Index

A

AbInitioModel (class in modelcif.model) AlignedPositionsIdentity (class in modelcif.alignment) AlignedResiduePairsIdentity (class in modelcif.alignment) Alignment (class in modelcif.reference) AlignmentMode (class in modelcif.alignment) alignments (modelcif.reference.TargetReference attribute) (modelcif.System attribute) AlignmentType (class in modelcif.alignment) AlphaFoldDB (class in modelcif.reference)

Assembly (class in modelcif) AsymUnit (class in modelcif) AsymUnitRange (class in modelcif) Atom (class in modelcif.model) atom() (modelcif.Residue method) AtomFeature (class in modelcif) atoms (modelcif.CustomTemplate attribute) auth_seq_id (modelcif.Residue property) authors (modelcif.System attribute)

B

BackboneGenerationStep (class in modelcif.protocol) BLASTEValue (class in modelcif.alignment)

Boolean (class in modelcif.qa_metric) branch_descriptors (modelcif.Entity attribute) branch_links (modelcif.Entity attribute)

C

CanonicalSMILES (class in modelcif.descriptor) CIFFile (class in modelcif.associated) citations (modelcif.System attribute) CoevolutionMSAStep (class in modelcif.protocol)

comments (modelcif.System attribute) comp (modelcif.Residue property) ContactPredictionStep (class in modelcif.protocol) ContactProbability (class in modelcif.qa_metric) CustomTemplate (class in modelcif)

D

Data (class in modelcif.data) data_usage (modelcif.System attribute) Database (class in modelcif) DataGroup (class in modelcif.data)

DeletionSeqDif (class in modelcif.reference) description (modelcif.qa_metric.MetricMode property) Descriptor (class in modelcif.descriptor) Dihedral (class in modelcif.qa_metric) Distance (class in modelcif.qa_metric)

E

Energy (class in modelcif.qa_metric) EnergyEstimateStep (class in modelcif.protocol)

Entity (class in modelcif) EntityInstanceFeature (class in modelcif) ExperimentalValidationStep (class in modelcif.protocol)

F

Feature (class in modelcif) (class in modelcif.qa_metric) FeaturePairwise (class in modelcif.qa_metric)

File (class in modelcif.associated) file_format (modelcif.associated.CIFFile property) formula_weight (modelcif.Entity property)

G

get_atoms() (modelcif.model.Model method) get_url() (modelcif.associated.Repository method)

Global (class in modelcif.alignment) (class in modelcif.qa_metric) grants (modelcif.System attribute)

H

HHblitsEValue (class in modelcif.alignment)

HomologyModel (class in modelcif.model)

I

Identity (class in modelcif.alignment) InChI (class in modelcif.descriptor) InChIKey (class in modelcif.descriptor) ins_code (modelcif.Residue property) InsertionSeqDif (class in modelcif.reference)

IpTM (class in modelcif.qa_metric) is_branched() (modelcif.Entity method) is_polymeric() (modelcif.Entity method) IsomericSMILES (class in modelcif.descriptor) IUPACName (class in modelcif.descriptor)

L

Local (class in modelcif.alignment) (class in modelcif.qa_metric)

LocalPairwise (class in modelcif.qa_metric)

M

MeanSequenceIdentity (class in modelcif.alignment) MetricMode (class in modelcif.qa_metric) MetricType (class in modelcif.qa_metric) Model (class in modelcif.model) model_groups (modelcif.System attribute) ModelAssessmentStep (class in modelcif.protocol) modelcif module modelcif.alignment module modelcif.associated module modelcif.data module modelcif.descriptor module modelcif.dumper module modelcif.model module modelcif.protocol module modelcif.qa_metric module

modelcif.reader module modelcif.reference module ModelCIFVariant (class in modelcif.dumper) (class in modelcif.reader) ModelGroup (class in modelcif.model) ModelingStep (class in modelcif.protocol) ModelRefinementStep (class in modelcif.protocol) ModelSelectionStep (class in modelcif.protocol) module modelcif modelcif.alignment modelcif.associated modelcif.data modelcif.descriptor modelcif.dumper modelcif.model modelcif.protocol modelcif.qa_metric modelcif.reader modelcif.reference Multiple (class in modelcif.alignment)

N

name (modelcif.qa_metric.MetricMode property) NonPolymerFromTemplate (class in modelcif) NormalizedScore (class in modelcif.qa_metric)

not_modeled_residue_ranges (modelcif.model.Model attribute) NotModeledResidueRange (class in modelcif.model) num_map (modelcif.AsymUnit attribute) number_of_molecules (modelcif.WaterAsymUnit property)

O

other_details (modelcif.alignment.Identity property) (modelcif.model.Model property) (modelcif.qa_metric.MetricType property) (modelcif.reference.TargetReference property) (modelcif.reference.TemplateReference property)

P

PAE (class in modelcif.qa_metric) Pair (class in modelcif.alignment) Pairwise (class in modelcif.alignment) parent (modelcif.Assembly attribute) PDB (class in modelcif.reference) PLDDT (class in modelcif.qa_metric) PLDDT01 (class in modelcif.qa_metric) PLDDTAllAtom (class in modelcif.qa_metric)

PLDDTAllAtom01 (class in modelcif.qa_metric) PLDDTToPolymer (class in modelcif.qa_metric) PolyResidueFeature (class in modelcif) Protocol (class in modelcif.protocol) protocols (modelcif.System attribute) PTM (class in modelcif.qa_metric) PubChem (class in modelcif.reference) PubChemCID (class in modelcif.descriptor)

Q

qa_metrics (modelcif.model.Model attribute)

QAMetricsFile (class in modelcif.associated) quality (modelcif.qa_metric.Dihedral property)

R

read() (in module modelcif.reader) ReferenceDatabase (class in modelcif) repositories (modelcif.System attribute) Repository (class in modelcif.associated)

representatives (modelcif.model.ModelGroup attribute) Residue (class in modelcif) residue() (modelcif.AsymUnit method) (modelcif.Entity method) revisions (modelcif.System attribute)

S

Score (class in modelcif.alignment) segment() (modelcif.AsymUnit method) seq_id_range (modelcif.AsymUnit property) (modelcif.Entity property) (modelcif.WaterAsymUnit property) SeqDif (class in modelcif.reference) sequence (modelcif.AsymUnit property) (modelcif.WaterAsymUnit property) SequenceDesignStep (class in modelcif.protocol)

ShorterSequenceIdentity (class in modelcif.alignment) Software (class in modelcif) SoftwareGroup (class in modelcif) SoftwareParameter (class in modelcif) SoftwareWithParameters (class in modelcif) Step (class in modelcif.protocol) steps (modelcif.protocol.Protocol attribute) strand_id (modelcif.AsymUnit property) StructureValidationStep (class in modelcif.protocol) System (class in modelcif)

T

TargetReference (class in modelcif.reference) TargetTemplateAlignmentStep (class in modelcif.protocol) Template (class in modelcif) TemplateAtom (class in modelcif)

TemplateReference (class in modelcif.reference) TemplateSearchStep (class in modelcif.protocol) TemplateSegment (class in modelcif) TemplateSelectionStep (class in modelcif.protocol) Transformation (class in modelcif)

U

UniProt (class in modelcif.reference)

W

WaterAsymUnit (class in modelcif)

write() (in module modelcif.dumper)

Z

ZipFile (class in modelcif.associated)

ZScore (class in modelcif.qa_metric)