Index

_

__getitem__() (AAIndex method) (AlignedColumn method) (AlignedRegion method) (AlignmentHandle method), [1] (ConstSequenceHandle method) (ConstSequenceList method) (Point method)

__len__() (AlignedRegion method) (AlignmentHandle method) (ConstSequenceHandle method) (ConstSequenceList method) (ProfileHandle method) __str__() (AlignedColumn method) (ConstSequenceHandle method) (SecStructure method)

A

A3MToCS() (HHblits method) A3MToProfile() (HHblits method) aa_list (ContactWeightMatrix attribute) (PairSubstWeightMatrix attribute) AAIndex (class in ost.seq.alg.aaindex) AAIndexData (class in ost.seq.alg.aaindex) absolute_origin (ImageHandle attribute) Accessibility() (in module ost.mol.alg) AccessibilityAlgorithm (class in ost.mol.alg) Add() (AminoAcidSet method) (Scene method) (ToolOptionEnum method) add_angles (Settings attribute) add_barostat (Settings attribute) add_bonds (Settings attribute) add_cmaps (Settings attribute) add_dihedrals (Settings attribute) add_exclusions (Settings attribute) add_gbsa (Settings attribute) add_impropers (Settings attribute) add_nonbonded (Settings attribute) add_thermostat (Settings attribute) AddAAPseudoCounts() (in module ost.seq.alg), [1] AddAction() (ContextMenu method) AddAddRule() (GromacsBlockModifier method) AddAlignment() (in module ost.gui) AddAllInclusiveBonds() (EntityView method) AddAltAtomPos() (EditorBase method) AddAngle() (BuildingBlock method) (Forcefield method) (GromacsBlockModifier method) AddAssembly() (LinearIndexer method) AddAtom() (BuildingBlock method) (ChainView method) (EntityView method) (ResidueView method) AddAtomRenamingRule() (Forcefield method) AddAuthorsToCitation() (MMCifInfo method) AddBioUnit() (MMCifInfo method) AddBlockModifier() (Forcefield method) AddBond() (BuildingBlock method) (EntityView method) (Forcefield method) (GromacsBlockModifier method) AddBuildingBlock() (Forcefield method) AddChain() (EntityView method) (MMCifInfoBioUnit method) AddCharacters() (LinearCharacterContainer method) AddCitation() (MMCifInfo method) AddCMap() (BuildingBlock method) (Forcefield method) (GromacsBlockModifier method) (Topology method) AddCol() (Table method) AddColumn() (ProfileHandle method) AddConstraint() (BuildingBlock method) (Forcefield method) AddDeleteAtom() (GromacsBlockModifier method) AddDihedral() (BuildingBlock method) (Forcefield method) (GromacsBlockModifier method) AddDistanceConstraint() (Topology method) AddEntity() (in module ost.gui) AddEntityBranchLink() (MMCifInfo method) AddExclusion() (BuildingBlock method) (Topology method) AddFrames() (CoordGroupHandle method) AddFromFiles() (in module ost.mol.mm.antechamber) AddFromPath() (in module ost.mol.mm.antechamber) AddHarmonicAngle() (Topology method) AddHarmonicBond() (Topology method) AddHarmonicDistanceRestraint() (Topology method) AddHarmonicImproper() (Topology method) AddHarmonicPositionRestraint() (Topology method) AddHydrogenConstructor() (Forcefield method) AddHydrogenRule() (GromacsHydrogenConstructor method) AddImplicitGenborn() (Forcefield method) AddImproper() (BuildingBlock method) (Forcefield method) (GromacsBlockModifier method) AddIon() (in module ost.mol.mm.antechamber) AddLJ() (Forcefield method) AddLJPair() (Forcefield method) (Topology method) AddMass() (Forcefield method) AddMMCifEntityIdTr() (MMCifInfo method) AddMMCifPDBChainTr() (MMCifInfo method) AddNullPseudoCounts() (in module ost.seq.alg) AddOperation() (MMCifInfo method) AddOperations() (MMCifInfoBioUnit method) AddPDBMMCifChainTr() (MMCifInfo method) AddPeriodicDihedral() (Topology method) AddPeriodicImproper() (Topology method) AddPersistentWidget() (MainArea method), [1] AddPositionConstraint() (Simulation method) (Topology method) AddPositionConstraints() (Simulation method) AddPositions() (LinearPositionContainer method) AddProfile() (ProfileDB method) AddReplaceRule() (GromacsBlockModifier method) AddResidue() (ChainView method) (EntityView method) AddResidueRenamingRule() (Forcefield method) AddRevision() (MMCifInfo method) (MMCifInfoRevisions method) AddRow() (Table method) AddSequence() (AlignmentHandle method) (ConstSequenceList method) AddSink() (MultiLogSink method) AddSymmetricCompound() (SymmetrySettings method) AddTorsion() (EditorBase method) AddTransitionPseudoCounts() (in module ost.seq.alg)

AddUreyBradleyAngle() (Topology method) AddWidget() (MainArea method) (PanelManager method) AddWidgetByName() (PanelManager method) AddWidgetToPool() (PanelManager method), [1] Align() (ChainMapper method) align_id (MMCifInfoStructRefSeq attribute) aligned_patches (BlastHit attribute) aligned_seqs (MMCifInfoStructRef attribute) AlignedColumn (class in ost.seq) AlignedCuboid (class in ost.geom) AlignedPatch (class in ost.bindings.blast) AlignedRegion (class in ost.seq) alignment (cluster attribute) (MappedLDDTScorer attribute) AlignmentFromChainView() (in module ost.seq.alg) AlignmentFromSequenceList() (in module ost.seq) AlignmentFromString() (in module ost.io) AlignmentHandle (class in ost.seq) alignments (OligoLDDTScorer attribute) (QSscorer property) AlignmentToString() (in module ost.io) AlignToSEQRES() (in module ost.seq.alg) aln (AlignedPatch attribute) (HHblitsHit attribute) (Scorer property) alns (MappingResult property) (QSScorer property) alt_name (AtomSpec attribute) AminoAcid (class in ost.conop) AminoAcidSet (class in ost.conop) AminoAcidToResidueName() (in module ost.conop) AnalyzeAngle() (in module ost.mol.alg) AnalyzeAromaticRingInteraction() (in module ost.mol.alg) AnalyzeAtomPos() (in module ost.mol.alg) AnalyzeCenterOfMassPos() (in module ost.mol.alg) AnalyzeDihedralAngle() (in module ost.mol.alg) AnalyzeDistanceBetwAtoms() (in module ost.mol.alg) AnalyzeDistanceBetwCenterOfMass() (in module ost.mol.alg) AnalyzeHelixKink() (in module ost.mol.alg.helix_kinks) AnalyzeMinDistance() (in module ost.mol.alg) AnalyzeMinDistanceBetwCenterOfMassAndView() (in module ost.mol.alg) AnalyzeRMSD() (in module ost.mol.alg) angle (FindMemParam attribute) Angle() (in module ost.geom) angle_table (StereoChemicalProps attribute) AngleViolationInfo (class in ost.mol.alg.stereochemistry) AnnoType (class in ost.seq.alg.aaindex) append() (SurfaceTriIDList method) (SurfaceVertexList method) AppendResidue() (EditorBase method) Apply() (ImageHandle method) ApplyIP() (ImageHandle method) ApplyLBFGS() (Simulation method) ApplyOnBuildingBlock() (GromacsBlockModifier method) (GromacsHydrogenConstructor method) (HeuristicHydrogenConstructor method) ApplyOnResidue() (GromacsBlockModifier method) (GromacsHydrogenConstructor method) (HeuristicHydrogenConstructor method) ApplySD() (Simulation method) ApplyTransform() (XCSEditor method), [1] AreIntersecting() (in module ost.geom) AreParallel() (in module ost.geom) assign_elem (MolckSettings attribute) assign_torsions (Processor attribute) AssignBackboneTorsions() (in module ost.conop) AssignDSSP() (in module ost.bindings.dssp) AssignFFSpecificNames() (Forcefield method) AssignPreset() (SubstWeightMatrix method) AssignSecStruct() (in module ost.mol.alg) AssignSSToA3M() (HHblits method) At() (Ellipse2 method) (Line2 method) (Line3 method) AtAngle() (Ellipse2 method) Atom (SurfaceVertex attribute) atom1 (MMCifInfoEntityBranchLink attribute) atom2 (MMCifInfoEntityBranchLink attribute) atom_count (EntityHandle attribute) (EntityView attribute) (ResidueHandle attribute) (ResidueView attribute) atom_one (BondSpec attribute) atom_specs (Compound attribute) atom_two (BondSpec attribute) AtomHandle (class in ost.mol) atoms (ChainHandle attribute) (ChainView attribute) (CoordGroupHandle attribute) (EntityHandle attribute) (EntityView attribute) (ResidueHandle attribute) (ResidueView attribute) AtomSpec (class in ost.conop) AtomView (class in ost.mol) Attach() (SurfaceHandle method) attached_view (ConstSequenceHandle attribute) AttachObserver() (Scene method) AttachView() (AlignmentHandle method) (ConstSequenceHandle method) authors (MMCifInfoCitation attribute) AutoAutoslab() (Scene method) Autoslab() (Scene method) AutoslabMax() (Scene method) AverageDistanceMatrixFromTraj() (in module ost.mol.alg.trajectory_analysis) avg_entropy (ProfileHandle attribute) axis (FindMemParam attribute) axis_a (Cuboid attribute) axis_b (Cuboid attribute) axis_c (Cuboid attribute) AxisRotation() (in module ost.geom)

B

b_factor (AtomHandle attribute) background (Scene attribute) barostat_frequency (Settings attribute) barostat_pressure (Settings attribute) barostat_temperature (Settings attribute) bb_lddt (Scorer property) bb_lddt_scorer (Scorer property) bb_local_lddt (Scorer property) bb_rmsd (ReprResult property) Begin() (ToolOptionEnum method) best_score (QSscorer property) biounits (MMCifInfo attribute) bit_score (AlignedPatch attribute) Blast() (in module ost.bindings.blast) BlastError (class in ost.bindings.blast) BlastHit (class in ost.bindings.blast) BlockModifier (class in ost.mol.mm) BLOSUMNullModel() (ProfileColumn method) bond_count (ResidueHandle attribute) bond_order (BondHandle attribute) (MMCifInfoEntityBranchLink attribute) bond_specs (Compound attribute) bond_table (StereoChemicalProps attribute) BondExists() (in module ost.mol) BondHandle (class in ost.mol) bonds (AtomHandle attribute) BondSpec (class in ost.conop)

BondViolationInfo (class in ost.mol.alg.stereochemistry) book_publisher (MMCifInfoCitation attribute) book_publisher_city (MMCifInfoCitation attribute) bounds (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (EntityView attribute) (ResidueHandle attribute) (ResidueView attribute) BrownianIntegrator (class in ost.mol.mm) BuildingBlock (class in ost.mol.mm) BuildQueryMSA() (HHblits method) built-in function CheckStructure() CleanlDDTReferences() CreateDistanceList() CreateDistanceListFromMultipleReferences() DistanceRMSDTest() DRMSD() GetlDDTPerResidueStats() LDDTHA() LocalDistDiffTest(), [1], [2], [3] PreparelDDTGlobalRDMap() PrintGlobalRDMap() PrintlDDTPerResidueStats() PrintResidueRDMap() ButterworthHighPassFilter (class in ost.img.alg) ButterworthLowPassFilter (class in ost.img.alg)

