Index

A

additional_maps (emdb.models.entry.EMDBEntry attribute) AdditionalMapFile (class in emdb.models.files) admin (emdb.models.entry.EMDBEntry attribute) alphafolddb (emdb.models.annotations.EMDBMacromoleculeSample attribute) AlphaFoldDBAnnotation (class in emdb.models.annotations) angstrom_resolution (emdb.models.plots.PlotFSC attribute)

annotation_details (emdb.models.files.BaseMapFile attribute) arbitrary_types_allowed (emdb.models.search.EMDBSearchResults.Config attribute) atom_inclusion (emdb.models.validation.EMDBValidationScores attribute) average_color (emdb.models.validation.EMDBModelScore attribute) average_score (emdb.models.validation.EMDBModelScore attribute) axis_order (emdb.models.files.BaseMapFile attribute)

B

bar (emdb.models.validation.EMDBModelScore attribute) BaseFile (class in emdb.models.files)

BaseMapFile (class in emdb.models.files) BasePlot (class in emdb.models.plots)

C

cath (emdb.models.annotations.EMDBMacromoleculeSample attribute) CathAnnotation (class in emdb.models.annotations) ccc (emdb.models.validation.EMDBValidationScores attribute) cell (emdb.models.files.BaseMapFile attribute) chains (emdb.models.validation.EMDBModelScore attribute) chebi (emdb.models.annotations.EMDBMacromoleculeSample attribute) ChEBIAnnotation (class in emdb.models.annotations) chembl (emdb.models.annotations.EMDBMacromoleculeSample attribute)

ChEMBLAnnotation (class in emdb.models.annotations) citations (emdb.models.entry.EMDBEntry attribute) complex_portal (emdb.models.annotations.EMDBSupramoleculeSample attribute) ComplexPortalAnnotation (class in emdb.models.annotations) contour_list (emdb.models.files.BaseMapFile attribute) counts (emdb.models.plots.PlotDataHistogram attribute) csv_search() (emdb.client.EMDB method) cutoff_0_143 (emdb.models.plots.PlotFSC attribute) cutoff_0_5 (emdb.models.plots.PlotFSC attribute)

D

data_type (emdb.models.files.BaseMapFile attribute) density_distribution (emdb.models.validation.EMDBValidationPlots attribute) deposited_files (emdb.models.entry.EMDBEntry property) details (emdb.models.files.BaseMapFile attribute) (emdb.models.files.MaskFile attribute)

dimensions (emdb.models.files.BaseMapFile attribute) download() (emdb.models.files.BaseFile method) download_all_files() (emdb.models.entry.EMDBEntry method) drugbank (emdb.models.annotations.EMDBMacromoleculeSample attribute) DrugBankAnnotation (class in emdb.models.annotations)

E

EMDB (class in emdb.client) emdb.client module emdb.exceptions module emdb.models.annotations module emdb.models.entry module emdb.models.files module emdb.models.lazy_entry module emdb.models.plots module emdb.models.search module emdb.models.validation module emdb_id (emdb.models.annotations.EMDBAnnotations attribute) EMDBAnnotations (class in emdb.models.annotations) EMDBAPIError EMDBBaseAnnotation (class in emdb.models.annotations) EMDBEntry (class in emdb.models.entry)

EMDBError EMDBFileNotFoundError EMDBInvalidIDError EMDBMacromoleculeSample (class in emdb.models.annotations) EMDBMetadataCIFFile (class in emdb.models.files) EMDBMetadataXMLFile (class in emdb.models.files) EMDBModelScore (class in emdb.models.validation) EMDBNetworkError EMDBNotFoundError EMDBRateLimitError EMDBSearchResults (class in emdb.models.search) EMDBSearchResults.Config (class in emdb.models.search) EMDBSupramoleculeSample (class in emdb.models.annotations) EMDBValidation (class in emdb.models.validation) EMDBValidationGeneral (class in emdb.models.validation) EMDBValidationPlots (class in emdb.models.validation) EMDBValidationScores (class in emdb.models.validation) empiar (emdb.models.annotations.EMDBAnnotations attribute) EMPIARAnnotation (class in emdb.models.annotations) end (emdb.models.annotations.CathAnnotation attribute) (emdb.models.annotations.InterProAnnotation attribute) (emdb.models.annotations.PfamAnnotation attribute) entries (emdb.models.search.EMDBSearchResults attribute) estimated_volume (emdb.models.plots.PlotVolumeEstimate attribute)

