Index

A

accessible_atoms() (molecupy.structures.atoms.Atom method) add_atom() (molecupy.structures.molecules.AtomicStructure method) add_atoms_to_data_file() (in module molecupy.converters.model2pdbdatafile) add_bind_site() (molecupy.structures.models.Model method) add_chain() (molecupy.structures.complexes.Complex method) (molecupy.structures.models.Model method) add_chains_to_model() (in module molecupy.converters.pdbdatafile2model) add_complex() (molecupy.structures.models.Model method) add_complexes_to_data_file() (in module molecupy.converters.model2pdbdatafile) add_connections_to_data_file() (in module molecupy.converters.model2pdbdatafile) add_record() (molecupy.pdb.pdbfile.PdbFile method) add_residue() (molecupy.structures.chains.ResiduicSequence method) (molecupy.structures.chains.ResiduicStructure method)

add_small_molecule() (molecupy.structures.models.Model method) add_small_molecules_to_model() (in module molecupy.converters.pdbdatafile2model) alpha_carbon() (molecupy.structures.molecules.Residue method) alpha_helices() (molecupy.structures.chains.Chain method) AlphaHelix (class in molecupy.structures.chains) Atom (class in molecupy.structures.atoms) atom_id() (molecupy.structures.atoms.GhostAtom method) atom_name() (molecupy.structures.atoms.GhostAtom method) AtomicStructure (class in molecupy.structures.molecules) atoms() (molecupy.structures.atoms.Bond method) (molecupy.structures.molecules.AtomicStructure method) authors() (molecupy.pdb.pdb.Pdb method)

B

beta_strands() (molecupy.structures.chains.Chain method) BetaStrand (class in molecupy.structures.chains) bind_site() (molecupy.structures.molecules.SmallMolecule method) bind_sites() (molecupy.structures.models.Model method) BindSite (class in molecupy.structures.chains) Bond (class in molecupy.structures.atoms) bond_length() (molecupy.structures.atoms.Bond method) bond_residue_atoms() (in module molecupy.converters.pdbdatafile2model)

bond_residues_together() (in module molecupy.converters.pdbdatafile2model) bond_to() (molecupy.structures.atoms.Atom method) bonded_atoms() (molecupy.structures.atoms.Atom method) bonds() (molecupy.structures.atoms.Atom method) break_bond_with() (molecupy.structures.atoms.Atom method) BrokenHelixError BrokenStrandError

C

caveat() (molecupy.pdb.pdb.Pdb method) center_of_mass() (molecupy.structures.molecules.AtomicStructure method) Chain (class in molecupy.structures.chains) chain() (molecupy.structures.chains.AlphaHelix method) (molecupy.structures.chains.BetaStrand method) (molecupy.structures.molecules.Residue method) chain_id() (molecupy.structures.chains.Chain method) chains() (molecupy.structures.complexes.Complex method) (molecupy.structures.models.Model method) classification() (molecupy.pdb.pdb.Pdb method) (molecupy.pdb.pdbdatafile.PdbDataFile method) comment() (molecupy.structures.chains.AlphaHelix method) Complex (class in molecupy.structures.complexes) complex() (molecupy.structures.chains.Chain method) complex_id() (molecupy.structures.complexes.Complex method)

complex_name() (molecupy.structures.complexes.Complex method) complexes() (molecupy.structures.models.Model method) connect_atoms() (in module molecupy.converters.pdbdatafile2model) connect_to() (molecupy.structures.molecules.Residue method) contacts_with() (molecupy.structures.molecules.AtomicStructure method) content() (molecupy.pdb.pdbfile.PdbRecord method) continuous_sequence() (molecupy.structures.chains.BindSite method) convert_to_string() (molecupy.pdb.pdbfile.PdbFile method) create_atom_records() (in module molecupy.converters.pdbdatafile2pdbfile) create_compnd_records() (in module molecupy.converters.pdbdatafile2pdbfile) create_conect_records() (in module molecupy.converters.pdbdatafile2pdbfile)

D

data_file() (molecupy.pdb.pdb.Pdb method) delete() (molecupy.structures.atoms.Bond method) deposition_date() (molecupy.pdb.pdb.Pdb method) disconnect_from() (molecupy.structures.molecules.Residue method) distance_to() (molecupy.structures.atoms.Atom method) downstream_residue() (molecupy.structures.molecules.Residue method) duplicate_chain() (molecupy.structures.models.Model method) duplicate_complex() (molecupy.structures.models.Model method)

duplicate_small_molecule() (molecupy.structures.models.Model method) DuplicateAtomsError DuplicateBindSitesError DuplicateChainsError DuplicateComplexesError DuplicateResiduesError DuplicateSmallMoleculesError