C

ca_chains (QSscoreEntity property) ca_entity (QSscoreEntity property) cad_score (Scorer property) CADResult (class in ost.bindings.cadscore) CADScore() (in module ost.bindings.cadscore) CalculateBestFitLine() (in module ost.mol.alg.structure_analysis) CalculateBestFitPlane() (in module ost.mol.alg.structure_analysis) CalculateContactProbability() (in module ost.seq.alg) CalculateContactScore() (in module ost.seq.alg) CalculateContactSubstitutionScore() (in module ost.seq.alg) CalculateDistanceDifferenceMatrix() (in module ost.mol.alg.structure_analysis) CalculateHelixAxis() (in module ost.mol.alg.structure_analysis) CalculateHelixKink() (in module ost.mol.alg.helix_kinks) CalculateMutualInformation() (in module ost.seq.alg) CalculateRMSD() (in module ost.mol.alg) CalculateSurface() (in module ost.bindings.msms) CalculateSurfaceArea() (in module ost.bindings.msms) (in module ost.bindings.naccess) CalculateSurfaceVolume() (in module ost.bindings.msms) calpha_only (IOProfile attribute) (MappedLDDTScorer attribute) (OligoLDDTScorer attribute) (QSscoreEntity attribute) (QSscorer attribute) CanOperateOn() (Tool method) Capture() (CoordGroupHandle method) CaptureInto() (CoordGroupHandle method) cas (MMCifInfoCitation attribute) casp_flag (MMCifInfoStructDetails attribute) center (Cuboid attribute) (Entity attribute) (Scene attribute) center_of_atoms (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (EntityView attribute) (ResidueHandle attribute) (ResidueView attribute) center_of_mass (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (EntityView attribute) (ResidueHandle attribute) (ResidueView attribute) CenterOn() (Scene method) CenterSpatialOrigin() (ImageHandle method) central_atom (ResidueHandle attribute) (ResidueView attribute) central_normal (ResidueHandle attribute) (ResidueView attribute) chain (ResidueHandle attribute) (ResidueView attribute) chain_count (EntityHandle attribute) (EntityView attribute) chain_mapper (LigandScorer property) (Scorer property) chain_mapping (QSscorer property) chain_mapping_scheme (QSscorer property) chain_name (MMCifInfoStructRefSeq attribute) chain_names (QSEntity property) ChainHandle (class in ost.mol) chainintervals (MMCifInfoBioUnit attribute) ChainMapper (class in ost.mol.alg.chain_mapping) chains (EntityHandle attribute) (EntityView attribute) (MMCifInfoBioUnit attribute) ChainType (class in ost.mol) ChainTypeFromString() (in module ost.mol) ChainView (class in ost.mol) ChangeDisplayMode() (in module ost.gui) charge (AtomHandle attribute) check_bond_feasibility (Processor attribute) CheckStereoChemistry() (in module ost.mol.alg) CheckStructure() built-in function chem_class (Compound attribute) (ResidueHandle attribute) (ResidueView attribute) chem_group_alignments (ChainMapper property) chem_group_ref_seqs (ChainMapper property) chem_group_types (ChainMapper property) chem_groups (ChainMapper property) (MappingResult property) (QSscoreEntity property) (QSScorer property) chem_mapping (MappingResult property) (OligoLDDTScorer attribute) (QSscorer property) chem_type (Compound attribute) (ResidueHandle attribute) (ResidueView attribute) ChemClass (class in ost.mol) ChemType (class in ost.mol) Circle2 (class in ost.geom) citation_type (MMCifInfoCitation attribute) citations (MMCifInfo attribute) ClashEvent (class in ost.mol.alg) ClashInfo (class in ost.mol.alg.stereochemistry) ClashingDistances (class in ost.mol.alg) ClashingDistances() (ClashingDistances method) ClashingInfo (class in ost.mol.alg) CleanlDDTReferences() built-in function

Cleanup() (HHblits method) (in module ost.conop.cleanup) CleanUpElementColumn() (in module ost.mol.alg) CleanupFailed() (HHblits method) ClearCache() (CompoundLib method) ClearProps() (GenericPropertyContainer method) ClearRange() (LinearCharacterContainer method) (LinearPositionContainer method) Click() (Tool method) ClipAlignment() (in module ost.seq.alg) ClustalW() (in module ost.bindings.clustalw) clustalw_bin (QSscorer property) cluster (class in ost.bindings.kclust) cmm_frequency (Settings attribute) cname (lDDTLocalScore attribute) ColorBy() (Entity method) ColorByElement() (Entity method) colored (MolckSettings attribute) columns (ProfileHandle attribute) command (HHblitsHeader attribute) CompDivide() (in module ost.geom) COMPLEX_SPATIAL (in module ost.img) CompMultiply() (in module ost.geom) Compound (class in ost.conop) CompoundLib (class in ost.conop) ComputeEnrichment() (Table method) ComputeEnrichmentAUC() (Table method) ComputeLogROCAUC() (Table method) ComputeMCC() (Table method) ComputeROC() (Table method) ComputeROCAUC() (Table method) connect (Processor attribute) Connect() (BuildingBlock method) (EditorBase method) connect_hetatm (Processor attribute) ConnectBranchLink() (MMCifInfoEntityBranchLink method) ConnectBranchLinks() (MMCifInfo method) ConopAction (class in ost.conop) Conservation() (in module ost.seq.alg) conserved_dist (lDDTLocalScore attribute) constrain_bonds (Settings attribute) constrain_hbonds (Settings attribute) ConstSequenceHandle (class in ost.seq) ConstSequenceList (class in ost.seq) contact_d (QSEntity property) ContactPredictionScoreResult (class in ost.seq.alg) contacts (QSscoreEntity property) contacts_ca (QSscoreEntity property) ContactWeightMatrix (class in ost.seq.alg) ContextActionType (in module ost.gui) ContextActionTypes (in module ost.gui) ContextMenu (class in ost.gui) ContextProfileDB (class in ost.seq.alg) CoordFrame (class in ost.mol) CoordGroupHandle (class in ost.mol) CoordToIndex() (ImageHandle method) Copy() (AlignmentHandle method) (CompoundLib method) (ConstSequenceHandle method) (EntityHandle method) (EntityView method) (ImageHandle method) CopyConserved() (in module ost.mol.alg) CopyFrame() (CoordGroupHandle method) CopyNonConserved() (in module ost.mol.alg) CopyResidue() (in module ost.mol.alg) Correl() (Table method) Count() (Table method) CPK (in module ost.gfx) cpu_properties (Settings attribute) Create() (CompoundLib static method) (TopologyCreator method) CreateAlignment() (in module ost.seq) CreateApolarSet() (AminoAcidSet static method) CreateAromaticSet() (AminoAcidSet static method) CreateCoordGroup() (in module ost.mol) CreateDist2Mean() (in module ost.seq.alg) CreateDistanceList() built-in function CreateDistanceListFromMultipleReferences() built-in function CreateDistanceMap() (in module ost.seq.alg) CreateEmptyView() (EntityHandle method) (EntityView method) CreateEntity() (in module ost.mol) CreateEntityFromView() (in module ost.mol) CreateFullView() (EntityHandle method) (EntityView method) CreateMeanlDDTHA() (in module ost.seq.alg) CreatePolarSet() (AminoAcidSet static method) CreateSequence() (in module ost.seq) CreateSequenceList() (in module ost.seq) CreateVarianceMap() (in module ost.seq.alg) CreateViewFromAtomList() (in module ost.mol) Cross() (in module ost.geom) Cuboid (class in ost.geom) CuboidAxis (class in ost.geom) cuda_properties (Settings attribute) CUSTOM (in module ost.gfx) custom_plugin_directory (Settings attribute) CustomCompound (class in ost.mol.alg.lddt) Cut() (AlignmentHandle method) cutoffs (lDDTSettings attribute)

D

date (HHblitsHeader attribute) (MMCifInfoObsolete attribute) date_original (MMCifInfoRevisions attribute) db_access (MMCifInfoStructRef attribute) db_begin (MMCifInfoStructRefSeq attribute) db_end (MMCifInfoStructRefSeq attribute) db_id (MMCifInfoStructRef attribute) db_name (MMCifInfoStructRef attribute) DefaultAngleStereoChemicalParams() (in module ost.mol.alg) DefaultBondStereoChemicalParams() (in module ost.mol.alg) DefaultClashingDistances() (in module ost.mol.alg) DefaultCompoundLibIsSet() (in module ost.testutils) DeleteAllAtoms() (EditorBase method) DeleteAtom() (EditorBase method) DeleteAtoms() (EditorBase method) DeleteChain() (EditorBase method) DeleteResidue() (EditorBase method) DeleteResidues() (EditorBase method) description (ChainHandle attribute) descriptor (MMCifInfoStructDetails attribute) Det() (in module ost.geom) details (MMCifInfoBioUnit attribute) (MMCifInfoStructRefSeqDif attribute) DFT (class in ost.img.alg) dialect (Compound attribute) (IOProfile attribute) Difference() (in module ost.mol)

difs (MMCifInfoStructRefSeq attribute) direction (Line2 attribute) (Line3 attribute) DiscreteShrink (class in ost.img.alg) Dist2Mean (class in ost.seq.alg) Distance() (in module ost.geom) DistanceMap (class in ost.seq.alg) DistanceMatrixFromPairwiseDistances() (in module ost.mol.alg.trajectory_analysis) DistanceRMSDTest() built-in function Distances (class in ost.seq.alg) DistRMSDFromTraj() (in module ost.mol.alg.trajectory_analysis) DockQ (DockQResult property) DockQ() (in module ost.bindings.dockq) (in module ost.mol.alg.dockq) dockq_ave (Scorer property) dockq_ave_full (Scorer property) dockq_scores (Scorer property) dockq_wave (Scorer property) dockq_wave_full (Scorer property) DockQResult (class in ost.bindings.dockq) doi (MMCifInfoCitation attribute) domain (ImageHandle attribute) Dot() (in module ost.geom) DoubleClick() (Tool method) DRMSD() built-in function

E

EditICS() (EntityHandle method) EditorBase (class in ost.mol) EditXCS() (EntityHandle method) element (AtomHandle attribute) (AtomSpec attribute) Ellipse2 (class in ost.geom) Empty() (AminoAcidSet method) EnableTabbedMode() (MainArea method) end (AlignedRegion attribute) End() (ToolOptionEnum method) energy (FindMemParam attribute) ent (QSscoreEntity attribute) ent_to_cm_1 (QSscorer property) ent_to_cm_2 (QSscorer property) Entity (class in ost.gfx) entity (CoordGroupHandle attribute) EntityHandle (class in ost.mol) EntityToPDBStr() (in module ost.io) EntityToSDFStr() (in module ost.io) EntityView (class in ost.mol) entropy (ProfileColumn attribute) entry_id (MMCifInfoStructDetails attribute) Equal() (in module ost.geom)

error (Query attribute) EulerTransformation() (in module ost.geom) evalue (AlignedPatch attribute) (HHblitsHit attribute) Export() (Scene method) ExportCsv() (Dist2Mean method) (VarianceMap method) ExportDat() (Dist2Mean method) (VarianceMap method) ExportJson() (Dist2Mean method) (VarianceMap method) ExportPov() (Scene method) extend() (SurfaceTriIDList method) (SurfaceVertexList method) Extend() (Table method) Extent (class in ost.img) extent (CuboidAxis attribute) (ImageHandle attribute) Extract() (ImageHandle method) (ProfileHandle method) ExtractRotation() (Mat4 method) ExtractTemplateData() (in module ost.db) ExtractTranslation() (Mat4 method) ExtractValidPositions() (in module ost.db)

