Index

A

add_atom() (ihm.model.Model method) (ihm.startmodel.StartingModel method) add_distance_restraint() (ihm.flr.FRETDistanceRestraintGroup method) add_entry() (ihm.flr.Experiment method) add_lifetime() (ihm.flr.RefMeasurement method) add_model() (ihm.model.DCDWriter method) add_primary() (ihm.dataset.Dataset method) add_ref_measurement() (ihm.flr.RefMeasurementGroup method) add_seq_dif() (ihm.startmodel.StartingModel method) add_sphere() (ihm.model.Model method) Alignment (class in ihm.reference) alignments (ihm.reader.SystemReader attribute) (ihm.reference.Sequence attribute) Alphabet (class in ihm) alphafold2 (in module ihm.citations) AlphaFoldDBLocation (class in ihm.location) analyses (ihm.protocol.Protocol attribute) (ihm.reader.SystemReader attribute)

Analysis (class in ihm.analysis) analysis_steps (ihm.reader.SystemReader attribute) assemblies (ihm.reader.SystemReader attribute) Assembly (class in ihm) asym_units (ihm.reader.SystemReader attribute) (ihm.System attribute) AsymUnit (class in ihm) AsymUnitRange (class in ihm) Atom (class in ihm) (class in ihm.model) atom() (ihm.Residue method) AtomCrossLink (class in ihm.restraint) AtomFeature (class in ihm.restraint) AtomicSegment (class in ihm.representation) auth_seq_id (ihm.Residue attribute) authors (ihm.System attribute) Axis (class in ihm.geometry)

B

BinaryCifReader (class in ihm.format_bcif) BinaryCifWriter (class in ihm.format_bcif) BioGRIDLocation (class in ihm.location) BMRBLocation (class in ihm.location) bmso (in module ihm.cross_linkers)

branch_descriptors (ihm.Entity attribute) branch_links (ihm.Entity attribute) BranchDescriptor (class in ihm) BranchLink (class in ihm) bs3 (in module ihm.cross_linkers)

C

case_sensitive (ihm.dictionary.ItemType attribute) categories (ihm.dictionary.Dictionary attribute) Category (class in ihm.dictionary) category() (ihm.format.CifWriter method) (ihm.format_bcif.BinaryCifWriter method) Center (class in ihm.geometry) CenterGeometricRestraint (class in ihm.restraint) centers (ihm.reader.SystemReader attribute) chem_comps (ihm.reader.SystemReader attribute) chem_descriptors (ihm.reader.SystemReader attribute) ChemComp (class in ihm) ChemDescriptor (class in ihm) CIFParser (class in ihm.metadata) CifParserError CifReader (class in ihm.format) CifWriter (class in ihm.format) Citation (class in ihm) citations (ihm.reader.SystemReader attribute) (ihm.System attribute)

clustering_feature (ihm.model.Ensemble attribute) clustering_method (ihm.model.Ensemble attribute) ClusterStep (class in ihm.analysis) colabfold (in module ihm.citations) Collection (class in ihm) collections (ihm.System attribute) comments (ihm.System attribute) comp (ihm.Residue attribute) ComparativeModelDataset (class in ihm.dataset) complete_assembly (ihm.System attribute) contains() (ihm.flr.Experiment method) copy_if_present() (ihm.reader.Handler method) cross_link_pseudo_sites (ihm.reader.SystemReader attribute) cross_links (ihm.reader.SystemReader attribute) (ihm.restraint.CrossLinkRestraint attribute) CrossLink (class in ihm.restraint) CrossLinkFit (class in ihm.restraint) CrossLinkPseudoSite (class in ihm.restraint) CrossLinkRestraint (class in ihm.restraint) CXMSDataset (class in ihm.dataset)

