Index

A

add_atom() (ihm.model.Model method) (ihm.startmodel.StartingModel method) add_connectivity() (ihm.multi_state_scheme.MultiStateScheme 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_relaxation_time() (ihm.multi_state_scheme.MultiStateScheme 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 property) authors (ihm.System attribute) Axis (class in ihm.geometry)

B

BinaryCIFParser (class in ihm.metadata) BinaryCifReader (class in ihm.format_bcif) BinaryCifWriter (class in ihm.format_bcif) BioGRIDLocation (class in ihm.location) BMRbigLocation (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 property) categories (ihm.dictionary.Dictionary attribute) (ihm.Revision 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) ChangeKeywordFilter (class in ihm.format) ChangeValueFilter (class in ihm.format) 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) CifTokenReader (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 property) clustering_method (ihm.model.Ensemble property) 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 property) ComparativeModelDataset (class in ihm.dataset) complete_assembly (ihm.System attribute) Connectivity (class in ihm.multi_state_scheme) 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) CrossLinkGroupFit (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) Database (class in ihm) database_status (ihm.System attribute) DatabaseLocation (class in ihm.location) DatabaseStatus (class in ihm) 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) deposit_site (ihm.DatabaseStatus property) DerivedDistanceRestraint (class in ihm.restraint) description (ihm.dictionary.Category attribute) Details (class in ihm.source) details (ihm.Revision attribute) 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 property) (ihm.restraint.LowerBoundDistanceRestraint property) (ihm.restraint.UpperBoundDistanceRestraint attribute) distance_restraint_groups (ihm.flr.FLRData attribute) distance_upper_limit (ihm.restraint.DistanceRestraint attribute) (ihm.restraint.HarmonicDistanceRestraint property) (ihm.restraint.LowerBoundDistanceRestraint attribute) (ihm.restraint.UpperBoundDistanceRestraint property) DistanceRestraint (class in ihm.restraint) DNAAlphabet (class in ihm) DNAChemComp (class in ihm) DNAFootprintingDataset (class in ihm.dataset) 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) EPRDataset (class in ihm.dataset) EquilibriumConstant (class in ihm.multi_state_scheme) 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 property) FeatureCrossLink (class in ihm.restraint) features (ihm.reader.SystemReader attribute) FeatureSegment (class in ihm.representation) FileLocation (class in ihm.location) Filter (class in ihm.format) filter_category() (ihm.format.Filter method) filter_loop_header() (ihm.format.Filter method) 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_kinetic_rate_fret_analysis_connection (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_relaxation_time_fret_analysis_connection (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 property) (ihm.Entity property) 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_connectivities() (ihm.multi_state_scheme.MultiStateScheme 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_loop_filter() (ihm.format.Filter method) get_lower() (ihm.reader.Handler method) get_relaxation_times() (ihm.multi_state_scheme.MultiStateScheme method) get_seq_dif() (ihm.startmodel.StartingModel method) get_spheres() (ihm.model.Model method) get_states() (ihm.multi_state_scheme.MultiStateScheme method) get_system_writer() (ihm.dumper.Variant method) Grant (class in ihm) grants (ihm.System attribute) groups (ihm.Revision attribute)

H

HalfTorus (class in ihm.geometry) Handler (class in ihm.reader) HarmonicDistanceRestraint (class in ihm.restraint) hdx_restraints (ihm.reader.SystemReader attribute)

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

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.multi_state_scheme 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 property) 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) items (ihm.Revision attribute) ItemType (class in ihm.dictionary)

J

JPOSTLocation (class in ihm.location)

K

Keyword (class in ihm.dictionary) keywords (ihm.dictionary.Category attribute) kinetic_rate_fret_analysis_connections (ihm.flr.FLRData attribute)

kinetic_rates (ihm.reader.SystemReader attribute) KineticRate (class in ihm.multi_state_scheme) KineticRateEquilibriumConstant (class in ihm.multi_state_scheme) KineticRateFretAnalysisConnection (class in ihm.flr)

L

LifetimeFitModel (class in ihm.flr) linked_items (ihm.dictionary.Dictionary attribute) LocalizationDensity (class in ihm.model) Location (class in ihm.location) location (ihm.dataset.Dataset property) 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) match_token_category() (ihm.format.Filter method) match_token_keyword() (ihm.format.Filter method) 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) module ihm ihm.analysis ihm.citations ihm.cross_linkers ihm.dataset ihm.dictionary ihm.dumper ihm.flr ihm.format ihm.format_bcif ihm.geometry ihm.location ihm.metadata ihm.model ihm.multi_state_scheme ihm.protocol ihm.reader ihm.reference ihm.representation ihm.restraint ihm.source ihm.startmodel

MRCParser (class in ihm.metadata) MSESeqDif (class in ihm.startmodel) multi_state_scheme_connectivities (ihm.reader.SystemReader attribute) multi_state_schemes (ihm.reader.SystemReader attribute) (ihm.System attribute) MultiResidueSegment (class in ihm.representation) MultiStateScheme (class in ihm.multi_state_scheme) 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)

not_modeled_residue_ranges (ihm.model.Model attribute) NotModeledResidueRange (class in ihm.model) NUM_ALIGNED_WITH_GAPS (ihm.startmodel.SequenceIdentityDenominator attribute) NUM_ALIGNED_WITHOUT_GAPS (ihm.startmodel.SequenceIdentityDenominator attribute) num_map (ihm.AsymUnit attribute) num_models_deposited (ihm.model.Ensemble property) (ihm.model.Subsample property) number_of_molecules (ihm.WaterAsymUnit property)

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.Parser method) (ihm.metadata.PDBParser 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) PopulationEquilibriumConstant (class in ihm.multi_state_scheme) pred_cont_restraint_groups (ihm.reader.SystemReader attribute) pred_cont_restraints (ihm.reader.SystemReader attribute) PredictedContactRestraint (class in ihm.restraint) PredictedContactsDataset (class in ihm.dataset) PRIDELocation (class in ihm.location) Probe (class in ihm.flr) ProbeDescriptor (class in ihm.flr) ProbeList (class in ihm.flr) process_site (ihm.DatabaseStatus property) ProcessEdge (class in ihm.model) ProcessStep (class in ihm.model) ProteomeXchangeLocation (class in ihm.location) 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.CifTokenReader method) (ihm.format_bcif.BinaryCifReader method) reason (ihm.model.NotModeledResidueRange property) recvd_initial_deposition_date (ihm.DatabaseStatus property) 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) relaxation_time_fret_analysis_connections (ihm.flr.FLRData attribute) relaxation_times (ihm.reader.SystemReader attribute) RelaxationTime (class in ihm.multi_state_scheme) RelaxationTimeFretAnalysisConnection (class in ihm.flr) relion (in module ihm.citations) RemoveItemFilter (class in ihm.format) ReplaceCategoryFilter (class in ihm.format) 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 property) residue2 (ihm.restraint.ResidueCrossLink property) 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) Revision (class in ihm) RevisionDetails (class in ihm) revisions (ihm.reader.SystemReader attribute) (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 property) (ihm.Entity property) (ihm.WaterAsymUnit property) SeqDif (class in ihm.reference) (class in ihm.startmodel) Sequence (class in ihm.reference) sequence (ihm.AsymUnit property) (ihm.WaterAsymUnit property) 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) status_code (ihm.DatabaseStatus property) 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 property) 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 property) (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) unit (ihm.multi_state_scheme.RelaxationTime property) 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)

XRayDiffractionDataset (class in ihm.dataset) 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)