F

fault_tolerant (IOProfile attribute) FermiHighPassFilter (class in ost.img.alg) FermiLowPassFilter (class in ost.img.alg) FFReader (class in ost.mol.mm) FFT (class in ost.img.alg) FileLogSink (class in ost) FileNotFound FillAngleStereoChemicalParams() (in module ost.mol.alg) FillAngleStereoChemicalParamsFromFile() (in module ost.mol.alg) FillBondStereoChemicalParams() (in module ost.mol.alg) FillBondStereoChemicalParamsFromFile() (in module ost.mol.alg) FillClashingDistances() (in module ost.mol.alg) FillClashingDistancesFromFile() (in module ost.mol.alg) Filter() (CoordGroupHandle method) (Table method) FilterClashes() (in module ost.mol.alg) FilterContacts() (in module ost.mol.alg.qsscoring) Finalize() (TrajWriter method) FindAtom() (ChainHandle method) (ChainView method) (EntityHandle method) (EntityView method) (ResidueHandle method) (ResidueView method) FindBondToAtom() (AtomHandle method) FindChain() (EntityHandle method) (EntityView method) FindCompound() (CompoundLib method) FindMembrane() (in module ost.mol.alg) FindMemParam (class in ost.mol.alg) FindResidue() (ChainHandle method) (ChainView method) (EntityHandle method) (EntityView method)

FindSequence() (AlignmentHandle method) (ConstSequenceList method) FindWithin() (EntityHandle method) (EntityView method) (SurfaceHandle method) first (BondHandle attribute) first_release (MMCifInfoRevisions attribute) fix_elements (RuleBasedProcessor attribute) fix_heavy_atoms (Settings attribute) FixTransform() (XCSEditor method) Fnat (DockQResult property) fnat (Scorer property) Fnonnat (DockQResult property) fnonnat (Scorer property) Forcefield (class in ost.mol.mm) forcefield (Settings attribute) ForceUpdate() (XCSEditor method) formula (Compound attribute) fov (Scene attribute) fraction_superposed (SuperpositionResult attribute) FractionalIndexToCoord() (ImageHandle method) FREQUENCY (in module ost.img) FromBytes() (ost.io.OMF static method) FromCRF() (ContextProfileDB method) FromDockQOutput() (DockQResult static method) FromEntity() (ost.io.OMF static method) FromFile() (ost.io.OMF static method) FromFlatMapping() (QSScorer method) FromMappingResult() (QSScorer static method) FromMMCIF() (ost.io.OMF static method) FromResidue() (CustomCompound static method)

G

gapless_string (ConstSequenceHandle attribute) GaussianFilter (class in ost.img.alg) GaussianHighPassFilter (class in ost.img.alg) GaussianLowPassFilter (class in ost.img.alg) GaussianSmooth() (Table method) GDT() (in module ost.bindings.lga) gdt_1 (ReprResult property) gdt_2 (ReprResult property) gdt_4 (ReprResult property) gdt_8 (ReprResult property) gdt_ha (TMScoreResult attribute) gdt_ts (TMScoreResult attribute) gdtha (Scorer property) GDTResult (class in ost.bindings.lga) gdtts (Scorer property) generate_disulfid_bonds (Settings attribute) GenericPropertyContainer (class in ost) geometric_center (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (EntityView attribute) (ResidueHandle attribute) (ResidueView attribute) Get() (Dist2Mean method) (RemoteRepository method) (VarianceMap method) GetA() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) (Ellipse2 method) GetAbsoluteOrigin() (ImageHandle method) GetAdjustedClashingDistance() (ClashingDistances method) GetAdjustedReferenceDistance() (ClashEvent method) GetAlignedSeq() (MMCifInfoStructRef method) GetAlignment() (QSscoreEntity method) GetAlignmentHandle() (AlignedRegion method) GetAllowedRange() (StereoChemicalAngleViolation method) (StereoChemicalBondViolation method) GetAlphaHelixContent() (in module ost.mol.alg.structure_analysis) GetAltAtomGroupNames() (ResidueHandle method) GetAngle() (CoordFrame method) (EntityView method) (Forcefield method) GetAngleCount() (StereoChemistryInfo method) GetAngleParam() (in module ost.mol.alg.stereochemistry) GetAngles() (BuildingBlock method) (QSscoreEntity method) GetAngleViolationList() (StereoChemistryInfo method) GetAngleWidth() (StereoChemicalAngleViolation method) GetArea() (Circle2 method) (Ellipse2 method) GetAssemblies() (LinearIndexer method) GetAtom1() (MMCifInfoEntityBranchLink method) GetAtom2() (MMCifInfoEntityBranchLink method) GetAtomCount() (CoordGroupHandle method) (EntityHandle method) (EntityView method) (ResidueHandle method) (ResidueView method) GetAtomList() (ChainHandle method) (CoordGroupHandle method) (EntityHandle method) (EntityView method) (ResidueHandle method) (ResidueView method) GetAtomName() (UniqueAtomIdentifier method) GetAtomPos() (CoordFrame method) (CoordGroupHandle method) GetAtoms() (BuildingBlock method) (Interaction method) GetAtomType() (Forcefield method) GetAttachedView() (ConstSequenceHandle method) GetAU() (ost.io.OMF method) GetAUChain() (ost.io.OMF method) GetAuthorList() (MMCifInfoCitation method) GetAverage() (Distances method) GetAverageOffset() (ClashingInfo method) GetAverageScore() (ProfileHandle method) GetAvgZscoreAngles() (StereoChemistryInfo method) GetAvgZscoreBonds() (StereoChemistryInfo method) GetAxis() (QSscoreEntity method) GetB() (Ellipse2 method) GetBadAngleCount() (StereoChemistryInfo method) GetBadAngles() (in module ost.mol.alg.stereochemistry) GetBadBondCount() (StereoChemistryInfo method) GetBadBonds() (in module ost.mol.alg.stereochemistry) GetBins() (Histogram method), [1] GetBioUnits() (MMCifInfo method) GetBlockModifier() (Forcefield method) GetBlocksize() (DiscreteShrink method) GetBond() (Forcefield method) GetBondCount() (AtomHandle method) (EntityView method) (ResidueHandle method) (StereoChemistryInfo method) GetBondLength() (StereoChemicalBondViolation method) GetBondList() (AtomHandle method) (EntityView method) GetBondOrder() (BondHandle method) (MMCifInfoEntityBranchLink method) GetBondParam() (in module ost.mol.alg.stereochemistry) GetBondPartners() (AtomHandle method) GetBonds() (BuildingBlock method) GetBondViolationList() (StereoChemistryInfo method) GetBookPublisher() (MMCifInfoCitation method) GetBookPublisherCity() (MMCifInfoCitation method) GetBoolProp() (GenericPropertyContainer method) GetBoundingBox() (Ellipse2 method) GetBounds() (ResidueHandle method) (ResidueView method) GetBU() (ost.io.OMF method) GetBuildingBlock() (Forcefield method) GetBuildingBlockNames() (Forcefield method) GetCAS() (MMCifInfoCitation method) GetCASPFlag() (MMCifInfoStructDetails method) GetCenter() (Circle2 method) GetCenterOfAtoms() (ChainView method) (EntityHandle method) (EntityView method) (ResidueHandle method) (ResidueView method) GetCenterOfMass() (ChainView method) (EntityHandle method) (EntityView method) (ResidueHandle method) (ResidueView method) GetCenterOfMassPos() (CoordFrame method) GetCentralAtom() (ResidueHandle method) (ResidueView method) GetCentralNormal() (ResidueHandle method) (ResidueView method) GetChain() (QSEntity method) (ResidueHandle method) (ResidueView method) GetChainCount() (EntityHandle method) (EntityView method) GetChainIntervalList() (MMCifInfoBioUnit method) GetChainLengths() (LinearIndexer method) GetChainList() (EntityHandle method) (EntityView method) (MMCifInfoBioUnit method) GetChainName() (UniqueAtomIdentifier method) GetChainNames() (LinearIndexer method) GetCharacter() (LinearCharacterContainer method) GetCharacters() (LinearCharacterContainer method) GetCharge() (AtomHandle method) (BuildingBlock method) (Topology method) GetCharges() (BuildingBlock method) (Topology method) GetChemClass() (ResidueHandle method) (ResidueView method) GetChemMapping() (ChainMapper method) GetChemType() (ResidueHandle method) (ResidueView method) GetCircumference() (Circle2 method) GetCitations() (MMCifInfo method) GetCitationType() (MMCifInfoCitation method) GetClashCount() (ClashingInfo method) GetClashes() (in module ost.mol.alg.stereochemistry) GetClashingDistance() (ClashingDistances method) GetClashList() (ClashingInfo method) GetCMap() (Forcefield method) GetCMapIndices() (Topology method), [1] GetCMapParameters() (Topology method) GetCMaps() (BuildingBlock method) GetColIndex() (Table method) GetColNames() (Table method) GetComplex() (ImageHandle method) GetConstraint() (Forcefield method) GetConstraints() (BuildingBlock method) GetContacts() (in module ost.mol.alg.qsscoring) GetContextMenu() (SceneWin method) GetCount() (AlignmentHandle method) (ConstSequenceList method) GetCoverage() (AlignmentHandle method) GetCreationDate() (CompoundLib method) GetCTerModifier() (Forcefield method) GetCurrentAltGroupName() (ResidueHandle method) GetCurrentDisplayMode() (in module ost.gui) GetCurrentLogSink() (in module ost) GetData() (Dist2Mean method) (VarianceMap method) GetDataElement() (Distances method) GetDataRange() (LinearIndexer method), [1] GetDataSize() (Distances method) GetDate() (MMCifInfoObsolete method) (MMCifInfoRevisions method) GetDateOriginal() (MMCifInfoRevisions method) GetDefault() (ToolOptionFloat method) (ToolOptionInt method) GetDefaultLib() (in module ost.conop) GetDefaultStereoData() (in module ost.mol.alg.stereochemistry) GetDefaultStereoLinkData() (in module ost.mol.alg.stereochemistry) GetDefaultSymmetrySettings() (in module ost.mol.alg.lddt) GetDescription() (ChainHandle method) GetDescriptor() (MMCifInfoStructDetails method) GetDetails() (MMCifInfoBioUnit method) GetDihedralAngle() (CoordFrame method) GetDihedrals() (BuildingBlock method) (Forcefield method) GetDirection() (Line2 method) (Line3 method) GetDisplayModes() (in module ost.gui) GetDistanceBetwAtoms() (CoordFrame method) GetDistanceBetwCenterOfMass() (CoordFrame method) (in module ost.mol.alg.structure_analysis) GetDistanceConstraintIndex() (Topology method) GetDistanceConstraintIndices() (Topology method) GetDistanceConstraintParameters() (Topology method) GetDistances() (DistanceMap method) GetDOI() (MMCifInfoCitation method) GetDomain() (ImageHandle method) GetElement() (AtomHandle method) GetEnd() (Rectangle2 method) GetEnergy() (Simulation method) GetEntity() (AtomHandle method) (ChainView method) (CoordGroupHandle method) (Simulation method) GetEntityBranchByChain() (MMCifInfo method) GetEntityBranchChainNames() (MMCifInfo method) GetEntityBranchChains() (MMCifInfo method) GetEntityBranchLinks() (MMCifInfo method) GetEntryID() (MMCifInfoStructDetails method) GetEps() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) GetEpsilon() (Topology method) GetEpsilons() (Topology method) GetErrorTolerance() (VariableLangevinIntegrator method) (VariableVerletIntegrator method) GetException() (TerminiExceptions method) GetExclusions() (BuildingBlock method) GetExtent() (CuboidAxis method) (ImageHandle method) GetFirst() (BondHandle method) GetFirstAtom() (ClashEvent method) (StereoChemicalAngleViolation method) (StereoChemicalBondViolation method) GetFirstNonGap() (ConstSequenceHandle method) GetFirstRelease() (MMCifInfoRevisions method) GetFlatChainMapping() (ReprResult method) GetFlatMapping() (MappingResult method) GetFloatProp() (GenericPropertyContainer method) GetForcefield() (FFReader method) GetForces() (Simulation method) GetFOV() (Scene method) GetFrameCount() (CoordGroupHandle method) GetFrameFromEntity() (in module ost.mol.alg.structure_analysis) GetFreq() (ProfileColumn method) GetFrequencySampling() (ImageHandle method) GetFriction() (BrownianIntegrator method) (LangevinIntegrator method) (VariableLangevinIntegrator method) GetFudgeLJ() (Forcefield method) GetFudgeQQ() (Forcefield method) GetFuncType() (Interaction method) GetGamma() (Ellipse2 method) GetGaplessString() (ConstSequenceHandle method) GetGBSARadii() (Topology method) GetGBSARadius() (Topology method) GetGeometricCenter() (ChainView method) (EntityHandle method) (EntityView method) (ResidueHandle method) (ResidueView method) GetGeometricEnd() (EntityView method) GetGeometricStart() (EntityView method) GetHalfExtent() (CuboidAxis method) GetHandle() (AtomView method) (ChainView method) (EntityView method) (ResidueView method) GetHarmonicAngleIndices() (Topology method), [1] GetHarmonicAngleParameters() (Topology method) GetHarmonicBondIndices() (Topology method), [1] GetHarmonicBondParameters() (Topology method) GetHarmonicDistanceRestraintIndices() (Topology method) GetHarmonicDistanceRestraintParameters() (Topology method) GetHarmonicImproperIndices() (Topology method) GetHarmonicImproperParameters() (Topology method) GetHarmonicImpropersIndices() (Topology method) GetHarmonicPositionRestraintIndices() (Topology method) GetHarmonicPositionRestraintParameters() (Topology method) GetHashCode() (AtomHandle method) (AtomView method) (BondHandle method) (ChainHandle method) (ChainView method) (ResidueHandle method) (ResidueView method) GetHeader() (lDDTLocalScore method) GetHeight() (Rectangle2 method) GetHMMData() (ProfileColumn method) GetHydrogenConstructor() (Forcefield method) GetIconPath() (Tool method) GetID() (MMCifInfoBioUnit method) (MMCifInfoObsolete method) (MMCifInfoTransOp method) GetImplicitGenborn() (Forcefield method) GetImpropers() (BuildingBlock method) (Forcefield method) GetIndex() (AlignedColumn method) (AtomHandle method) (ResidueHandle method) (ResidueView method) (ToolOptionEnum method)

