Bio.PDB package

Subpackages

• Bio.PDB.mmtf package
  • Submodules
    • Bio.PDB.mmtf.DefaultParser module
      • StructureDecoder
    • Bio.PDB.mmtf.mmtfio module
      • MMTFIO
  • Module contents
    • get_from_decoded()
    • MMTFParser
      • MMTFParser.get_structure_from_url()
      • MMTFParser.get_structure()

Submodules

• Bio.PDB.AbstractPropertyMap module
  • AbstractPropertyMap
    • AbstractPropertyMap.__init__()
    • AbstractPropertyMap.__contains__()
    • AbstractPropertyMap.__getitem__()
    • AbstractPropertyMap.__len__()
    • AbstractPropertyMap.keys()
    • AbstractPropertyMap.__iter__()
  • AbstractResiduePropertyMap
    • AbstractResiduePropertyMap.__init__()
  • AbstractAtomPropertyMap
    • AbstractAtomPropertyMap.__init__()
• Bio.PDB.Atom module
  • Atom
    • Atom.__init__()
    • Atom.__eq__()
    • Atom.__ne__()
    • Atom.__gt__()
    • Atom.__ge__()
    • Atom.__lt__()
    • Atom.__le__()
    • Atom.__hash__()
    • Atom.__repr__()
    • Atom.__sub__()
    • Atom.strictly_equals()
    • Atom.set_serial_number()
    • Atom.set_bfactor()
    • Atom.set_coord()
    • Atom.set_altloc()
    • Atom.set_occupancy()
    • Atom.set_sigatm()
    • Atom.set_siguij()
    • Atom.set_anisou()
    • Atom.set_charge()
    • Atom.set_radius()
    • Atom.flag_disorder()
    • Atom.is_disordered()
    • Atom.set_parent()
    • Atom.detach_parent()
    • Atom.get_sigatm()
    • Atom.get_siguij()
    • Atom.get_anisou()
    • Atom.get_parent()
    • Atom.get_serial_number()
    • Atom.get_name()
    • Atom.get_id()
    • Atom.get_full_id()
    • Atom.get_coord()
    • Atom.get_bfactor()
    • Atom.get_occupancy()
    • Atom.get_fullname()
    • Atom.get_altloc()
    • Atom.get_level()
    • Atom.get_charge()
    • Atom.get_radius()
    • Atom.transform()
    • Atom.get_vector()
    • Atom.copy()
  • DisorderedAtom
    • DisorderedAtom.__init__()
    • DisorderedAtom.__iter__()
    • DisorderedAtom.__repr__()
    • DisorderedAtom.center_of_mass()
    • DisorderedAtom.disordered_get_list()
    • DisorderedAtom.disordered_add()
    • DisorderedAtom.disordered_remove()
    • DisorderedAtom.transform()
• Bio.PDB.Chain module
  • Chain
    • Chain.__init__()
    • Chain.__gt__()
    • Chain.__ge__()
    • Chain.__lt__()
    • Chain.__le__()
    • Chain.__getitem__()
    • Chain.__contains__()
    • Chain.__delitem__()
    • Chain.__repr__()
    • Chain.get_unpacked_list()
    • Chain.has_id()
    • Chain.get_residues()
    • Chain.get_atoms()
    • Chain.atom_to_internal_coordinates()
    • Chain.internal_to_atom_coordinates()
    • Chain.__orig_bases__
    • Chain.__parameters__
• Bio.PDB.DSSP module
  • Usage
  • Examples
  • version()
  • ss_to_index()
  • dssp_dict_from_pdb_file()
  • make_dssp_dict()
  • DSSP
    • DSSP.__init__()
• Bio.PDB.Dice module
  • ChainSelector
    • ChainSelector.__init__()
    • ChainSelector.accept_model()
    • ChainSelector.accept_chain()
    • ChainSelector.accept_residue()
    • ChainSelector.accept_atom()
  • extract()
• Bio.PDB.Entity module
  • Entity
    • Entity.level
    • Entity.__init__()
    • Entity.parent
    • Entity.child_list
    • Entity.child_dict
    • Entity.__len__()
    • Entity.__getitem__()
    • Entity.__delitem__()
    • Entity.__contains__()
    • Entity.__iter__()