E

element() (molecupy.structures.atoms.GhostAtom method)

experimental_techniques() (molecupy.pdb.pdb.Pdb method)

F

formula() (molecupy.structures.molecules.AtomicStructure method)

G

get_as_string() (molecupy.pdb.pdbfile.PdbRecord method) get_atom_by_element() (molecupy.structures.molecules.AtomicStructure method) get_atom_by_id() (molecupy.structures.molecules.AtomicStructure method) get_atom_by_name() (molecupy.structures.molecules.AtomicStructure method) get_atoms_by_element() (molecupy.structures.molecules.AtomicStructure method) get_atoms_by_name() (molecupy.structures.molecules.AtomicStructure method) get_bind_site_by_id() (molecupy.structures.models.Model method) get_bond_with() (molecupy.structures.atoms.Atom method) get_chain_by_id() (molecupy.structures.models.Model method) get_complex_by_id() (molecupy.structures.models.Model method) get_complex_by_name() (molecupy.structures.models.Model method) get_complexes_by_name() (molecupy.structures.models.Model method) get_helix_by_id() (molecupy.structures.chains.Chain method) get_pdb_from_file() (in module molecupy.pdb.access) get_pdb_remotely() (in module molecupy.pdb.access)

get_record_by_name() (molecupy.pdb.pdbfile.PdbFile method) get_records_by_name() (molecupy.pdb.pdbfile.PdbFile method) get_residue_by_id() (molecupy.structures.chains.ResiduicStructure method) get_residue_by_name() (molecupy.structures.chains.ResiduicStructure method) get_residues_by_name() (molecupy.structures.chains.ResiduicStructure method) get_small_molecule_by_id() (molecupy.structures.models.Model method) get_small_molecule_by_name() (molecupy.structures.models.Model method) get_small_molecules_by_name() (molecupy.structures.models.Model method) get_strand_by_id() (molecupy.structures.chains.Chain method) GhostAtom (class in molecupy.structures.atoms) give_model_alpha_helices() (in module molecupy.converters.pdbdatafile2model) give_model_beta_strands() (in module molecupy.converters.pdbdatafile2model) give_model_complexes() (in module molecupy.converters.pdbdatafile2model) give_model_sites() (in module molecupy.converters.pdbdatafile2model)

H

helix_class() (molecupy.structures.chains.AlphaHelix method)

helix_id() (molecupy.structures.chains.AlphaHelix method)

I

internal_contacts() (molecupy.structures.molecules.AtomicStructure method) InvalidPdbCodeError

is_missing() (molecupy.structures.molecules.Residue method) is_obsolete() (molecupy.pdb.pdb.Pdb method)

J

journal() (molecupy.pdb.pdb.Pdb method)

K

keywords() (molecupy.pdb.pdb.Pdb method)

L

ligand() (molecupy.structures.chains.BindSite method) local_atoms() (molecupy.structures.atoms.Atom method)

location() (molecupy.structures.atoms.Atom method) LongBondWarning

M

make_disulphide_bonds() (in module molecupy.converters.pdbdatafile2model) make_link_bonds() (in module molecupy.converters.pdbdatafile2model) map_sites_to_ligands() (in module molecupy.converters.pdbdatafile2model) mass() (molecupy.structures.atoms.GhostAtom method) (molecupy.structures.molecules.AtomicStructure method) Model (class in molecupy.structures.models) model() (molecupy.pdb.pdb.Pdb method) (molecupy.structures.atoms.GhostAtom method) (molecupy.structures.chains.BindSite method) (molecupy.structures.chains.Chain method) (molecupy.structures.complexes.Complex method) (molecupy.structures.molecules.SmallMolecule method) model_annotations() (molecupy.pdb.pdb.Pdb method) model_count() (molecupy.pdb.pdb.Pdb method) model_from_pdb_data_file() (in module molecupy.converters.pdbdatafile2model) models() (molecupy.pdb.pdb.Pdb method) molecule() (molecupy.structures.atoms.GhostAtom method) molecule_id() (molecupy.structures.molecules.SmallMolecule method) molecule_name() (molecupy.structures.molecules.SmallMolecule method) molecupy.converters.model2pdbdatafile (module)

molecupy.converters.pdbdatafile2model (module) molecupy.converters.pdbdatafile2pdbfile (module) molecupy.converters.pdbfile2pdbdatafile (module) molecupy.exceptions (module) molecupy.pdb.access (module) molecupy.pdb.pdb (module) molecupy.pdb.pdbdatafile (module) molecupy.pdb.pdbfile (module) molecupy.structures.atoms (module) molecupy.structures.chains (module) molecupy.structures.complexes (module) molecupy.structures.models (module) molecupy.structures.molecules (module) MultipleResidueConnectionError