GetInsCode() (ResNum method) GetIntpolComplex() (ImageHandle method) GetIntpolReal() (ImageHandle method) GetIntProp() (GenericPropertyContainer method) GetISBN() (MMCifInfoCitation method) GetJsonString() (Dist2Mean method) (VarianceMap method) GetKineticEnergy() (Simulation method) GetLastDate() (MMCifInfoRevisions method) GetLastMajor() (MMCifInfoRevisions method) GetLastMinor() (MMCifInfoRevisions method) GetLastNonGap() (ConstSequenceHandle method) GetlDDTMapping() (ChainMapper method) GetlDDTPerResidueStats() built-in function GetLength() (AlignedRegion method) (AlignmentHandle method) (BondHandle method) GetLimit() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) (FermiHighPassFilter method) (FermiLowPassFilter method) (GaussianHighPassFilter method) (GaussianLowPassFilter method) (HighPassFilter method) (LowPassFilter method) GetLJ() (Forcefield method) GetLJPairIndex() (Topology method) GetLJPairIndices() (Topology method) GetLJPairParameters() (Topology method) GetLowerLimit() (ToolOptionFloat method) (ToolOptionInt method) GetMainArea() (Perspective method) GetMajor() (MMCifInfoRevisions method) GetMapping() (ChainMapper method) GetMass() (AtomHandle method) (BuildingBlock method) (ChainView method) (EntityHandle method) (EntityView method) (Forcefield method) (MMCifInfoStructDetails method) (ResidueHandle method) (ResidueView method) (Topology method) GetMasses() (BuildingBlock method) (Topology method) GetMassMethod() (MMCifInfoStructDetails method) GetMatchingBackboneViews() (AlignmentHandle method) GetMatrix() (MMCifInfoTransOp method) GetMax() (AlignedCuboid method) (Distances method) GetMaxAdjustedDistance() (ClashingDistances method) GetMaxLength() (ConstSequenceList method) GetMaxWeight() (SubstWeightMatrix method) GetMenu() (PanelManager method) (Perspective method) GetMenuBar() (Perspective method) GetMethod() (MMCifInfo method) GetMethodDetails() (MMCifInfoBioUnit method) GetMin() (AlignedCuboid method) (Distances method) GetMinDistanceBetweenViews() (in module ost.mol.alg.structure_analysis) GetMinDistBetwCenterOfMassAndView() (in module ost.mol.alg.structure_analysis) GetMinLength() (ConstSequenceList method) GetMinor() (MMCifInfoRevisions method) GetMinWeight() (SubstWeightMatrix method) GetMMCifEntityIdTr() (MMCifInfo method) GetMMCifPDBChainTr() (MMCifInfo method) GetMode() (EditorBase method) GetModelDetails() (MMCifInfoStructDetails method) GetModelDistance() (ClashEvent method) GetModelTypeDetails() (MMCifInfoStructDetails method) GetName() (AtomHandle method) (ChainHandle method) (ChainView method) (ConstSequenceHandle method) (EntityHandle method) (EntityView method) (QSscoreEntity method) (ResidueHandle method) (ResidueView method) (Table method) (Tool method) GetNames() (Interaction method) (ProfileDB method) GetNChainContacts() (lDDTScorer method) GetNext() (ResidueHandle method) (ResidueView method) GetNMappings() (ChainMapper method) GetNormal() (Plane method) GetNormStdDev() (Distances method) GetNTerModifier() (Forcefield method) GetNum() (MMCifInfoRevisions method) (ResNum method) GetNumber() (ResidueHandle method) (ResidueView method) GetNumCMaps() (Topology method) GetNumDistanceConstraints() (Topology method) GetNumElements() (LinearCharacterContainer method) (LinearPositionContainer method) GetNumExclusions() (Topology method) GetNumHarmonicAngles() (Topology method) GetNumHarmonicBonds() (Topology method) GetNumHarmonicDistanceRestraints() (Topology method) GetNumHarmonicImpropers() (Topology method) GetNumHarmonicPositionRestraints() (Topology method) GetNumLJPairs() (Topology method) GetNumParticles() (Topology method) GetNumPeriodicDihedrals() (Topology method) GetNumPeriodicImpropers() (Topology method) GetNumPositionConstraints() (Topology method) GetNumpyMatrix() (Table method) GetNumpyMatrixAsArray() (Table method) GetNumResidues() (Dist2Mean method) (LinearIndexer method) GetNumStructures() (Dist2Mean method) (DistanceMap method) GetNumUreyBradleyAngles() (Topology method) GetOBCScaling() (Topology method) GetOBCScalings() (Topology method) GetObsoleteInfo() (MMCifInfo method) GetOffset() (ConstSequenceHandle method) GetOligoLDDTScorer() (QSscorer method) GetOmegaTorsion() (ResidueHandle method) (ResidueView method) GetOneLetterCode() (ConstSequenceHandle method) (ResidueHandle method) (ResidueView method) GetOperations() (MMCifInfo method) (MMCifInfoBioUnit method) GetOperationsIntervalList() (MMCifInfoBioUnit method) GetOptimalPrefactors() (Table method) GetOrigin() (Ellipse2 method) (Line2 method) (Line3 method) (Plane method) (Sphere method) GetOriginalPos() (AtomHandle method) GetOSTVersionUsed() (CompoundLib method) GetOther() (BondHandle method) GetP() (Plane method) GetPageFirst() (MMCifInfoCitation method) GetPageLast() (MMCifInfoCitation method) GetPairScore() (AAIndexData method) GetPanels() (Perspective method) GetParam() (Interaction method) GetPDBID() (MMCifInfoObsolete method) GetPDBMMCifChainTr() (MMCifInfo method) GetPeriodicBoxExtents() (Simulation method) GetPeriodicDihedralIndices() (Topology method), [1] GetPeriodicDiheralParameters() (Topology method) GetPeriodicImproperIndices() (Topology method) GetPeriodicImproperParameters() (Topology method) GetPeriodicImpropersIndices() (Topology method) GetPerResidueScores() (MappedLDDTScorer method) GetPhiTorsion() (ResidueHandle method) (ResidueView method) GetPixelSampling() (ImageHandle method) GetPlatform() (in module ost.settings) GetPos() (AlignmentHandle method) (AtomHandle method) (BondHandle method) (ConstSequenceHandle method) (QSEntity method) GetPosition() (LinearPositionContainer method) GetPositions() (EntityHandle method) (LinearPositionContainer method) (Simulation method) GetPotentialEnergy() (Simulation method) GetPrev() (ResidueHandle method) (ResidueView method) GetProb() (HMMData method) GetProfile() (ProfileDB method) GetPropAsString() (GenericPropertyContainer method) GetPsiTorsion() (ResidueHandle method) (ResidueView method) GetPublishedIn() (MMCifInfoCitation method) GetPubMed() (MMCifInfoCitation method) GetQObject() (ContextMenu method) (in module ost.gui) (PanelManager method) (SceneWin method) GetQSScoreMapping() (ChainMapper method) GetQualifiedAtomName() (UniqueAtomIdentifier method) GetQualifiedName() (AtomHandle method) (ResidueHandle method) (ResidueView method) GetRadius() (AtomHandle method) (Circle2 method) (Sphere method) GetRandomNumberSeed() (BrownianIntegrator method) (LangevinIntegrator method) (VariableLangevinIntegrator method) GetReal() (ImageHandle method) GetReplacedPDBID() (MMCifInfoObsolete method) GetRepr() (ChainMapper method) GetResidue() (AlignedColumn method) (AlignmentHandle method) (AtomHandle method) (ConstSequenceHandle method) GetResidueByIndex() (ChainView method) GetResidueCount() (ChainHandle method) (EntityHandle method) (EntityView method) GetResidueIndex() (AlignmentHandle method) (ConstSequenceHandle method) GetResidueList() (ChainHandle method) (ChainView method) (EntityHandle method) (EntityView method) GetResidueName() (UniqueAtomIdentifier method) GetResNum() (UniqueAtomIdentifier method) GetResolution() (MMCifInfo method) GetRevisions() (MMCifInfo method) GetRigidMapping() (ChainMapper method) GetRMSD() (CoordFrame method) GetRowCount() (AlignedColumn method) GetRTC() (Scene method) GetScore() (AAIndexData method) (ContactPredictionScoreResult method) (ProfileColumn method) GetSecond() (BondHandle method) GetSecondAtom() (ClashEvent method) (StereoChemicalAngleViolation method) (StereoChemicalBondViolation method) GetSecStructure() (ResidueHandle method) (ResidueView method) GetSequence() (AlignmentHandle method) (QSEntity method) GetSequenceOffset() (AlignmentHandle method) GetSequenceRole() (AlignmentHandle method) GetSequences() (AlignmentHandle method) GetSigma() (GaussianFilter method) (Topology method) GetSigmas() (Topology method) GetSize() (DistanceMap method) (ImageHandle method) (MMCifInfoRevisions method) (VarianceMap method) GetSpatialOrigin() (ImageHandle method) GetSpatialSampling() (ImageHandle method) GetStart() (Rectangle2 method) GetStatus() (MMCifInfoRevisions method) GetStdDev() (Distances method) GetStereoChemicalPropsFile() (in module ost.io) GetStop() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) GetStringProp() (GenericPropertyContainer method) GetStructDetails() (MMCifInfo method) GetSubData() (Dist2Mean method) (VarianceMap method) GetT() (FermiHighPassFilter method) (FermiLowPassFilter method) GetTemperature() (BrownianIntegrator method) (LangevinIntegrator method) (VariableLangevinIntegrator method) GetThirdAtom() (StereoChemicalAngleViolation method) GetTitle() (MMCifInfoCitation method) (MMCifInfoStructDetails method) GetToolOptions() (Tool method) GetTopology() (Simulation method) GetTraj() (TrajObserver method) GetTransform() (Scene method) GetTriIDList() (SurfaceHandle method) GetType() (BuildingBlock method) (ChainHandle method) (ImageHandle method) (MMCifInfoTransOp method) GetTypes() (BuildingBlock method) (Interaction method) GetUnique() (Table method) GetUnknownAtomsOfResidue() (in module ost.conop) GetUpperLimit() (ToolOptionFloat method) (ToolOptionInt method) GetUreyBradleyAngleIndices() (Topology method), [1] GetUreyBradleyAngleParameters() (Topology method) GetValue() (in module ost.settings) (ToolOptionEnum method) (ToolOptionFloat method) (ToolOptionInt method) GetVector() (CuboidAxis method) (MMCifInfoTransOp method) GetVelocities() (Simulation method) GetVerbosityLevel() (in module ost) GetVersion() (in module ost.bindings.msms) GetVertex() (SurfaceHandle method) GetVertexIDList() (SurfaceHandle method) GetVolume() (MMCifInfoCitation method) GetWeight() (SubstWeightMatrix method) GetWeightedStdDev() (Distances method) GetWidth() (Rectangle2 method) GetYear() (MMCifInfoCitation method) global_score (QSscorer property) globalAA (CADResult attribute) GlobalAlign() (in module ost.seq.alg) GlobalRDMap (built-in class) GromacsBlockModifier (class in ost.mol.mm) GromacsHydrogenConstructor (class in ost.mol.mm)

