDB)

Split 4 Residue linker from FAB. Linker may be longer than this, but I think this is about it.

jade.antibody.util module

jade.antibody.util.get_all_cdr_sele(cdr, stem=0)

If any stem residues are given, will include stem residues in selection.

jade.antibody.util.get_overhang_sele(pymol_writer, cdr, overhang=3)

Gets the selection for terminal superposition in PyMol