N

name() (molecupy.pdb.pdbfile.PdbRecord method) NoAtomsError

NoResiduesError number() (molecupy.pdb.pdbfile.PdbRecord method)

O

obsolete_date() (molecupy.pdb.pdb.Pdb method)

P

Pdb (class in molecupy.pdb.pdb) pdb_code() (molecupy.pdb.pdb.Pdb method) pdb_data_file_from_model() (in module molecupy.converters.model2pdbdatafile) pdb_data_file_from_pdb_file() (in module molecupy.converters.pdbfile2pdbdatafile) pdb_data_file_from_string() (in module molecupy.pdb.access) pdb_file() (molecupy.pdb.pdbfile.PdbRecord method) pdb_file_from_pdb_data_file() (in module molecupy.converters.pdbdatafile2pdbfile) pdb_file_from_string() (in module molecupy.pdb.access) pdb_from_string() (in module molecupy.pdb.access) PdbDataFile (class in molecupy.pdb.pdbdatafile) PdbFile (class in molecupy.pdb.pdbfile) PdbRecord (class in molecupy.pdb.pdbfile) predict_bind_site() (molecupy.structures.molecules.AtomicStructure method) process_anisou_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_atom_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_author_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_caveat_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_cispep_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_compnd_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_conect_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_cryst1_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_dbref_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_expdta_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_formul_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_header_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_helix_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_het_records() (in module molecupy.converters.pdbfile2pdbdatafile)

process_hetatm_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_hetnam_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_hetsyn_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_jrnl_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_keywd_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_link_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_master_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_mdltyp_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_model_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_modres_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_mtrix_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_nummdl_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_obslte_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_origx_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_remark_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_revdat_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_scale_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_seqadv_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_seqres_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_sheet_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_site_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_source_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_split_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_sprsde_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_ssbond_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_ter_records() (in module molecupy.converters.pdbfile2pdbdatafile) process_title_records() (in module molecupy.converters.pdbfile2pdbdatafile)

R

radius_of_gyration() (molecupy.structures.molecules.AtomicStructure method) records() (molecupy.pdb.pdbfile.PdbFile method) remove_atom() (molecupy.structures.molecules.AtomicStructure method) remove_bind_site() (molecupy.structures.models.Model method) remove_chain() (molecupy.structures.complexes.Complex method) (molecupy.structures.models.Model method) remove_complex() (molecupy.structures.models.Model method) remove_record() (molecupy.pdb.pdbfile.PdbFile method) remove_residue() (molecupy.structures.chains.ResiduicStructure method) remove_small_molecule() (molecupy.structures.models.Model method)

replacement_code() (molecupy.pdb.pdb.Pdb method) Residue (class in molecupy.structures.molecules) residue_id() (molecupy.structures.molecules.Residue method) residue_name() (molecupy.structures.molecules.Residue method) residues() (molecupy.structures.chains.ResiduicSequence method) (molecupy.structures.chains.ResiduicStructure method) ResiduicSequence (class in molecupy.structures.chains) ResiduicStructure (class in molecupy.structures.chains) revisions() (molecupy.pdb.pdb.Pdb method) rotate() (molecupy.structures.molecules.AtomicStructure method)

S

save_as_pdb() (molecupy.structures.models.Model method) sense() (molecupy.structures.chains.BetaStrand method) sequence_string() (molecupy.structures.chains.ResiduicSequence method) site_id() (molecupy.structures.chains.BindSite method) small_molecules() (molecupy.structures.models.Model method) SmallMolecule (class in molecupy.structures.molecules)

source() (molecupy.pdb.pdbdatafile.PdbDataFile method) (molecupy.pdb.pdbfile.PdbFile method) (molecupy.structures.models.Model method) split_codes() (molecupy.pdb.pdb.Pdb method) strand_id() (molecupy.structures.chains.BetaStrand method) supercede_date() (molecupy.pdb.pdb.Pdb method) supercedes() (molecupy.pdb.pdb.Pdb method)

T

text() (molecupy.pdb.pdbfile.PdbRecord method) title() (molecupy.pdb.pdb.Pdb method) to_pdb_data_file() (molecupy.pdb.pdbfile.PdbFile method) (molecupy.structures.models.Model method)

to_pdb_file() (molecupy.pdb.pdbdatafile.PdbDataFile method) translate() (molecupy.structures.molecules.AtomicStructure method)

U

upstream_residue() (molecupy.structures.molecules.Residue method)

X

x() (molecupy.structures.atoms.Atom method)

Y

y() (molecupy.structures.atoms.Atom method)

Z

z() (molecupy.structures.atoms.Atom method)