D

data_transformations (ihm.reader.SystemReader attribute) DatabaseLocation (class in ihm.location) Dataset (class in ihm.dataset) dataset_groups (ihm.reader.SystemReader attribute) DatasetGroup (class in ihm.dataset) datasets (ihm.reader.SystemReader attribute) db_locations (ihm.reader.SystemReader attribute) DCDWriter (class in ihm.model) DeNovoModelDataset (class in ihm.dataset) densities (ihm.model.Ensemble attribute) (ihm.reader.SystemReader attribute) DerivedDistanceRestraint (class in ihm.restraint) description (ihm.dictionary.Category attribute) Details (class in ihm.source) dhso (in module ihm.cross_linkers) Dictionary (class in ihm.dictionary) disopred (in module ihm.citations) dist_restraint_groups (ihm.reader.SystemReader attribute) dist_restraints (ihm.reader.SystemReader attribute) distance_lower_limit (ihm.restraint.DistanceRestraint attribute) (ihm.restraint.HarmonicDistanceRestraint attribute) (ihm.restraint.LowerBoundDistanceRestraint attribute) (ihm.restraint.UpperBoundDistanceRestraint attribute)

distance_restraint_groups (ihm.flr.FLRData attribute) distance_upper_limit (ihm.restraint.DistanceRestraint attribute) (ihm.restraint.HarmonicDistanceRestraint attribute) (ihm.restraint.LowerBoundDistanceRestraint attribute) (ihm.restraint.UpperBoundDistanceRestraint attribute) DistanceRestraint (class in ihm.restraint) DNAAlphabet (class in ihm) DNAChemComp (class in ihm) DPeptideAlphabet (class in ihm) DPeptideChemComp (class in ihm) DSaccharideAlphaChemComp (class in ihm) DSaccharideBetaChemComp (class in ihm) DSaccharideChemComp (class in ihm) dsbu (in module ihm.cross_linkers) dsg (in module ihm.cross_linkers) dss (in module ihm.cross_linkers) dsso (in module ihm.cross_linkers) dump() (ihm.dumper.Dumper method) Dumper (class in ihm.dumper)

E

edc (in module ihm.cross_linkers) em2d_restraints (ihm.reader.SystemReader attribute) EM2DClassDataset (class in ihm.dataset) EM2DRestraint (class in ihm.restraint) EM2DRestraintFit (class in ihm.restraint) em3d_restraints (ihm.reader.SystemReader attribute) EM3DRestraint (class in ihm.restraint) EM3DRestraintFit (class in ihm.restraint) EMDBLocation (class in ihm.location) EMDensityDataset (class in ihm.dataset) EMMicrographsDataset (class in ihm.dataset) EMPIARLocation (class in ihm.location) EmptyStep (class in ihm.analysis) end_save_frame() (ihm.reader.Handler method) Ensemble (class in ihm.model)

EnsembleFRETDataset (class in ihm.dataset) ensembles (ihm.reader.SystemReader attribute) (ihm.System attribute) entities (ihm.reader.SystemReader attribute) (ihm.System attribute) Entity (class in ihm) EntityAssembly (class in ihm.flr) EntityRange (class in ihm) enumeration (ihm.dictionary.Keyword attribute) ExpCondition (class in ihm.flr) Experiment (class in ihm.flr) experimental_cross_links (ihm.restraint.CrossLinkRestraint attribute) experimental_xl_groups (ihm.reader.SystemReader attribute) experimental_xls (ihm.reader.SystemReader attribute) ExperimentalCrossLink (class in ihm.restraint) external_files (ihm.reader.SystemReader attribute)