H

half_extent (CuboidAxis attribute) HALF_FREQUENCY (in module ost.img) handle (AtomView attribute) (ChainView attribute) (EntityView attribute) (ResidueView attribute) HasAltAtomGroup() (ResidueHandle method) HasAltAtoms() (ResidueHandle method) HasAttachedView() (ConstSequenceHandle method) HasCol() (Table method) HasException() (TerminiExceptions method) hash_code (AtomHandle attribute) (AtomView attribute) (BondHandle attribute) (ChainHandle attribute) (ChainView attribute) (ResidueHandle attribute) (ResidueView attribute) HasName() (Interaction method) HasNameWildcard() (Interaction method) HasProp() (GenericPropertyContainer method) HasType() (Interaction method) HasTypeWildcard() (Interaction method)

HBond (class in ost.bindings.hbplus) HBondList() (in module ost.bindings.hbplus) HBondScore() (in module ost.bindings.hbplus) height (Rectangle2 attribute) HeuristicHydrogenConstructor (class in ost.mol.mm) HeuristicProcessor (class in ost.conop) HHblits (class in ost.bindings.hhblits3) HHblitsHeader (class in ost.bindings.hhblits3) HHblitsHit (class in ost.bindings.hhblits3) HHblitsNullModel() (ProfileColumn method) Hide() (in module ost.gui) (SceneWin method) HideAllBars() (Perspective method) HideSubWindow() (MainArea method) HighPassFilter (class in ost.img.alg) Histogram (class in ost.img.alg) hit_id (HHblitsHit attribute) hmm_data (ProfileColumn attribute) HMMData (class in ost.seq) HMMScore() (in module ost.seq.alg) HMMTransition (class in ost.seq) HSC (in module ost.gfx) HydrogenConstructor (class in ost.mol.mm)

I

ICSEditor (class in ost.mol) id (Compound attribute) (MMCifInfoBioUnit attribute) (MMCifInfoCitation attribute) (MMCifInfoObsolete attribute) (MMCifInfoTransOp attribute) ideal_bond_length_constraints (Settings attribute) identifier (BlastHit attribute) Identity() (Mat2 static method) (Mat3 static method) (Mat4 static method) ImageHandle (class in ost.img) in_sequence (ChainHandle attribute) (ChainView attribute) inchi (Compound attribute) inchi_key (Compound attribute) inconsistent_residues (ReprResult property) index (AtomHandle attribute) (ResidueHandle attribute) (ResidueView attribute) IndexToCoord() (ImageHandle method) init_temperature (Settings attribute) ins_code (ResNum attribute) InSequence() (ChainView method) (in module ost.mol) InsertAltAtom() (EditorBase method), [1] InsertAtom() (EditorBase method) InsertChain() (EditorBase method) Integrator (class in ost.mol.mm) integrator (Settings attribute) interacting_chains (QSEntity property) Interaction (class in ost.mol.mm) interface_qs_best (Scorer property) interface_qs_global (Scorer property) interfaces (Scorer property) Intersection() (in module ost.mol) IntersectionPoint() (in module ost.geom) Invert() (in module ost.geom) (SurfaceHandle method) IOProfile (class in ost.io) iRMS (DockQResult property) irmsd (Scorer property) is_assessed (lDDTLocalScore attribute) is_hetatom (AtomHandle attribute) is_leaving (AtomSpec attribute) is_ligand (ResidueHandle attribute) (ResidueView attribute) is_oligosaccharide (ChainHandle attribute) is_polymer (ChainHandle attribute) is_polynucleotide (ChainHandle attribute) is_polypeptide (ChainHandle attribute) is_polysaccharide (ChainHandle attribute) is_protein (ResidueHandle attribute) (ResidueView attribute) is_valid (QSscoreEntity attribute) IsAminoAcid() (ChemType method)

IsAtomIncluded() (ResidueView method) IsAtomSelected() (Query method) isbn (MMCifInfoCitation attribute) IsBondFeasible() (in module ost.conop) IsChainSelected() (Query method) IsCitationTypeBook() (MMCifInfoCitation method) IsCitationTypeJournal() (MMCifInfoCitation method) IsCitationTypeUnknown() (MMCifInfoCitation method) IsCoenzyme() (ChemType method) IsCoil() (SecStructure method) IsDrug() (ChemType method) IsEmpty() (ClashingDistances method) (StereoChemicalParams method) (Table method) IsExtended() (SecStructure method) IsFrequency() (ImageHandle method) IsHelical() (SecStructure method) IsHetAtom() (AtomHandle method) IsInPlane() (in module ost.geom) IsInSphere() (in module ost.geom) IsIon() (ChemType method) IsKnown() (ChemType method) IsLigand() (ResidueHandle method) (ResidueView method) IsNonCanonical() (ChemType method) IsNucleotide() (ChemType method) IsNucleotideLinking() (ChemClass method) (ResidueHandle method) (ResidueView method) IsOligosaccharide() (ChainHandle method) IsOnLine() (in module ost.geom) IsParametrized() (Interaction method) IsPeptideLinking() (ChemClass method) (ResidueHandle method) (ResidueView method) IsPlatformAvailable() (Simulation static method) IsPolymer() (ChainHandle method) IsPolynucleotide() (ChainHandle method) IsPolypeptide() (ChainHandle method) IsPolysaccharide() (ChainHandle method) IsProtein() (ResidueHandle method) (ResidueView method) IsResidueSelected() (Query method) IsSaccharide() (ChemType method) IsSpatial() (ImageHandle method) IsValid() (AtomHandle method) (BondHandle method) (ChainHandle method) (ChainView method) (CoordGroupHandle method) (EntityHandle method) (EntityView method) (ImageHandle method) (ResidueHandle method) (ResidueView method) IsWater() (ChemType method) IterativeSuperposeSVD() (in module ost.mol.alg)

J

join_spread_atom_records (IOProfile attribute) JSONSummary() (DockQResult method) (MappingResult method) (ReprResult method)

K

kClust() (in module ost.bindings.kclust) keep_ff_specific_naming (Settings attribute)

keys() (AAIndex method) kill_electrostatics (Settings attribute)

L

label (lDDTSettings attribute) LangevinIntegrator (class in ost.mol.mm) lDDT (ReprResult property) lddt (Scorer property) lDDT() (lDDTScorer method) lddt_mdl (OligoLDDTScorer property) lddt_pli (LigandScorer property) lddt_pli_details (LigandScorer property) lddt_pli_matrix (LigandScorer property) lddt_ref (OligoLDDTScorer property) lddt_scorer (MappedLDDTScorer attribute) (Scorer property) lDDTBSScorer (class in ost.mol.alg.scoring) LDDTHA() built-in function lDDTLocalScore (built-in class) lDDTScorer (class in ost.mol.alg.lddt) lDDTSettings (class in ost.mol.alg) length (BondHandle attribute) Length() (in module ost.geom) Length2() (in module ost.geom) LigandScorer (class in ost.mol.alg.ligand_scoring) Line2 (class in ost.geom) Line3 (class in ost.geom) LINE_TRACE (in module ost.gfx) LinearCharacterContainer (class in ost.db) LinearIndexer (class in ost.db) LinearPositionContainer (class in ost.db) Load() (CompoundLib static method) (ContextProfileDB method) (Forcefield static method) (LinearCharacterContainer method) (LinearIndexer method) (LinearPositionContainer method) (ProfileDB method) (RemoteRepository method) (Simulation static method) (Table static method) (Topology method)

LoadAlignment() (in module ost.io) LoadAMBERForcefield() (in module ost.mol.mm) LoadCHARMMForcefield() (in module ost.mol.mm) LoadConstantContactWeightMatrix() (in module ost.seq.alg) LoadDefaultContactWeightMatrix() (in module ost.seq.alg) LoadDefaultPairSubstWeightMatrix() (in module ost.seq.alg) LoadDSSP() (in module ost.bindings.dssp) LoadEntity() (in module ost.io) LoadImage() (in module ost.io), [1] LoadMMCIF() (in module ost.io) LoadPDB() (in module ost.io) LoadSequence() (in module ost.io) LoadSequenceList() (in module ost.io) LoadSequenceProfile() (in module ost.io) local_cad_score (Scorer property) local_lddt (lDDTLocalScore attribute) (Scorer property) localAA (CADResult attribute) LocalAlign() (in module ost.seq.alg) LocalDistDiffTest() built-in function, [1], [2], [3] Locate() (in module ost.settings) LogDebug() (in module ost) LogError() (in module ost) LogInfo() (in module ost) LogLevel (class in ost) LogMessage() (LogSink method) LogScript() (in module ost) LogSink (class in ost) LogTrace() (in module ost) LogVerbose() (in module ost) LogWarning() (in module ost) LowPassFilter (class in ost.img.alg) LRMS (DockQResult property) lrmsd (Scorer property)

