Bio.PDB软件包

子包

• Bio.PDB.QCP Superimposer软件包
  • 模块内容
    • QCPSuperimposer
      • QCPSuperimposer.__init__()
      • QCPSuperimposer.set()
      • QCPSuperimposer.run()
      • QCPSuperimposer.get_transformed()
      • QCPSuperimposer.get_rotran()
      • QCPSuperimposer.get_init_rms()
      • QCPSuperimposer.get_rms()
• Bio.PDB.mmtf软件包
  • 子模块
    • Bio.PDB.mmtf.DefaultParser模块
    • Bio.PDB.mmtf.mmtfio模块
  • 模块内容

子模块

• Bio.PDB.AbstractPropertyMap模块
  • AbstractPropertyMap
    • AbstractPropertyMap.__init__()
    • AbstractPropertyMap.__contains__()
    • AbstractPropertyMap.__getitem__()
    • AbstractPropertyMap.__len__()
    • AbstractPropertyMap.keys()
    • AbstractPropertyMap.__iter__()
  • AbstractResiduePropertyMap
    • AbstractResiduePropertyMap.__init__()
  • AbstractAtomPropertyMap
    • AbstractAtomPropertyMap.__init__()
• Bio.PDB.Atom模块
  • Atom
    • Atom.__init__()
    • Atom.__eq__()
    • Atom.__ne__()
    • Atom.__gt__()
    • Atom.__ge__()
    • Atom.__lt__()
    • Atom.__le__()
    • Atom.__hash__()
    • Atom.__repr__()
    • Atom.__sub__()
    • 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模块
  • 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()
• Bio.PDB.DSSP模块
  • 用法
  • 示例
  • ss_to_index()
  • dssp_dict_from_pdb_file()
  • make_dssp_dict()
  • DSSP
    • DSSP.__init__()
• Bio.PDB.骰子模块
  • ChainSelector
    • ChainSelector.__init__()
    • ChainSelector.accept_model()
    • ChainSelector.accept_chain()
    • ChainSelector.accept_residue()
    • ChainSelector.accept_atom()
  • extract()
• Bio.PDB.实体模块
  • Entity
    • Entity.__init__()
    • 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.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()
  • 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.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模块
  • 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模块
  • HSExposureCA
    • HSExposureCA.__init__()
    • HSExposureCA.pcb_vectors_pymol()
  • HSExposureCB
    • HSExposureCB.__init__()
  • ExposureCN
    • ExposureCN.__init__()
• Bio.PDB.MMCIF2Dict模块
  • MMCIF2Dict
    • MMCIF2Dict.__init__()
• Bio.PDB.MMCIFParser模块
  • MMCIFParser
    • MMCIFParser.__init__()
    • MMCIFParser.get_structure()
  • FastMMCIFParser
    • FastMMCIFParser.__init__()
    • FastMMCIFParser.get_structure()
• Bio.PDB.Model模块
  • Model
    • Model.__init__()
    • Model.__repr__()
    • Model.get_chains()
    • Model.get_residues()
    • Model.get_atoms()
    • Model.atom_to_internal_coordinates()
    • Model.internal_to_atom_coordinates()
• Bio.PDB.NACCESS模块
  • run_naccess()
  • process_rsa_data()
  • process_asa_data()
  • NACCESS
    • NACCESS.__init__()
  • NACCESS_atomic
    • NACCESS_atomic.__init__()
• Bio.PDB.NeighborSearch模块
  • NeighborSearch
    • NeighborSearch.__init__()
    • NeighborSearch.search()
    • NeighborSearch.search_all()
• Bio.PDB.PDBExceptions模块
  • PDBException
  • PDBConstructionException
  • PDBConstructionWarning
• Bio.PDB.PDBIO模块
  • 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模块
  • 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.download_entire_pdb()
    • PDBList.download_obsolete_entries()
    • PDBList.get_seqres_file()
• Bio.PDB.PDBParser模块
  • PDBParser
    • PDBParser.__init__()
    • PDBParser.get_structure()
    • PDBParser.get_header()
    • PDBParser.get_trailer()
• Bio.PDB.PICIO模块
  • read_PIC()
  • enumerate_atoms()
  • pdb_date()
  • write_PIC()
• Bio.PDB.PSEA模块
  • run_psea()
  • psea()
  • psea2HEC()
  • annotate()
  • PSEA
    • PSEA.__init__()
    • PSEA.get_seq()
• Bio.PDB多肽模块
  • index_to_one()
  • one_to_index()
  • index_to_three()
  • three_to_index()
  • three_to_one()
  • one_to_three()
  • is_aa()
  • 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剩余模块
  • Residue
    • Residue.__init__()
    • Residue.__repr__()
    • Residue.add()
    • Residue.flag_disordered()
    • Residue.is_disordered()
    • Residue.get_resname()
    • Residue.get_unpacked_list()
    • Residue.get_segid()
    • Residue.get_atoms()
  • DisorderedResidue
