Bio.PDB package
Subpackages
Submodules
- Bio.PDB.AbstractPropertyMap module
- 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
- 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
- Bio.PDB.Dice module
- 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
- Bio.PDB.HSExposure module
- Bio.PDB.MMCIF2Dict module
- Bio.PDB.MMCIFParser module
- Bio.PDB.Model module
- Bio.PDB.NACCESS module
- Bio.PDB.NeighborSearch module
- Bio.PDB.PDBExceptions module
- Bio.PDB.PDBIO module
- 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
- Bio.PDB.PDBParser module
- Bio.PDB.PICIO module
- Bio.PDB.PSEA module
- Bio.PDB.Polypeptide module
- Bio.PDB.Residue module
- Bio.PDB.ResidueDepth module
- Bio.PDB.SASA module
- Bio.PDB.SCADIO module
- Bio.PDB.Selection module
- Bio.PDB.Structure module
- Bio.PDB.StructureAlignment module
- 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
- Bio.PDB.alphafold_db module
- Bio.PDB.binary_cif module
- Bio.PDB.cealign module
- Bio.PDB.ic_data module
- Bio.PDB.ic_rebuild module
- 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
Hedron
Dihedron
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
- Bio.PDB.parse_pdb_header module
- Bio.PDB.qcprot module
- 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.