F

feature_zones (emdb.models.plots.PlotFSC attribute) figure (emdb.models.entry.EMDBEntry attribute) FigureFile (class in emdb.models.files) filename (emdb.models.files.BaseFile attribute) format (emdb.models.files.BaseFile attribute) from_api() (emdb.models.annotations.CathAnnotation class method) (emdb.models.annotations.ChEBIAnnotation class method) (emdb.models.annotations.ChEMBLAnnotation class method) (emdb.models.annotations.ComplexPortalAnnotation class method) (emdb.models.annotations.DrugBankAnnotation class method) (emdb.models.annotations.EMDBAnnotations class method) (emdb.models.annotations.EMDBBaseAnnotation class method) (emdb.models.annotations.EMDBMacromoleculeSample class method) (emdb.models.annotations.EMDBSupramoleculeSample class method) (emdb.models.annotations.GeneOntologyAnnotation class method) (emdb.models.annotations.InterProAnnotation class method) (emdb.models.annotations.ORCIDAnnotation class method) (emdb.models.annotations.PfamAnnotation class method) (emdb.models.entry.EMDBEntry class method) (emdb.models.files.BaseFile class method) (emdb.models.files.BaseMapFile class method) (emdb.models.files.MaskFile class method) (emdb.models.search.EMDBSearchResults class method) (emdb.models.validation.EMDBModelScore class method) (emdb.models.validation.EMDBValidation class method) (emdb.models.validation.EMDBValidationGeneral class method) (emdb.models.validation.EMDBValidationPlots class method) (emdb.models.validation.EMDBValidationScores class method)

from_atom_inclusion() (emdb.models.validation.EMDBModelScore class method) fsc (emdb.models.plots.PlotFSC attribute) (emdb.models.validation.EMDBValidationPlots attribute) fsc_corrected (emdb.models.plots.PlotFSC attribute) fsc_masked (emdb.models.plots.PlotFSC attribute)

G

gene_ontology (emdb.models.annotations.EMDBMacromoleculeSample attribute) gene_ontology_cell (emdb.models.annotations.EMDBMacromoleculeSample attribute) gene_ontology_function (emdb.models.annotations.EMDBMacromoleculeSample attribute) gene_ontology_process (emdb.models.annotations.EMDBMacromoleculeSample attribute) GeneOntologyAnnotation (class in emdb.models.annotations)

general (emdb.models.validation.EMDBValidation attribute) get_annotations() (emdb.client.EMDB method) (emdb.models.entry.EMDBEntry method) get_entry() (emdb.client.EMDB method) get_validation() (emdb.client.EMDB method) (emdb.models.entry.EMDBEntry method)

H

half_maps (emdb.models.entry.EMDBEntry attribute)

halfbit (emdb.models.plots.PlotFSC attribute) HalfMapFile (class in emdb.models.files)

I

id (emdb.models.annotations.EMDBBaseAnnotation attribute) (emdb.models.annotations.EMDBMacromoleculeSample attribute) (emdb.models.annotations.EMDBSupramoleculeSample attribute) (emdb.models.entry.EMDBEntry attribute) (emdb.models.validation.EMDBValidation attribute)

interpro (emdb.models.annotations.EMDBMacromoleculeSample attribute) InterProAnnotation (class in emdb.models.annotations) intersections (emdb.models.plots.PlotFSC attribute)

L

label (emdb.models.files.BaseMapFile attribute) LazyEMDBEntry (class in emdb.models.lazy_entry)

level (emdb.models.plots.PlotFSC attribute) (emdb.models.plots.PlotVolumeEstimate attribute)