    • Entity.__eq__()
    • Entity.__ne__()
    • Entity.__gt__()
    • Entity.__ge__()
    • Entity.__lt__()
    • Entity.__le__()
    • Entity.__hash__()
    • Entity.id
    • Entity.strictly_equals()
    • Entity.get_level()
    • Entity.set_parent()
    • Entity.detach_parent()
    • Entity.detach_child()
    • Entity.add()
    • Entity.insert()
    • Entity.get_iterator()
    • Entity.get_list()
    • Entity.has_id()
    • Entity.get_parent()
    • Entity.get_id()
    • Entity.get_full_id()
    • Entity.transform()
    • Entity.center_of_mass()
    • Entity.copy()
    • Entity.__annotations__
    • Entity.__orig_bases__
    • Entity.__parameters__
  • DisorderedEntityWrapper
    • DisorderedEntityWrapper.__init__()
    • DisorderedEntityWrapper.__getattr__()
    • DisorderedEntityWrapper.__getitem__()
    • DisorderedEntityWrapper.__setitem__()
    • DisorderedEntityWrapper.__contains__()
    • DisorderedEntityWrapper.__iter__()
    • DisorderedEntityWrapper.__len__()
    • DisorderedEntityWrapper.__sub__()
    • DisorderedEntityWrapper.__gt__()
    • DisorderedEntityWrapper.__ge__()
    • DisorderedEntityWrapper.__lt__()
    • DisorderedEntityWrapper.__le__()
    • DisorderedEntityWrapper.copy()
    • DisorderedEntityWrapper.get_id()
    • DisorderedEntityWrapper.strictly_equals()
    • DisorderedEntityWrapper.disordered_has_id()
    • DisorderedEntityWrapper.detach_parent()
    • DisorderedEntityWrapper.get_parent()
    • DisorderedEntityWrapper.set_parent()
    • DisorderedEntityWrapper.disordered_select()
    • DisorderedEntityWrapper.disordered_add()
    • DisorderedEntityWrapper.disordered_remove()
    • DisorderedEntityWrapper.is_disordered()
    • DisorderedEntityWrapper.disordered_get_id_list()
    • DisorderedEntityWrapper.disordered_get()
    • DisorderedEntityWrapper.disordered_get_list()
• Bio.PDB.FragmentMapper module
  • Fragment
    • Fragment.__init__()
    • Fragment.get_resname_list()
    • Fragment.get_id()
    • Fragment.get_coords()
    • Fragment.add_residue()
    • Fragment.__len__()
    • Fragment.__sub__()
    • Fragment.__repr__()
  • FragmentMapper
    • FragmentMapper.__init__()
    • FragmentMapper.__contains__()
    • FragmentMapper.__getitem__()
• Bio.PDB.HSExposure module
  • HSExposureCA
    • HSExposureCA.__init__()
    • HSExposureCA.pcb_vectors_pymol()
  • HSExposureCB
    • HSExposureCB.__init__()
  • ExposureCN
    • ExposureCN.__init__()
• Bio.PDB.MMCIF2Dict module
  • MMCIF2Dict
    • MMCIF2Dict.__init__()
• Bio.PDB.MMCIFParser module
  • MMCIFParser
    • MMCIFParser.__init__()
    • MMCIFParser.get_structure()
  • FastMMCIFParser
    • FastMMCIFParser.__init__()
    • FastMMCIFParser.get_structure()
• Bio.PDB.Model module
  • Model
    • Model.__init__()
    • Model.__repr__()
    • Model.get_chains()
    • Model.get_residues()
    • Model.get_atoms()
    • Model.atom_to_internal_coordinates()
    • Model.__orig_bases__
    • Model.__parameters__
    • Model.internal_to_atom_coordinates()
• Bio.PDB.NACCESS module
  • run_naccess()
  • process_rsa_data()
  • process_asa_data()
  • NACCESS
    • NACCESS.__init__()
  • NACCESS_atomic
    • NACCESS_atomic.__init__()
• Bio.PDB.NeighborSearch module
  • NeighborSearch
    • NeighborSearch.__init__()
    • NeighborSearch.search()