M

MainArea (class in ost.gui) map_nonstd_res (MolckSettings attribute) MapNonStandardResidues() (in module ost.mol.alg) mapped_lddt_scorers (OligoLDDTScorer property) mapped_model_pos (Scorer property) mapped_residues (QSscorer property) mapped_target_pos (Scorer property) MappedLDDTScorer (class in ost.mol.alg.qsscoring) mapping (MappingResult property) (Scorer property) MappingResult (class in ost.mol.alg.chain_mapping) mass (AtomHandle attribute) (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (EntityView attribute) (MMCifInfoStructDetails attribute) (ResidueHandle attribute) (ResidueView attribute) mass_method (MMCifInfoStructDetails attribute) Mat2 (class in ost.geom) Mat3 (class in ost.geom) Mat4 (class in ost.geom) Match() (BuildingBlock method) (in module ost.seq) match_columns (HHblitsHeader attribute) MatchNames() (Interaction method) MatchResidueByGlobalAln() (in module ost.mol.alg) MatchResidueByIdx() (in module ost.mol.alg) MatchResidueByLocalAln() (in module ost.mol.alg) MatchResidueByNum() (in module ost.mol.alg) MatchTypes() (Interaction method) matrix (ContactPredictionScoreResult attribute) Max() (Table method) (VarianceMap method) max_ca_per_chain_for_cm (QSscorer attribute) max_mappings_extensive (QSscorer attribute) MaxIdx() (Table method) MaxRow() (Table method) mdl (OligoLDDTScorer attribute) mdl_bb_pos (ReprResult property) mdl_full_bb_pos (ReprResult property) mdl_residues (ReprResult property) mdl_view (ReprResult property) Mean() (Table method) MeanlDDT (class in ost.seq.alg) Median() (Table method) membrane_asa (FindMemParam attribute) membrane_axis (FindMemParam attribute) membrane_representation (FindMemParam attribute) Merge() (in module ost.table) (Topology method), [1] MergePairwiseAlignments() (in module ost.seq.alg) method (MMCifInfo attribute) method_details (MMCifInfoBioUnit attribute) Min() (Table method) (VarianceMap method) MinDistance() (in module ost.geom) MinIdx() (Table method) Minor() (in module ost.geom) MinRow() (Table method) MMAlignResult (class in ost.bindings) MMCifInfo (class in ost.io) MMCifInfoBioUnit (class in ost.io) MMCifInfoBioUnit.PDBize() (in module ost.io)

MMCifInfoCitation (class in ost.io) MMCifInfoEntityBranchLink (class in ost.io) MMCifInfoObsolete (class in ost.io) MMCifInfoRevisions (class in ost.io) MMCifInfoStructDetails (class in ost.io) MMCifInfoStructRef (class in ost.io) MMCifInfoStructRefSeq (class in ost.io) MMCifInfoStructRefSeqDif (class in ost.io) MMCifInfoTransOp (class in ost.io) model (MappingResult property) (Scorer property) model_bad_angles (Scorer property) model_bad_bonds (Scorer property) model_chain_name (MappedLDDTScorer attribute) model_clashes (Scorer property) model_contacts (DockQResult property) (Scorer property) model_details (MMCifInfoStructDetails attribute) model_interface_residues (Scorer property) model_type_details (MMCifInfoStructDetails attribute) module ost.bindings ost.bindings.blast ost.bindings.cadscore ost.bindings.clustalw ost.bindings.dockq ost.bindings.dssp ost.bindings.hbplus ost.bindings.hhblits3 ost.bindings.kclust ost.bindings.lga ost.bindings.naccess ost.bindings.tmtools ost.conop ost.conop.cleanup ost.geom ost.gfx ost.gui ost.img ost.img.alg ost.io ost.mol ost.mol.alg ost.mol.alg.chain_mapping ost.mol.alg.helix_kinks ost.mol.alg.ligand_scoring ost.mol.alg.qsscore ost.mol.alg.qsscoring ost.mol.alg.stereochemistry ost.mol.alg.structure_analysis ost.mol.alg.trajectory_analysis ost.mol.mm ost.mol.mm.antechamber ost.seq ost.seq.alg ost.settings ost.table ost.testutils Molck() (in module ost.mol.alg) MolckSettings (class in ost.mol.alg) MRC_AUTO_FORMAT (ost.io.Subformat attribute) MRC_NEW_FORMAT (ost.io.Subformat attribute) MRC_OLD_FORMAT (ost.io.Subformat attribute) MsmsProcessError (class in ost.bindings.msms) MultiLogSink (class in ost)

N

n_eff (HHblitsHeader attribute) n_target_not_mapped (Scorer property) name (AtomHandle attribute) (AtomSpec attribute) (ChainHandle attribute) (ChainView attribute) (ConstSequenceHandle attribute) (Entity attribute) (ResidueHandle attribute) (ResidueView attribute) native_contacts (DockQResult property) (Scorer property) ncycles (SuperpositionResult attribute) neff (HMMData attribute) (ProfileHandle attribute) neff_d (HMMData attribute) neff_i (HMMData attribute) next (ResidueHandle attribute) (ResidueView attribute)

no_hetatms (IOProfile attribute) nonbonded_cutoff (Settings attribute) nonbonded_method (Settings attribute) nonbonded_table (StereoChemicalProps attribute) nonmapped_interfaces (Scorer property) nonmapped_interfaces_contacts (Scorer property) normal (Plane attribute) Normal (SurfaceVertex attribute) Normalise() (ConstSequenceHandle method) Normalize() (in module ost.geom) NoSymmetryError nucleotide_linking (ResidueHandle attribute) (ResidueView attribute) null_model (ProfileHandle attribute) num (ResNum attribute) number (ResidueHandle attribute) (ResidueView attribute)

O

obsolete (MMCifInfo attribute) occupancy (AtomHandle attribute) offset (ConstSequenceHandle attribute) oligo_lddt (OligoLDDTScorer property) oligo_lddt_scorer (OligoLDDTScorer property) OligoLDDTScorer (class in ost.mol.alg.qsscoring) omega_torsion (ResidueHandle attribute) (ResidueView attribute) one_letter_code (Compound attribute) (ResidueHandle attribute) (ResidueView attribute) OneLetterCodeToAminoAcid() (in module ost.conop) OneLetterCodeToResidueName() (in module ost.conop) opencl_properties (Settings attribute) openmm_plugin_directory (Settings attribute) operations (MMCifInfo attribute) (MMCifInfoBioUnit attribute) operationsintervalls (MMCifInfoBioUnit attribute) opt_score (MappingResult property) order (BondSpec attribute) origin (Line2 attribute) (Line3 attribute) (Plane attribute) (Sphere attribute) original_name (QSscoreEntity attribute) original_pos (AtomHandle attribute) OrthogonalVector() (in module ost.geom) ost.bindings module ost.bindings.blast module ost.bindings.cadscore module ost.bindings.clustalw module ost.bindings.dockq module ost.bindings.dssp module ost.bindings.hbplus module ost.bindings.hhblits3 module ost.bindings.kclust module ost.bindings.lga module ost.bindings.naccess module ost.bindings.tmtools module ost.conop module ost.conop.cleanup module ost.geom module ost.gfx module ost.gui module ost.img module ost.img.alg module

ost.io module ost.io.CCP4 (built-in class) ost.io.DAT (built-in class) ost.io.DF3 (built-in class) ost.io.DM3 (built-in class) ost.io.DX (built-in class) ost.io.Endianess (built-in class) ost.io.Format (built-in class) ost.io.IPL (built-in class) ost.io.JPK (built-in class) ost.io.MRC (built-in class) ost.io.Nanoscope (built-in class) ost.io.OMF (class in ost.io) ost.io.PNG (built-in class) ost.io.Situs (built-in class) ost.io.Spider (built-in class) ost.io.Subformat (built-in class) ost.io.TIF (built-in class) ost.mol module ost.mol.alg module ost.mol.alg.chain_mapping module ost.mol.alg.helix_kinks module ost.mol.alg.ligand_scoring module ost.mol.alg.qsscore module ost.mol.alg.qsscoring module ost.mol.alg.stereochemistry module ost.mol.alg.structure_analysis module ost.mol.alg.trajectory_analysis module ost.mol.mm module ost.mol.mm.antechamber module ost.seq module ost.seq.alg module ost.settings module ost.table module ost.testutils module OST_BIG_ENDIAN (ost.io.Endianess attribute) OST_BIT16_FORMAT (ost.io.Format attribute) OST_BIT32_FORMAT (ost.io.Format attribute) OST_BIT8_FORMAT (ost.io.Format attribute) OST_DEFAULT_FORMAT (ost.io.Format attribute) OST_DOUBLE_FORMAT (ost.io.Format attribute) OST_FLOAT_FORMAT (ost.io.Format attribute) OST_LITTLE_ENDIAN (ost.io.Endianess attribute) OST_LOCAL_ENDIAN (ost.io.Endianess attribute) ost_query (ReprResult property) OST_VAX_DATA (ost.io.Endianess attribute)

P

p (Plane attribute) page_first (MMCifInfoCitation attribute) page_last (MMCifInfoCitation attribute) PAIR (AnnoType attribute) PairDist() (QSEntity method) PairedTTest() (Table method) PairSubstWeightMatrix (class in ost.seq.alg) PairwiseDistancesFromTraj() (in module ost.mol.alg.trajectory_analysis) PanelManager (class in ost.gui) PanelPosition (in module ost.gui) Parse() (AAIndexData static method) ParseA3M() (in module ost.bindings.hhblits3) ParseAtomNames() (in module ost.mol.alg) ParseBlastOutput() (in module ost.bindings.blast) ParseHeaderLine() (in module ost.bindings.hhblits3) ParseHHblitsOutput() (in module ost.bindings.hhblits3) ParseHHM() (in module ost.bindings.hhblits3) Paste() (ImageHandle method) PasteRotation() (Mat4 method) patch_dockq (Scorer property) patch_qs (Scorer property) pdb_id (MMCifInfoObsolete attribute) PDBStrToEntity() (in module ost.io) penalize_extra_chains (OligoLDDTScorer attribute) peptide_bonds (Processor attribute) peptide_linking (ResidueHandle attribute) (ResidueView attribute) Percentiles() (Table method) periodic_box_extent (Settings attribute) Perspective (class in ost.gui) phi_torsion (ResidueHandle attribute) (ResidueView attribute) Plane (class in ost.geom) platform (Settings attribute) Plot() (Table method) PlotBar() (Table method) PlotEnrichment() (Table method) PlotHexbin() (Table method) PlotHistogram() (Table method) PlotLogROC() (Table method) PlotROC() (Table method)