M

macromolecules (emdb.models.annotations.EMDBAnnotations attribute) map_file (emdb.models.files.MaskFile attribute) masked_local_res_histogram (emdb.models.validation.EMDBValidationPlots attribute) MaskFile (class in emdb.models.files) masks (emdb.models.entry.EMDBEntry attribute) metadata_files (emdb.models.entry.EMDBEntry attribute) method (emdb.models.entry.EMDBEntry attribute) metric (emdb.models.validation.EMDBModelScore attribute) mmfsc (emdb.models.validation.EMDBValidationPlots attribute) model_config (emdb.models.annotations.AlphaFoldDBAnnotation attribute) (emdb.models.annotations.CathAnnotation attribute) (emdb.models.annotations.ChEBIAnnotation attribute) (emdb.models.annotations.ChEMBLAnnotation attribute) (emdb.models.annotations.ComplexPortalAnnotation attribute) (emdb.models.annotations.DrugBankAnnotation attribute) (emdb.models.annotations.EMDBAnnotations attribute) (emdb.models.annotations.EMDBBaseAnnotation attribute) (emdb.models.annotations.EMDBMacromoleculeSample attribute) (emdb.models.annotations.EMDBSupramoleculeSample attribute) (emdb.models.annotations.EMPIARAnnotation attribute) (emdb.models.annotations.GeneOntologyAnnotation attribute) (emdb.models.annotations.InterProAnnotation attribute) (emdb.models.annotations.ORCIDAnnotation attribute) (emdb.models.annotations.PDBAnnotation attribute) (emdb.models.annotations.PDBeKbAnnotation attribute) (emdb.models.annotations.PfamAnnotation attribute) (emdb.models.annotations.Scop2Annotation attribute) (emdb.models.annotations.UniProtAnnotation attribute) (emdb.models.entry.EMDBEntry attribute) (emdb.models.files.AdditionalMapFile attribute) (emdb.models.files.BaseFile attribute) (emdb.models.files.BaseMapFile attribute) (emdb.models.files.EMDBMetadataCIFFile attribute) (emdb.models.files.EMDBMetadataXMLFile attribute) (emdb.models.files.FigureFile attribute) (emdb.models.files.HalfMapFile attribute) (emdb.models.files.MaskFile attribute) (emdb.models.files.ModelCifFile attribute) (emdb.models.files.PrimaryMapFile attribute) (emdb.models.plots.BasePlot attribute) (emdb.models.plots.PlotDataHistogram attribute) (emdb.models.plots.PlotDataXY attribute) (emdb.models.plots.PlotFSC attribute) (emdb.models.plots.PlotVolumeEstimate attribute) (emdb.models.search.EMDBSearchResults attribute) (emdb.models.validation.EMDBModelScore attribute) (emdb.models.validation.EMDBValidation attribute) (emdb.models.validation.EMDBValidationGeneral attribute) (emdb.models.validation.EMDBValidationPlots attribute) (emdb.models.validation.EMDBValidationScores attribute)

model_map_ratio (emdb.models.validation.EMDBValidationGeneral attribute) model_post_init() (emdb.models.annotations.EMDBAnnotations method) (emdb.models.entry.EMDBEntry method) (emdb.models.files.AdditionalMapFile method) (emdb.models.files.BaseFile method) (emdb.models.files.BaseMapFile method) (emdb.models.files.EMDBMetadataCIFFile method) (emdb.models.files.EMDBMetadataXMLFile method) (emdb.models.files.FigureFile method) (emdb.models.files.HalfMapFile method) (emdb.models.files.MaskFile method) (emdb.models.files.ModelCifFile method) (emdb.models.files.PrimaryMapFile method) (emdb.models.search.EMDBSearchResults method) (emdb.models.validation.EMDBValidation method) (emdb.models.validation.EMDBValidationPlots method) model_volume (emdb.models.validation.EMDBValidationGeneral attribute) ModelCifFile (class in emdb.models.files) modelling (emdb.models.entry.EMDBEntry attribute) module emdb.client emdb.exceptions emdb.models.annotations emdb.models.entry emdb.models.files emdb.models.lazy_entry emdb.models.plots emdb.models.search emdb.models.validation

O

onebit (emdb.models.plots.PlotFSC attribute) orcid (emdb.models.annotations.EMDBAnnotations attribute)

ORCIDAnnotation (class in emdb.models.annotations) origin (emdb.models.files.BaseMapFile attribute)

P

pdb (emdb.models.annotations.EMDBAnnotations attribute) pdb_id (emdb.models.files.ModelCifFile attribute) (emdb.models.plots.PlotFSC attribute) (emdb.models.validation.EMDBModelScore attribute) pdb_models (emdb.models.entry.EMDBEntry attribute) PDBAnnotation (class in emdb.models.annotations) pdbekb (emdb.models.annotations.EMDBMacromoleculeSample attribute) PDBeKbAnnotation (class in emdb.models.annotations) pfam (emdb.models.annotations.EMDBMacromoleculeSample attribute) PfamAnnotation (class in emdb.models.annotations)

phaserandomization (emdb.models.plots.PlotFSC attribute) pixel_spacing (emdb.models.files.BaseMapFile attribute) plot() (emdb.models.plots.BasePlot method) PlotDataHistogram (class in emdb.models.plots) PlotDataXY (class in emdb.models.plots) PlotFSC (class in emdb.models.plots) plots (emdb.models.validation.EMDBValidation attribute) PlotVolumeEstimate (class in emdb.models.plots) primary_map (emdb.models.entry.EMDBEntry attribute) PrimaryMapFile (class in emdb.models.files) provenance (emdb.models.annotations.EMDBBaseAnnotation attribute)