    • NeighborSearch.search_all()
• Bio.PDB.PDBExceptions module
  • PDBException
  • PDBConstructionException
  • PDBConstructionWarning
  • PDBIOException
• Bio.PDB.PDBIO module
  • Select
    • Select.__repr__()
    • Select.accept_model()
    • Select.accept_chain()
    • Select.accept_residue()
    • Select.accept_atom()
  • StructureIO
    • StructureIO.__init__()
    • StructureIO.set_structure()
  • PDBIO
    • PDBIO.__init__()
    • PDBIO.save()
• Bio.PDB.PDBList module
  • PDBList
    • PDBList.PDB_REF
    • PDBList.__init__()
    • PDBList.get_status_list()
    • PDBList.get_recent_changes()
    • PDBList.get_all_entries()
    • PDBList.get_all_obsolete()
    • PDBList.retrieve_pdb_file()
    • PDBList.update_pdb()
    • PDBList.download_pdb_files()
    • PDBList.get_all_assemblies()
    • PDBList.retrieve_assembly_file()
    • PDBList.download_all_assemblies()
    • PDBList.download_entire_pdb()
    • PDBList.download_obsolete_entries()
    • PDBList.get_seqres_file()
• Bio.PDB.PDBMLParser module
  • PDBMLParser
    • PDBMLParser.__init__()
    • PDBMLParser.get_structure()
• Bio.PDB.PDBParser module
  • PDBParser
    • PDBParser.__init__()
    • PDBParser.get_structure()
    • PDBParser.get_header()
    • PDBParser.get_trailer()
• Bio.PDB.PICIO module
  • read_PIC()
  • read_PIC_seq()
  • enumerate_atoms()
  • pdb_date()
  • write_PIC()
• Bio.PDB.PSEA module
  • run_psea()
  • psea()
  • psea2HEC()
  • annotate()
  • PSEA
    • PSEA.__init__()
    • PSEA.get_seq()
• Bio.PDB.Polypeptide module
  • index_to_one()
  • one_to_index()
  • index_to_three()
  • three_to_index()
  • is_aa()
  • is_nucleic()
  • Polypeptide
    • Polypeptide.get_ca_list()
    • Polypeptide.get_phi_psi_list()
    • Polypeptide.get_tau_list()
    • Polypeptide.get_theta_list()
    • Polypeptide.get_sequence()
    • Polypeptide.__repr__()
  • CaPPBuilder
    • CaPPBuilder.__init__()
  • PPBuilder
    • PPBuilder.__init__()
• Bio.PDB.Residue module
  • Residue
    • Residue.__init__()
    • Residue.__repr__()
    • Residue.strictly_equals()
    • Residue.add()
    • Residue.flag_disordered()
    • Residue.is_disordered()
    • Residue.get_resname()
    • Residue.get_unpacked_list()
    • Residue.get_segid()
    • Residue.get_atoms()
    • Residue.__orig_bases__
    • Residue.__parameters__
  • DisorderedResidue
    • DisorderedResidue.__init__()
    • DisorderedResidue.__repr__()
    • DisorderedResidue.add()
    • DisorderedResidue.sort()
    • DisorderedResidue.disordered_add()
    • DisorderedResidue.disordered_remove()
• Bio.PDB.ResidueDepth module
  • get_surface()
  • min_dist()
  • residue_depth()
  • ca_depth()
  • ResidueDepth
    • ResidueDepth.__init__()
• Bio.PDB.SASA module
  • ShrakeRupley
    • ShrakeRupley.__init__()
    • ShrakeRupley.compute()
• Bio.PDB.SCADIO module
  • write_SCAD()
• Bio.PDB.Selection module
  • uniqueify()
  • get_unique_parents()
  • unfold_entities()
• Bio.PDB.Structure module
  • Structure
    • Structure.__init__()
    • Structure.__repr__()
    • Structure.get_models()
    • Structure.get_chains()
    • Structure.get_residues()
    • Structure.get_atoms()
    • Structure.atom_to_internal_coordinates()
    • Structure.internal_to_atom_coordinates()
    • Structure.__orig_bases__
    • Structure.__parameters__