F

Feature (class in ihm.restraint) feature (ihm.analysis.Step attribute) FeatureCrossLink (class in ihm.restraint) features (ihm.reader.SystemReader attribute) FeatureSegment (class in ihm.representation) FileLocation (class in ihm.location) FilterStep (class in ihm.analysis) finalize() (ihm.dumper.Dumper method) (ihm.reader.Handler method) fits (ihm.restraint.AtomCrossLink attribute) (ihm.restraint.EM2DRestraint attribute) (ihm.restraint.EM3DRestraint attribute) (ihm.restraint.FeatureCrossLink attribute) (ihm.restraint.ResidueCrossLink attribute) (ihm.restraint.SASRestraint attribute) flr_data (ihm.reader.SystemReader attribute) (ihm.System attribute) flr_entity_assemblies (ihm.reader.SystemReader attribute) flr_exp_conditions (ihm.reader.SystemReader attribute) flr_experiments (ihm.reader.SystemReader attribute) flr_fps_av_modeling (ihm.reader.SystemReader attribute) flr_fps_av_parameters (ihm.reader.SystemReader attribute) flr_fps_global_parameters (ihm.reader.SystemReader attribute) flr_fps_mean_probe_positions (ihm.reader.SystemReader attribute) flr_fps_modeling (ihm.reader.SystemReader attribute) flr_fps_mpp_atom_position_groups (ihm.reader.SystemReader attribute) flr_fps_mpp_atom_positions (ihm.reader.SystemReader attribute) flr_fps_mpp_modeling (ihm.reader.SystemReader attribute) flr_fret_analyses (ihm.reader.SystemReader attribute) flr_fret_calibration_parameters (ihm.reader.SystemReader attribute) flr_fret_distance_restraint_groups (ihm.reader.SystemReader attribute) flr_fret_distance_restraints (ihm.reader.SystemReader attribute) flr_fret_forster_radius (ihm.reader.SystemReader attribute) flr_fret_model_distances (ihm.reader.SystemReader attribute) flr_fret_model_qualities (ihm.reader.SystemReader attribute) flr_inst_settings (ihm.reader.SystemReader attribute)

flr_instruments (ihm.reader.SystemReader attribute) flr_lifetime_fit_models (ihm.reader.SystemReader attribute) flr_peak_assignments (ihm.reader.SystemReader attribute) flr_poly_probe_conjugates (ihm.reader.SystemReader attribute) flr_poly_probe_positions (ihm.reader.SystemReader attribute) flr_probes (ihm.reader.SystemReader attribute) flr_ref_measurement_groups (ihm.reader.SystemReader attribute) flr_ref_measurement_lifetimes (ihm.reader.SystemReader attribute) flr_ref_measurements (ihm.reader.SystemReader attribute) flr_sample_conditions (ihm.reader.SystemReader attribute) flr_sample_probe_details (ihm.reader.SystemReader attribute) flr_samples (ihm.reader.SystemReader attribute) FLRData (class in ihm.flr) formula_weight (ihm.ChemComp attribute) (ihm.Entity attribute) fps_modeling (ihm.flr.FLRData attribute) FPSAVModeling (class in ihm.flr) FPSAVParameter (class in ihm.flr) FPSGlobalParameters (class in ihm.flr) FPSMeanProbePosition (class in ihm.flr) FPSModeling (class in ihm.flr) FPSMPPAtomPosition (class in ihm.flr) FPSMPPAtomPositionGroup (class in ihm.flr) FPSMPPModeling (class in ihm.flr) fret_model_distances (ihm.flr.FLRData attribute) fret_model_qualities (ihm.flr.FLRData attribute) FRETAnalysis (class in ihm.flr) FRETCalibrationParameters (class in ihm.flr) FRETDataset (class in ihm.dataset) FRETDistanceRestraint (class in ihm.flr) FRETDistanceRestraintGroup (class in ihm.flr) FRETForsterRadius (class in ihm.flr) FRETModelDistance (class in ihm.flr) FRETModelQuality (class in ihm.flr) from_accession() (ihm.reference.UniProtSequence class method) from_pubmed_id() (ihm.Citation class method)

G

GeneticInteractionsDataset (class in ihm.dataset) geom_restraints (ihm.reader.SystemReader attribute) GeometricObject (class in ihm.geometry) GeometricRestraint (class in ihm.restraint) geometries (ihm.reader.SystemReader attribute) get() (ihm.reader.RangeIDMapper method) get_all() (ihm.reader.IDMapper method) get_atoms() (ihm.model.Model method) (ihm.startmodel.StartingModel method) get_audit_conform_handler() (ihm.reader.Variant method) get_bool() (ihm.reader.Handler method) get_by_id() (ihm.reader.IDMapper method)

get_by_id_or_none() (ihm.reader.IDMapper method) get_dumpers() (ihm.dumper.Variant method) get_entry_by_index() (ihm.flr.Experiment method) get_float() (ihm.reader.Handler method) get_handlers() (ihm.reader.Variant method) get_int() (ihm.reader.Handler method) get_int_or_string() (ihm.reader.Handler method) get_lower() (ihm.reader.Handler method) get_seq_dif() (ihm.startmodel.StartingModel method) get_spheres() (ihm.model.Model method) get_system_writer() (ihm.dumper.Variant method) Grant (class in ihm) grants (ihm.System attribute)