Point (class in ost.img) polynuc_seqs (ChainMapper property) polypep_seqs (ChainMapper property) PopLogSink() (in module ost) PopVerbosityLevel() (in module ost) pos (AtomHandle attribute) (BondHandle attribute) (FindMemParam attribute) Position (SurfaceVertex attribute) positions (EntityHandle attribute) PredictContacts() (in module ost.seq.alg) PreparelDDTGlobalRDMap() built-in function prev (ResidueHandle attribute) (ResidueView attribute) PrintAllDistances() (ClashingDistances method) PrintAllParameters() (StereoChemicalParams method) PrintGlobalRDMap() built-in function PrintlDDTPerResidueStats() built-in function PrintParameters() (lDDTSettings method) PrintResidueRDMap() built-in function prob (HHblitsHit attribute) Process() (Processor method) Processor (class in ost.conop) processor (IOProfile attribute) ProcessStructure() (ChainMapper method) ProfileColumn (class in ost.seq) ProfileDB (class in ost.seq) ProfileHandle (class in ost.seq) Prune() (EditorBase method) psi_torsion (ResidueHandle attribute) (ResidueView attribute) published_in (MMCifInfoCitation attribute) pubmed (MMCifInfoCitation attribute) PushLogSink() (in module ost) PushVerbosityLevel() (in module ost) pvalue (HHblitsHit attribute) PythonShell (class in ost.gui)

Q

qs_best (Scorer property) qs_ent_1 (QSscorer attribute) qs_ent_2 (QSscorer attribute) qs_global (Scorer property) qs_scorer (Scorer property) qsent1 (QSScorer property) qsent2 (QSScorer property) QSEntity (class in ost.mol.alg.qsscore) QSscoreEntity (class in ost.mol.alg.qsscoring) QSscoreError

QSScorer (class in ost.mol.alg.qsscore) QSscorer (class in ost.mol.alg.qsscoring) quack_mode (IOProfile attribute) qualified_name (AtomHandle attribute) (ResidueHandle attribute) (ResidueView attribute) quality_problems (lDDTLocalScore attribute) Query (class in ost.mol) query (HHblitsHeader attribute) QueryFlag (class in ost.mol) QueryQuoteName() (in module ost.mol)

R

r_free (MMCifInfo attribute) r_work (MMCifInfo attribute) radius (AtomHandle attribute) (lDDTSettings attribute) (Sphere attribute) reaction_field_dielecric (Settings attribute) read_conect (IOProfile attribute) ReadGromacsForcefield() (FFReader method) ReadITP() (FFReader method) ReadResidueDatabase() (FFReader method) ReadStereoChemicalPropsFile() (in module ost.io) Rectangle2 (class in ost.geom) ref (OligoLDDTScorer attribute) ref_bb_pos (ReprResult property) ref_full_bb_pos (ReprResult property) ref_residues (ReprResult property) ref_view (ReprResult property) reference_chain_name (MappedLDDTScorer attribute) reference_properties (Settings attribute) Register() (Simulation method) RemoteGet() (in module ost.io.remote) RemoteLoad() (in module ost.io.remote) RemoteRepository (class in ost.io.remote) Remove() (AminoAcidSet method) (Scene method) remove_cmm_motion (Settings attribute) RemoveAlignment() (in module ost.gui) RemoveAll() (Scene method) RemoveAssembly() (LinearIndexer method) RemoveAtom() (BuildingBlock method) (EntityView method) (ResidueView method) RemoveChain() (EntityView method) RemoveCol() (Table method) removed_chains (QSscoreEntity attribute) RemoveEntity() (in module ost.gui) RemoveInteractionsToNext() (BuildingBlock method) RemoveInteractionsToPrev() (BuildingBlock method) RemoveProp() (GenericPropertyContainer method) RemoveResidue() (ChainView method) (EntityView method) RemoveResidues() (ChainView method) RemoveSequence() (AlignmentHandle method) RemoveSink() (MultiLogSink method) RemoveWidget() (PanelManager method) RenameAtom() (EditorBase method) RenameChain() (EditorBase method) RenameCol() (Table method) RenameResidue() (EditorBase method) RenderGL() (Scene method) Renumber() (in module ost.seq.alg.renumber) RenumberAllResidues() (EditorBase method) RenumberChain() (EditorBase method), [1] ReorderAllResidues() (EditorBase method) ReorderResidues() (EditorBase method) Replace() (AlignmentHandle method) replace_pdb_id (MMCifInfoObsolete attribute) ReplaceAtom() (BuildingBlock method) (Interaction method) representative_id (cluster attribute) ReprResult (class in ost.mol.alg.chain_mapping) RequestRedraw() (Scene method) res_num_alignment (QSscorer attribute)

ResetCharge() (Simulation method) ResetDistanceConstraint() (Simulation method) ResetExclusions() (Topology method) ResetGBSA() (Simulation method) ResetHarmonicAngle() (Simulation method) ResetHarmonicBond() (Simulation method) ResetHarmonicDistanceRestraint() (Simulation method) ResetHarmonicImproper() (Simulation method) ResetHarmonicPositionRestraint() (Simulation method) ResetLJ() (Simulation method) ResetLJPair() (Simulation method) ResetMass() (Simulation method) ResetPeriodicDihedral() (Simulation method) ResetPeriodicImproper() (Simulation method) ResetPositionConstraints() (Simulation method) (Topology method) ResetUreyBradleyAngle() (Simulation method) residue (AtomHandle attribute) residue_count (ChainHandle attribute) (EntityHandle attribute) (EntityView attribute) ResidueHandle (class in ost.mol) ResidueNamesMatch() (in module ost.mol.alg) ResidueNameToAminoAcid() (in module ost.conop) ResidueNameToOneLetterCode() (in module ost.conop) ResidueRDMap (built-in class) residues (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (EntityView attribute) ResidueToAminoAcid() (in module ost.conop) ResidueView (class in ost.mol) Resize() (Scene method) ResNum (class in ost.mol) resolution (MMCifInfo attribute) revisions (MMCifInfo attribute) Rhythm() (TrajObserver method) (TrajWriter method) rigid_water (Settings attribute) rm_hyd_atoms (MolckSettings attribute) rm_non_std (MolckSettings attribute) rm_oxt_atoms (MolckSettings attribute) rm_unk_atoms (MolckSettings attribute) rm_zero_occ_atoms (MolckSettings attribute) rmsd (LigandScorer property) (Scorer property) (SuperpositionResult attribute) rmsd_below_five (TMScoreResult attribute) rmsd_common (TMScoreResult attribute) rmsd_details (LigandScorer property) rmsd_matrix (LigandScorer property) RMSD_Matrix_From_Traj() (in module ost.mol.alg.trajectory_analysis) rmsd_superposed_atoms (SuperpositionResult attribute) rname (lDDTLocalScore attribute) rnum (lDDTLocalScore attribute) (MMCifInfoStructRefSeqDif attribute) role (ConstSequenceHandle attribute) RotateTorsionAngle() (ICSEditor method), [1] rotation (MMCifInfoTransOp attribute) RowMean() (Table method) RuleBasedProcessor (class in ost.conop) RunAntechamber() (in module ost.mol.mm.antechamber) RunTests() (in module ost.testutils)

S

Save() (ContextProfileDB method) (Forcefield method) (LinearCharacterContainer method) (LinearIndexer method) (LinearPositionContainer method) (ProfileDB method) (Simulation method) (Table method) (Topology method) SaveAlignment() (in module ost.io) SaveEntity() (in module ost.io) SaveImage() (in module ost.io), [1] SavePDB() (in module ost.io) SaveSequence() (in module ost.io) SaveSequenceList() (in module ost.io) sc_lddt (OligoLDDTScorer property) sc_lddt_scorers (OligoLDDTScorer property) Scene (class in ost.gfx) SceneWin (class in ost.gui) score (AlignedPatch attribute) (HHblitsHit attribute) Score() (QSScorer method) ScoreBS() (lDDTBSScorer method) ScoreInterface() (QSScorer method) Scorer (class in ost.mol.alg.scoring) SCRMSD() (in module ost.mol.alg.ligand_scoring) SDFStrToEntity() (in module ost.io) Search() (HHblits method) SearchColNames() (Table method) searched_hmms (HHblitsHeader attribute) sec_structure (ResidueHandle attribute) (ResidueView attribute) second (BondHandle attribute) SecStructure (class in ost.mol) SecStructure.Type (class in ost.mol) Select() (ChainView method) (EntityHandle method) (EntityView method) (ResidueView method) (Table method) selection (Entity attribute) SemiGlobalAlign() (in module ost.seq.alg) seq_begin (MMCifInfoStructRefSeq attribute) seq_end (MMCifInfoStructRefSeq attribute) seqid (AlignedPatch attribute) sequence (ProfileHandle attribute) sequence_count (AlignmentHandle attribute) sequence_separation (lDDTSettings attribute) SequenceFromChain() (in module ost.seq) SequenceFromString() (in module ost.io) SequenceHandle (class in ost.seq) SequenceIdentity() (in module ost.seq.alg) SequenceList (class in ost.seq) SequenceListFromString() (in module ost.io) SequenceListToString() (in module ost.io) SequenceProfileFromString() (in module ost.io) sequences (AlignmentHandle attribute) (cluster attribute) SequencesHaveEqualLength() (ConstSequenceList method) SequenceSimilarity() (in module ost.seq.alg) SequenceToString() (in module ost.io) SequenceViewer (class in ost.gui) SetA() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) (Ellipse2 method) SetAbsoluteOrigin() (ImageHandle method) SetAngle() (ICSEditor method) SetAtom1() (MMCifInfoEntityBranchLink method) SetAtom2() (MMCifInfoEntityBranchLink method) SetAtomOriginalPos() (XCSEditor method) SetAtomPos() (CoordGroupHandle method) (XCSEditor method) SetAtomTransformedPos() (XCSEditor method) SetAuthorList() (MMCifInfoCitation method) SetB() (Ellipse2 method) SetBackground() (Scene method) SetBlocksize() (DiscreteShrink method) SetBlur() (Scene method) SetBondLength() (ICSEditor method) SetBondOrder() (BondHandle method) (MMCifInfoEntityBranchLink method) SetBookPublisher() (MMCifInfoCitation method) SetBookPublisherCity() (MMCifInfoCitation method) SetBoolProp() (GenericPropertyContainer method) SetCAS() (MMCifInfoCitation method) SetCASPFlag() (MMCifInfoStructDetails method) SetCenter() (Circle2 method) SetCentralAtom() (ResidueHandle method) (ResidueView method) SetChainDescription() (EditorBase method) SetChainList() (MMCifInfoBioUnit method) SetChainType() (EditorBase method) SetCharge() (Topology method) SetCharges() (Topology method) SetChemLibInfo() (CompoundLib method) SetCitationType() (MMCifInfoCitation method) SetCitationTypeBook() (MMCifInfoCitation method) SetCitationTypeJournal() (MMCifInfoCitation method) SetCitationTypeUnknown() (MMCifInfoCitation method) SetClashingDistance() (ClashingDistances method) SetCMapParameters() (Topology method) SetColor() (Entity method) SetComplex() (ImageHandle method) SetDate() (MMCifInfoObsolete method) SetDateOriginal() (MMCifInfoRevisions method) SetDefaultLib() (in module ost.conop) SetDescriptor() (MMCifInfoStructDetails method) SetDetails() (MMCifInfoBioUnit method) SetDistanceConstraintParameters() (Topology method) SetDOI() (MMCifInfoCitation method) SetEnd() (Rectangle2 method) SetEntryID() (MMCifInfoStructDetails method) SetEps() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) SetEpsilon() (Topology method) SetEpsilons() (Topology method) SetErrorTolerance() (VariableLangevinIntegrator method) (VariableVerletIntegrator method) SetException() (TerminiExceptions method) SetFloatProp() (GenericPropertyContainer method) SetFog() (Scene method) SetFogColor() (Scene method) SetFogOffsets() (Scene method) SetForcefield() (FFReader method) SetFOV() (Scene method) SetFramePositions() (CoordGroupHandle method) SetFreq() (ProfileColumn method) SetFriction() (BrownianIntegrator method) (LangevinIntegrator method) (VariableLangevinIntegrator method) SetFudgeLJ() (Forcefield method) (Topology method) SetFudgeQQ() (Forcefield method) (Topology method) SetGamma() (Ellipse2 method) SetGBSARadii() (Topology method) SetGBSARadius() (Topology method) SetGenPairs() (Forcefield method) SetHarmonicAngleParameters() (Topology method) SetHarmonicBondParameters() (Topology method) SetHarmonicDistanceRestraintParameters() (Topology method) SetHarmonicImproperParameters() (Topology method) SetHarmonicPositionRestraintParameters() (Topology method) SetHMMData() (ProfileColumn method) SetID() (MMCifInfoBioUnit method) (MMCifInfoObsolete method) (MMCifInfoTransOp method) SetIndex() (ToolOptionEnum method) SetIntProp() (GenericPropertyContainer method) SetISBN() (MMCifInfoCitation method) SetIsLigand() (ResidueHandle method) (ResidueView method) SetIsProtein() (ResidueHandle method) SetLightDir() (Scene method) SetLightProp() (Scene method) SetLimit() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) (FermiHighPassFilter method) (FermiLowPassFilter method) (GaussianHighPassFilter method) (GaussianLowPassFilter method) (HighPassFilter method) (LowPassFilter method)