• Bio.PDB.StructureAlignment module
  • StructureAlignment
    • StructureAlignment.__init__()
    • StructureAlignment.get_maps()
    • StructureAlignment.get_iterator()
• Bio.PDB.StructureBuilder module
  • StructureBuilder
    • StructureBuilder.__init__()
    • StructureBuilder.set_header()
    • StructureBuilder.set_line_counter()
    • StructureBuilder.init_structure()
    • StructureBuilder.init_model()
    • StructureBuilder.init_chain()
    • StructureBuilder.init_seg()
    • StructureBuilder.init_residue()
    • StructureBuilder.init_atom()
    • StructureBuilder.set_anisou()
    • StructureBuilder.set_siguij()
    • StructureBuilder.set_sigatm()
    • StructureBuilder.get_structure()
    • StructureBuilder.set_symmetry()
• Bio.PDB.Superimposer module
  • Superimposer
    • Superimposer.__init__()
    • Superimposer.set_atoms()
    • Superimposer.apply()
• Bio.PDB.alphafold_db module
  • get_predictions()
  • download_cif_for()
  • get_structural_models_for()
• Bio.PDB.binary_cif module
  • BinaryCIFParser
    • BinaryCIFParser.__init__()
    • BinaryCIFParser.get_structure()
• Bio.PDB.cealign module
  • Reference
  • CEAligner
    • CEAligner.__init__()
    • CEAligner.get_guide_coord_from_structure()
    • CEAligner.set_reference()
    • CEAligner.align()
• Bio.PDB.ic_data module
• Bio.PDB.ic_rebuild module
  • structure_rebuild_test()
  • report_IC()
  • IC_duplicate()
  • compare_residues()
  • write_PDB()
• Bio.PDB.internal_coords module
  • IC_Chain
    • IC_Chain.MaxPeptideBond
    • IC_Chain.ParallelAssembleResidues
    • IC_Chain.AAsiz
    • IC_Chain.atomArray
    • IC_Chain.dCoordSpace
    • IC_Chain.dcsValid
    • IC_Chain.__init__()
    • IC_Chain.__deepcopy__()
    • IC_Chain.clear_ic()
    • IC_Chain.build_atomArray()
    • IC_Chain.build_edraArrays()
    • IC_Chain.assemble_residues()
    • IC_Chain.assemble_residues_ser()
    • IC_Chain.init_edra()
    • IC_Chain.init_atom_coords()
    • IC_Chain.update_dCoordSpace()
    • IC_Chain.propagate_changes()
    • IC_Chain.internal_to_atom_coordinates()
    • IC_Chain.atom_to_internal_coordinates()
    • IC_Chain.distance_plot()
    • IC_Chain.dihedral_signs()
    • IC_Chain.distplot_to_dh_arrays()
    • IC_Chain.distance_to_internal_coordinates()
    • IC_Chain.copy_initNCaCs()
    • IC_Chain.make_extended()
    • IC_Chain.__annotations__
  • IC_Residue
    • IC_Residue.accept_resnames
    • IC_Residue.no_altloc
    • IC_Residue.gly_Cbeta
    • IC_Residue.pic_accuracy
    • IC_Residue.accept_backbone
    • IC_Residue.accept_sidechain
    • IC_Residue.accept_mainchain
    • IC_Residue.accept_hydrogens
    • IC_Residue.accept_deuteriums
    • IC_Residue.accept_atoms
    • IC_Residue.__init__()
    • IC_Residue.__deepcopy__()
    • IC_Residue.__contains__()
    • IC_Residue.rak()
    • IC_Residue.__repr__()
    • IC_Residue.pretty_str()
    • IC_Residue.set_flexible()
    • IC_Residue.set_hbond()
    • IC_Residue.clear_transforms()
    • IC_Residue.assemble()
    • IC_Residue.split_akl()
    • IC_Residue.atom_sernum
    • IC_Residue.atom_chain
    • IC_Residue.pdb_residue_string()
    • IC_Residue.pic_flags
    • IC_Residue.picFlagsDefault
    • IC_Residue.picFlagsDict
    • IC_Residue.pick_angle()
    • IC_Residue.get_angle()
    • IC_Residue.set_angle()