H

HalfTorus (class in ihm.geometry) Handler (class in ihm.reader)

HarmonicDistanceRestraint (class in ihm.restraint) HDXDataset (class in ihm.dataset) hhpred (in module ihm.citations)

I

IDMapper (class in ihm.reader) ignored_keywords (ihm.reader.Handler attribute) IgnoreVariant (class in ihm.dumper) ihm (module) ihm.analysis (module) ihm.citations (module) ihm.cross_linkers (module) ihm.dataset (module) ihm.dictionary (module) ihm.dumper (module) ihm.flr (module) ihm.format (module) ihm.format_bcif (module) ihm.geometry (module) ihm.location (module) ihm.metadata (module) ihm.model (module) ihm.protocol (module) ihm.reader (module)

ihm.reference (module) ihm.representation (module) ihm.restraint (module) ihm.source (module) ihm.startmodel (module) IHMVariant (class in ihm.dumper) (class in ihm.reader) imp (in module ihm.citations) IndependentSubsample (class in ihm.model) InnerSurfaceGeometricRestraint (class in ihm.restraint) InputFileLocation (class in ihm.location) ins_code (ihm.Residue attribute) Instrument (class in ihm.flr) InstSetting (class in ihm.flr) IntegrativeModelDataset (class in ihm.dataset) IProXLocation (class in ihm.location) is_branched() (ihm.Entity method) is_polymeric() (ihm.Entity method) item_type (ihm.dictionary.Keyword attribute) ItemType (class in ihm.dictionary)

J

JPOSTLocation (class in ihm.location)

K

Keyword (class in ihm.dictionary)

keywords (ihm.dictionary.Category attribute)

L

LifetimeFitModel (class in ihm.flr) linked_items (ihm.dictionary.Dictionary attribute) LocalizationDensity (class in ihm.model) Location (class in ihm.location) locations (ihm.System attribute) loop() (ihm.format.CifWriter method) (ihm.format_bcif.BinaryCifWriter method)

LowerBoundDistanceRestraint (class in ihm.restraint) LowerUpperBoundDistanceRestraint (class in ihm.restraint) LPeptideAlphabet (class in ihm) LPeptideChemComp (class in ihm) LSaccharideAlphaChemComp (class in ihm) LSaccharideBetaChemComp (class in ihm) LSaccharideChemComp (class in ihm)

M

mandatory (ihm.dictionary.Category attribute) (ihm.dictionary.Keyword attribute) Manipulated (class in ihm.source) MassIVELocation (class in ihm.location) MassSpecDataset (class in ihm.dataset) MEAN_LENGTH (ihm.startmodel.SequenceIdentityDenominator attribute) mmseqs2 (in module ihm.citations) Model (class in ihm.model)

model_groups (ihm.reader.SystemReader attribute) ModelArchiveLocation (class in ihm.location) ModelGroup (class in ihm.model) modeller (in module ihm.citations) models (ihm.reader.SystemReader attribute) MRCParser (class in ihm.metadata) MSESeqDif (class in ihm.startmodel) MultiResidueSegment (class in ihm.representation) MutagenesisDataset (class in ihm.dataset)

N

name (ihm.dictionary.Category attribute) (ihm.dictionary.Keyword attribute) Natural (class in ihm.source) NMRDataset (class in ihm.dataset) NonPolyFeature (class in ihm.restraint) NonPolymerChemComp (class in ihm)

not_in_file (ihm.reader.Handler attribute) NUM_ALIGNED_WITH_GAPS (ihm.startmodel.SequenceIdentityDenominator attribute) NUM_ALIGNED_WITHOUT_GAPS (ihm.startmodel.SequenceIdentityDenominator attribute) num_models_deposited (ihm.model.Ensemble attribute) (ihm.model.Subsample attribute) number_of_molecules (ihm.WaterAsymUnit attribute)