Q

qscore (emdb.models.validation.EMDBValidationScores attribute)

R

rawmap_contour_level (emdb.models.validation.EMDBValidationGeneral attribute) rawmap_density_distribution (emdb.models.validation.EMDBValidationPlots attribute) rawmap_mmcif (emdb.models.validation.EMDBValidationPlots attribute) rawmap_rotationally_averaged_power_spectrum (emdb.models.validation.EMDBValidationPlots attribute) recommended_contour_level (emdb.models.plots.PlotDataXY attribute) (emdb.models.plots.PlotVolumeEstimate attribute) (emdb.models.validation.EMDBValidation attribute)

related_emdb_ids (emdb.models.entry.EMDBEntry attribute) related_pdb_ids (emdb.models.entry.EMDBEntry attribute) residues (emdb.models.validation.EMDBModelScore attribute) resolution (emdb.models.entry.EMDBEntry attribute) (emdb.models.plots.PlotDataXY attribute) (emdb.models.plots.PlotFSC attribute) (emdb.models.validation.EMDBValidation attribute) rotationally_averaged_power_spectrum (emdb.models.validation.EMDBValidationPlots attribute)

S

sample (emdb.models.entry.EMDBEntry attribute) sample_id (emdb.models.annotations.EMDBBaseAnnotation attribute) save() (emdb.models.plots.BasePlot method) scop2 (emdb.models.annotations.EMDBMacromoleculeSample attribute) Scop2Annotation (class in emdb.models.annotations) score (emdb.models.annotations.ComplexPortalAnnotation attribute) scores (emdb.models.validation.EMDBValidation attribute) search() (emdb.client.EMDB method) size_kbytes (emdb.models.files.BaseFile attribute) smoc (emdb.models.validation.EMDBValidationScores attribute) source_path (emdb.models.files.AdditionalMapFile property) (emdb.models.files.BaseFile property) (emdb.models.files.BaseMapFile property) (emdb.models.files.EMDBMetadataCIFFile property) (emdb.models.files.EMDBMetadataXMLFile property) (emdb.models.files.FigureFile property) (emdb.models.files.HalfMapFile property) (emdb.models.files.MaskFile property) (emdb.models.files.ModelCifFile property) (emdb.models.files.PrimaryMapFile property)

spacing (emdb.models.files.BaseMapFile attribute) start (emdb.models.annotations.CathAnnotation attribute) (emdb.models.annotations.InterProAnnotation attribute) (emdb.models.annotations.PfamAnnotation attribute) statistics (emdb.models.files.BaseMapFile attribute) structure_determination_list (emdb.models.entry.EMDBEntry attribute) supramolecules (emdb.models.annotations.EMDBAnnotations attribute) surface_ratio (emdb.models.validation.EMDBValidationGeneral attribute) symmetry (emdb.models.files.BaseMapFile attribute)

T

title (emdb.models.annotations.ChEBIAnnotation attribute) (emdb.models.annotations.ChEMBLAnnotation attribute) (emdb.models.annotations.ComplexPortalAnnotation attribute) (emdb.models.annotations.DrugBankAnnotation attribute) (emdb.models.annotations.GeneOntologyAnnotation attribute) (emdb.models.annotations.InterProAnnotation attribute) (emdb.models.annotations.ORCIDAnnotation attribute) (emdb.models.annotations.PfamAnnotation attribute) (emdb.models.plots.BasePlot attribute)

type (emdb.models.annotations.EMDBMacromoleculeSample attribute) (emdb.models.annotations.EMDBSupramoleculeSample attribute) (emdb.models.annotations.GeneOntologyAnnotation attribute) (emdb.models.plots.PlotFSC attribute)

U

uniprot (emdb.models.annotations.EMDBMacromoleculeSample attribute)

UniProtAnnotation (class in emdb.models.annotations) unmasked_local_res_histogram (emdb.models.validation.EMDBValidationPlots attribute)

V

values (emdb.models.plots.PlotDataHistogram attribute) volume (emdb.models.plots.PlotVolumeEstimate attribute)

volume_estimate (emdb.models.validation.EMDBValidationGeneral attribute) (emdb.models.validation.EMDBValidationPlots attribute)

X

x (emdb.models.plots.PlotDataXY attribute)

x_label (emdb.models.plots.BasePlot attribute)

Y

y (emdb.models.plots.PlotDataXY attribute)

y_label (emdb.models.plots.BasePlot attribute)