    • DisorderedResidue.__init__()
    • DisorderedResidue.__repr__()
    • DisorderedResidue.add()
    • DisorderedResidue.sort()
    • DisorderedResidue.disordered_add()
    • DisorderedResidue.disordered_remove()
• Bio.PDB.ResidueDepth模块
  • get_surface()
  • min_dist()
  • residue_depth()
  • ca_depth()
  • ResidueDepth
    • ResidueDepth.__init__()
• Bio.PDB.SASA模块
  • ShrakeRupley
    • ShrakeRupley.__init__()
    • ShrakeRupley.compute()
• Bio.PDB.SCADIO模块
  • write_SCAD()
• Bio.PDB.选择模块
  • uniqueify()
  • get_unique_parents()
  • unfold_entities()
• Bio.PDB结构模块
  • 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()
• Bio.PDB.结构对齐模块
  • StructureAlignment
    • StructureAlignment.__init__()
    • StructureAlignment.get_maps()
    • StructureAlignment.get_iterator()
• Bio.PDB.结构构建器模块
  • 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模块
  • Superimposer
    • Superimposer.__init__()
    • Superimposer.set_atoms()
    • Superimposer.apply()
• Bio.PDB.celign模块
• Bio.PDB.ic_数据模块
• Bio.PDB.ic_重建模块
  • structure_rebuild_test()
  • report_IC()
  • IC_duplicate()
  • compare_residues()
  • write_PDB()
• Bio.PDB.内部_坐标模块
  • IC_Chain
    • IC_Chain.MaxPeptideBond
    • IC_Chain.__init__()
    • IC_Chain.clear_ic()
    • IC_Chain.set_residues()
    • IC_Chain.link_residues()
    • IC_Chain.assemble_residues()
    • IC_Chain.coords_to_structure()
    • IC_Chain.init_edra()
    • IC_Chain.init_atom_coords()
    • IC_Chain.internal_to_atom_coordinates()
    • IC_Chain.atom_to_internal_coordinates()
    • IC_Chain.write_SCAD()
  • IC_Residue
    • IC_Residue.accept_resnames
    • IC_Residue.AllBonds
    • IC_Residue.__init__()
    • IC_Residue.rak()
    • IC_Residue.build_rak_cache()
    • IC_Residue.accept_mainchain
    • IC_Residue.accept_hydrogens
    • IC_Residue.accept_deuteriums
    • IC_Residue.accept_atoms
    • IC_Residue.gly_Cbeta
    • IC_Residue.atm241()
    • IC_Residue.__repr__()
    • IC_Residue.pretty_str()
    • IC_Residue.load_PIC()
    • IC_Residue.link_dihedra()
    • IC_Residue.set_flexible()
    • IC_Residue.set_hbond()
    • IC_Residue.default_startpos()
    • IC_Residue.get_startpos()
    • IC_Residue.clear_transforms()
    • IC_Residue.assemble()
    • IC_Residue.atom_to_internal_coordinates()
    • IC_Residue.build_glyCB()
    • IC_Residue.write_PIC()
    • IC_Residue.coords_to_residue()
    • IC_Residue.relative_atom_re
    • IC_Residue.pick_angle()
    • IC_Residue.get_angle()
    • IC_Residue.set_angle()
    • 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.__init__()
    • Edron.gen_acs()
    • 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()
    • Hedron.cic
  • Dihedron
    • Dihedron.__init__()
    • Dihedron.__repr__()
    • Dihedron.set_hedra()
    • Dihedron.angle
    • Dihedron.cic
  • AtomKey
    • AtomKey.atom_re
    • AtomKey.endnum_re
    • AtomKey.fieldNames
    • AtomKey.fieldsDef
      • AtomKey.fieldsDef.__getnewargs__()
      • AtomKey.fieldsDef.__new__()
      • AtomKey.fieldsDef.__repr__()
      • AtomKey.fieldsDef.__slots__
      • AtomKey.fieldsDef.altloc
      • AtomKey.fieldsDef.atm
      • AtomKey.fieldsDef.icode
      • AtomKey.fieldsDef.occ
      • AtomKey.fieldsDef.resname
      • AtomKey.fieldsDef.respos
    • AtomKey.fields
    • AtomKey.d2h
    • AtomKey.__init__()
    • AtomKey.__repr__()
    • AtomKey.__hash__()
    • AtomKey.altloc_match()
    • AtomKey.__ne__()
    • AtomKey.__eq__()
    • AtomKey.__gt__()
    • AtomKey.__ge__()
    • AtomKey.__lt__()
    • AtomKey.__le__()
  • set_accuracy_95()
  • HedronMatchError
  • MissingAtomError
• Bio.PDB.mmcifio模块
  • MMCIFIO
    • MMCIFIO.__init__()
    • MMCIFIO.set_dict()
    • MMCIFIO.save()
• Bio.PDB.parse_PDB_Header模块
  • parse_pdb_header()
• Bio.PDB.qcprot模块
• Bio.PDB.Vector模块
  • 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()

模块内容

处理大分子晶体结构的课程。

包括：PDB和MMCIF解析器、结构类、使PDB的本地副本保持最新的模块、PDB文件的选择性IO等。

原作者：托马斯·哈梅莱克(Thomas Hamelryck)。撰稿人：-Peter Cock-Joe Greener-Rob Miller-Lenna X.Peterson-Joao Rodrigues-Kristian Rther-Eric Talevich-以及许多其他人。