O

OldFileError omitted (ihm.reader.Handler attribute) ordered_processes (ihm.System attribute) ordered_procs (ihm.reader.SystemReader attribute) ordered_steps (ihm.reader.SystemReader attribute) OrderedProcess (class in ihm.model) orphan_assemblies (ihm.System attribute) orphan_chem_descriptors (ihm.System attribute) orphan_dataset_groups (ihm.System attribute)

orphan_datasets (ihm.System attribute) orphan_features (ihm.System attribute) orphan_geometric_objects (ihm.System attribute) orphan_protocols (ihm.System attribute) orphan_pseudo_sites (ihm.System attribute) orphan_representations (ihm.System attribute) orphan_starting_models (ihm.System attribute) OTHER (ihm.startmodel.SequenceIdentityDenominator attribute) OuterSurfaceGeometricRestraint (class in ihm.restraint) OutputFileLocation (class in ihm.location)

P

parent (ihm.Assembly attribute) parents (ihm.dataset.Dataset attribute) parse_file() (ihm.metadata.CIFParser method) (ihm.metadata.MRCParser method) (ihm.metadata.PDBParser method) (ihm.metadata.Parser method) Parser (class in ihm.metadata) PDBDataset (class in ihm.dataset) PDBDevLocation (class in ihm.location) PDBHelix (class in ihm.startmodel) PDBLocation (class in ihm.location) PDBParser (class in ihm.metadata) PeakAssignment (class in ihm.flr) PeptideChemComp (class in ihm) photo_leucine (in module ihm.cross_linkers) phoX (in module ihm.cross_linkers) phyre2 (in module ihm.citations) Plane (class in ihm.geometry) pmi (in module ihm.citations)

poly_probe_conjugates (ihm.flr.FLRData attribute) PolyProbeConjugate (class in ihm.flr) PolyProbePosition (class in ihm.flr) pred_cont_restraint_groups (ihm.reader.SystemReader attribute) pred_cont_restraints (ihm.reader.SystemReader attribute) PredictedContactRestraint (class in ihm.restraint) PRIDELocation (class in ihm.location) Probe (class in ihm.flr) ProbeDescriptor (class in ihm.flr) ProbeList (class in ihm.flr) ProcessEdge (class in ihm.model) ProcessStep (class in ihm.model) Protocol (class in ihm.protocol) protocols (ihm.reader.SystemReader attribute) ProXLLocation (class in ihm.location) pseudo_sites (ihm.reader.SystemReader attribute) PseudoSite (class in ihm.restraint) PseudoSiteFeature (class in ihm.restraint) psipred (in module ihm.citations)

Q

qmeandisco (in module ihm.citations)

R

RandomSubsample (class in ihm.model) RangeIDMapper (class in ihm.reader) ranges (ihm.reader.SystemReader attribute) read() (in module ihm.dictionary) (in module ihm.reader) read_file() (ihm.format.CifReader method) (ihm.format_bcif.BinaryCifReader method) Reference (class in ihm.reference) references (ihm.reader.SystemReader attribute) RefMeasurement (class in ihm.flr) RefMeasurementGroup (class in ihm.flr) RefMeasurementLifetime (class in ihm.flr) relion (in module ihm.citations) report() (ihm.System method) repos (ihm.reader.SystemReader attribute) Repository (class in ihm.location)

Representation (class in ihm.representation) representations (ihm.reader.SystemReader attribute) RescoreStep (class in ihm.analysis) Residue (class in ihm) residue() (ihm.AsymUnit method) (ihm.Entity method) residue1 (ihm.restraint.ResidueCrossLink attribute) residue2 (ihm.restraint.ResidueCrossLink attribute) ResidueCrossLink (class in ihm.restraint) ResidueFeature (class in ihm.restraint) ResidueSegment (class in ihm.representation) Restraint (class in ihm.restraint) restraint_groups (ihm.System attribute) RestraintGroup (class in ihm.restraint) restraints (ihm.System attribute) RNAAlphabet (class in ihm) RNAChemComp (class in ihm)