    • IC_Residue.bond_rotate()
    • IC_Residue.bond_set()
    • IC_Residue.pick_length()
    • IC_Residue.get_length()
    • IC_Residue.set_length()
    • IC_Residue.applyMtx()
    • IC_Residue.__annotations__
  • Edron
    • Edron.edron_re
    • Edron.gen_key()
    • Edron.gen_tuple()
    • Edron.__init__()
    • Edron.__deepcopy__()
    • Edron.__contains__()
    • Edron.is_backbone()
    • Edron.__repr__()
    • Edron.__hash__()
    • Edron.__eq__()
    • Edron.__ne__()
    • Edron.__gt__()
    • Edron.__ge__()
    • Edron.__lt__()
    • Edron.__le__()
  • Hedron
    • Hedron.__init__()
    • Hedron.__repr__()
    • Hedron.angle
    • Hedron.len12
    • Hedron.len23
    • Hedron.get_length()
    • Hedron.set_length()
  • Dihedron
    • Dihedron.__init__()
    • Dihedron.__repr__()
    • Dihedron.angle
    • Dihedron.angle_dif()
    • Dihedron.angle_avg()
    • Dihedron.angle_pop_sd()
    • Dihedron.difference()
    • Dihedron.bits()
  • AtomKey
    • AtomKey.atom_re
    • AtomKey.fieldNames
    • AtomKey.fields
    • AtomKey.d2h
    • AtomKey.__init__()
    • AtomKey.__deepcopy__()
    • AtomKey.__repr__()
    • AtomKey.__hash__()
    • AtomKey.altloc_match()
    • AtomKey.is_backbone()
    • AtomKey.atm()
    • AtomKey.cr_class()
    • AtomKey.__ne__()
    • AtomKey.__eq__()
    • AtomKey.__gt__()
    • AtomKey.__ge__()
    • AtomKey.__lt__()
    • AtomKey.__le__()
  • set_accuracy_95()
  • HedronMatchError
  • MissingAtomError
• Bio.PDB.mmcifio module
  • MMCIFIO
    • MMCIFIO.__init__()
    • MMCIFIO.set_dict()
    • MMCIFIO.save()
• Bio.PDB.parse_pdb_header module
  • parse_pdb_header()
• Bio.PDB.qcprot module
  • qcp()
  • QCPSuperimposer
    • QCPSuperimposer.__init__()
    • QCPSuperimposer.set_atoms()
    • QCPSuperimposer.apply()
    • QCPSuperimposer.set()
    • QCPSuperimposer.run()
    • QCPSuperimposer.get_transformed()
    • QCPSuperimposer.get_rotran()
    • QCPSuperimposer.get_init_rms()
    • QCPSuperimposer.get_rms()
• Bio.PDB.vectors module
  • m2rotaxis()
  • vector_to_axis()
  • rotaxis2m()
  • rotaxis()
  • refmat()
  • rotmat()
  • calc_angle()
  • calc_dihedral()
  • Vector
    • Vector.__init__()
    • Vector.__repr__()
    • Vector.__neg__()
    • Vector.__add__()
    • Vector.__sub__()
    • Vector.__mul__()
    • Vector.__truediv__()
    • Vector.__pow__()
    • Vector.__getitem__()
    • Vector.__setitem__()
    • Vector.__contains__()
    • Vector.norm()
    • Vector.normsq()
    • Vector.normalize()
    • Vector.normalized()
    • Vector.angle()
    • Vector.get_array()
    • Vector.left_multiply()
    • Vector.right_multiply()
    • Vector.copy()
  • homog_rot_mtx()
  • set_Z_homog_rot_mtx()
  • set_Y_homog_rot_mtx()
  • set_X_homog_rot_mtx()
  • homog_trans_mtx()
  • set_homog_trans_mtx()
  • homog_scale_mtx()
  • get_spherical_coordinates()
  • coord_space()
  • multi_rot_Z()
  • multi_rot_Y()
  • multi_coord_space()

Module contents

Classes that deal with macromolecular crystal structures.

Includes: PDB and mmCIF parsers, a Structure class, a module to keep a local copy of the PDB up-to-date, selective IO of PDB files, etc.

Original Author: Thomas Hamelryck. Contributions by: - Peter Cock - Joe Greener - Rob Miller - Lenna X. Peterson - Joao Rodrigues - Kristian Rother - Eric Talevich - and many others.