S

SaccharideChemComp (class in ihm) Sample (class in ihm.flr) SampleCondition (class in ihm.flr) SampleProbeDetails (class in ihm.flr) sas_restraints (ihm.reader.SystemReader attribute) SASBDBLocation (class in ihm.location) SASDataset (class in ihm.dataset) SASRestraint (class in ihm.restraint) SASRestraintFit (class in ihm.restraint) sda (in module ihm.cross_linkers) Segment (class in ihm.representation) segment() (ihm.AsymUnit method) seq_id_range (ihm.AsymUnit attribute) (ihm.Entity attribute) (ihm.WaterAsymUnit attribute) SeqDif (class in ihm.reference) (class in ihm.startmodel) Sequence (class in ihm.reference) sequence (ihm.AsymUnit attribute) (ihm.WaterAsymUnit attribute) SequenceIdentity (class in ihm.startmodel) SequenceIdentityDenominator (class in ihm.startmodel) set() (ihm.reader.RangeIDMapper method) set_line_wrap() (in module ihm.dumper) SHORTER_LENGTH (ihm.startmodel.SequenceIdentityDenominator attribute) Software (class in ihm) software (ihm.reader.SystemReader attribute) (ihm.System attribute) Source (class in ihm.source)

Sphere (class in ihm.geometry) (class in ihm.model) src_gens (ihm.reader.SystemReader attribute) src_nats (ihm.reader.SystemReader attribute) src_syns (ihm.reader.SystemReader attribute) start_block() (ihm.format.CifWriter method) (ihm.format_bcif.BinaryCifWriter method) starting_models (ihm.reader.SystemReader attribute) StartingModel (class in ihm.startmodel) State (class in ihm.model) state_groups (ihm.reader.SystemReader attribute) (ihm.System attribute) StateGroup (class in ihm.model) states (ihm.reader.SystemReader attribute) Step (class in ihm.analysis) (class in ihm.protocol) steps (ihm.analysis.Analysis attribute) (ihm.model.OrderedProcess attribute) (ihm.protocol.Protocol attribute) strand_id (ihm.AsymUnit attribute) Subsample (class in ihm.model) subsamples (ihm.model.Ensemble attribute) swiss_model (in module ihm.citations) Synthetic (class in ihm.source) sysr (ihm.reader.Handler attribute) System (class in ihm) system (ihm.reader.Handler attribute) (ihm.reader.SystemReader attribute) system_reader (ihm.reader.Variant attribute) SystemReader (class in ihm.reader)

T

tbuphoX (in module ihm.cross_linkers) Template (class in ihm.startmodel) Torus (class in ihm.geometry)

Transformation (class in ihm.geometry) transformations (ihm.reader.SystemReader attribute) TransformedDataset (class in ihm.dataset)

U

UniProtSequence (class in ihm.reference) unknown (ihm.reader.Handler attribute) (in module ihm)

UnknownCategoryWarning UnknownKeywordWarning update_locations_in_repositories() (ihm.System method) UpperBoundDistanceRestraint (class in ihm.restraint)

V

validate() (ihm.dictionary.Dictionary method) ValidationStep (class in ihm.analysis) ValidatorError

Variant (class in ihm.dumper) (class in ihm.reader) VisualizationFileLocation (class in ihm.location)

W

WaterAsymUnit (class in ihm) WaterChemComp (class in ihm) WorkflowFileLocation (class in ihm.location)

write() (in module ihm.dumper) write_comment() (ihm.format.CifWriter method) (ihm.format_bcif.BinaryCifWriter method)

X

XAxis (class in ihm.geometry) xl_restraints (ihm.reader.SystemReader attribute)

XYPlane (class in ihm.geometry) XZPlane (class in ihm.geometry)

Y

YAxis (class in ihm.geometry)

YeastTwoHybridDataset (class in ihm.dataset) YZPlane (class in ihm.geometry)

Z

ZAxis (class in ihm.geometry)