SetLJPairParameters() (Topology method) SetMass() (MMCifInfoStructDetails method) (Topology method) SetMasses() (Topology method) SetMassMethod() (MMCifInfoStructDetails method) SetMatrix() (MMCifInfoTransOp method) SetMethod() (MMCifInfo method) SetMethodDetails() (MMCifInfoBioUnit method) SetModelDetails() (MMCifInfoStructDetails method) SetModelTypeDetails() (MMCifInfoStructDetails method) SetName() (ConstSequenceHandle method) (EntityHandle method) (EntityView method) (QSscoreEntity method) (Table method) SetNames() (Interaction method) SetNearFar() (Scene method) SetOBCScaling() (Topology method) SetOBCScalings() (Topology method) SetObsoleteInfo() (MMCifInfo method) SetOffset() (ConstSequenceHandle method) SetOrigin() (Ellipse2 method) (Sphere method) SetPageFirst() (MMCifInfoCitation method) SetPageLast() (MMCifInfoCitation method) SetParam() (Interaction method) (StereoChemicalParams method) SetPDBID() (MMCifInfoObsolete method) SetPeriodicBoxExtents() (Simulation method) SetPeriodicDiheralParameters() (Topology method) SetPeriodicImproperParameters() (Topology method) SetPixelSampling() (ImageHandle method) SetPositions() (Simulation method) SetProb() (HMMData method) SetPublishedIn() (MMCifInfoCitation method) SetPubMed() (MMCifInfoCitation method) SetQ() (GaussianFilter method) SetRadius() (Circle2 method) (Sphere method) SetRandomNumberSeed() (BrownianIntegrator method) (LangevinIntegrator method) (VariableLangevinIntegrator method) SetReal() (ImageHandle method) SetRenderMode() (Entity method) SetReplacedPDBID() (MMCifInfoObsolete method) SetResidueNumber() (EditorBase method) SetResolution() (MMCifInfo method) SetRevisionsDateOriginal() (MMCifInfo method) SetRTC() (Scene method) SetScore() (ContactPredictionScoreResult method) SetSequenceName() (AlignmentHandle method) SetSequenceOffset() (AlignmentHandle method) SetSequenceRole() (AlignmentHandle method) SetShadow() (Scene method) SetShadowQuality() (Scene method) SetSigma() (GaussianFilter method) (Topology method) SetSigmas() (Topology method) SetSpatialOrigin() (ImageHandle method) SetSpatialSampling() (ImageHandle method) SetStandardCTer() (Forcefield method) SetStandardNTer() (Forcefield method) SetStart() (Rectangle2 method) SetStereoEye() (Scene method) SetStereoInverted() (Scene method) SetStop() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) SetStringProp() (GenericPropertyContainer method) SetStructDetails() (MMCifInfo method) SetSymmetries() (QSscorer method) SetT() (FermiHighPassFilter method) (FermiLowPassFilter method) SetTemperature() (BrownianIntegrator method) (LangevinIntegrator method) (VariableLangevinIntegrator method) Settings (class in ost.mol.mm) settings (MappedLDDTScorer attribute) (OligoLDDTScorer attribute) SetTitle() (MMCifInfoCitation method) (MMCifInfoStructDetails method) SetTorsionAngle() (ICSEditor method), [1] SetTransform() (Scene method) (XCSEditor method), [1] SetType() (MMCifInfoTransOp method) SetTypes() (Interaction method) SetValue() (ToolOptionFloat method) (ToolOptionInt method) SetVector() (MMCifInfoTransOp method) SetVelocities() (Simulation method) SetVolume() (MMCifInfoCitation method) SetWeight() (SubstWeightMatrix method) SetYear() (MMCifInfoCitation method) ShannonEntropy() (in module ost.seq.alg) Show() (in module ost.gui) (SceneWin method) ShowSubWindow() (MainArea method) SIMPLE (in module ost.gfx) Simulation (class in ost.mol.mm), [1] SINGLE (AnnoType attribute) Size (class in ost.img) size (ImageHandle attribute) Size() (ProfileDB method) (ToolOptionEnum method) Slice() (ConstSequenceList method) SLINE (in module ost.gfx) solute_dielectric (Settings attribute) solvent_dielectric (Settings attribute) Sort() (Table method) sorted_indices (ContactPredictionScoreResult attribute) SPATIAL (in module ost.img) spatial_origin (ImageHandle attribute) SpearmanCorrel() (Table method) Sphere (class in ost.geom) ss_score (HHblitsHit attribute) start (AlignedRegion attribute) Stats() (Table method) StatusMessage() (Perspective method) StdDev() (Table method) Steps() (Simulation method) Stereo() (Scene method) StereoCheck() (in module ost.mol.alg.stereochemistry) stereochecked_aln (Scorer property) stereochecked_model (Scorer property) stereochecked_target (Scorer property) StereoChemicalAngleViolation (class in ost.mol.alg) StereoChemicalBondViolation (class in ost.mol.alg) StereoChemicalParams (class in ost.mol.alg) StereoChemicalParams() (StereoChemicalParams method) StereoChemicalProps (built-in class) StereoChemistryInfo (class in ost.mol.alg) StereoDataFromMON_LIB() (in module ost.mol.alg.stereochemistry) StreamLogSink (class in ost) strict_hydrogens (RuleBasedProcessor attribute) strict_interactions (Settings attribute) string (Query attribute) StringFromChainType() (in module ost.mol) struct_details (MMCifInfo attribute) struct_refs (MMCifInfo attribute) substructure (ReprResult property) SubstWeightMatrix (class in ost.seq.alg) SubstWeightMatrix.Preset (class in ost.seq.alg) Sum() (Table method) Superpose() (in module ost.mol.alg) superposed_mdl_bb_pos (ReprResult property) SuperposeFrames() (in module ost.mol.alg) SuperposeSVD() (in module ost.mol.alg) superposition (QSscorer property) SuperpositionDialog (class in ost.gui.dng.superpositiondialog) SuperpositionResult (class in ost.mol.alg) SUPPORTED_TYPES (Table attribute) SurfaceHandle (class in ost.mol) SurfaceTriIDList (class in ost.mol) SurfaceVertex (class in ost.mol) SurfaceVertex() (SurfaceVertex method) SurfaceVertexList (class in ost.mol) SwitchAtomPos() (ResidueHandle method) symm_1 (QSscorer property) symm_2 (QSscorer property) SymmetrySettings (class in ost.mol.alg.lddt)

T

Table (class in ost.table) Take() (ConstSequenceList method) target (ChainMapper property) (MappingResult property) (Scorer property) target_bad_angles (Scorer property) target_bad_bonds (Scorer property) target_clashes (Scorer property) target_interface_residues (Scorer property) termini_exceptions (Settings attribute) TerminiExceptions (class in ost.mol.mm) thermostat_collision_frequency (Settings attribute) thermostat_temperature (Settings attribute) three_letter_code (Compound attribute) tilt (FindMemParam attribute) tilt_axis (FindMemParam attribute) title (MMCifInfoCitation attribute) (MMCifInfoStructDetails attribute) tm_score (Scorer property) (TMScoreResult attribute) TMAlign() (in module ost.bindings.tmtools) TMAlignResult (class in ost.bindings) TMScore() (in module ost.bindings.tmtools) TMScoreResult (class in ost.bindings.tmtools) ToBytes() (ost.io.OMF method) ToFile() (ost.io.OMF method) ToJSON() (AngleViolationInfo method) (BondViolationInfo method) (ClashInfo method) Tool (class in ost.gui)

ToolOption (class in ost.gui) ToolOptionEnum (class in ost.gui) ToolOptionFloat (class in ost.gui) ToolOptionInt (class in ost.gui) Topology (class in ost.mol.mm) TopologyCreator (class in ost.mol.mm) ToString() (AlignmentHandle method) (lDDTLocalScore method) (lDDTSettings method) (MolckSettings method) (Table method) total_dist (lDDTLocalScore attribute) ToVec2() (Point method) ToVec3() (Point method) ToVec4() (Point method) TRACE (in module ost.gfx) TrajObserver (class in ost.mol.mm) TrajWriter (class in ost.mol.mm) transform (ReprResult property) (Scene attribute) (Scorer property) (TMScoreResult attribute) transformation (SuperpositionResult attribute) transformed_mapped_model_pos (Scorer property) translation (MMCifInfoTransOp attribute) Transpose() (in module ost.geom) TUBE (in module ost.gfx) type (ChainHandle attribute) (ImageHandle attribute) (MMCifInfoTransOp attribute)

U

Union() (in module ost.mol) UniqueAtomIdentifier (built-in class) unk_atom_treatment (RuleBasedProcessor attribute) unk_res_treatment (RuleBasedProcessor attribute) UnProject() (Scene method) UpdateICS() (XCSEditor method) UpdatePositions() (Entity method) (Simulation method)

UpdateView() (Entity method) UpdateXCS() (ICSEditor method) URLForID() (RemoteRepository method) USAlign() (in module ost.bindings.tmtools) usalign_mapping (Scorer property) use_dispersion_correction (Settings attribute)

V

valid (AtomHandle attribute) (BondHandle attribute) (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (EntityView attribute) (Query attribute) (ResidueHandle attribute) (ResidueView attribute) ValidateSEQRESAlignment() (in module ost.seq.alg) values() (AAIndex method) VariableLangevinIntegrator (class in ost.mol.mm) VariableVerletIntegrator (class in ost.mol.mm)

VarianceMap (class in ost.seq.alg) Vec2 (class in ost.geom) Vec3 (class in ost.geom) Vec4 (class in ost.geom) vector (CuboidAxis attribute) VerletIntegrator (class in ost.mol.mm) view (QSEntity property) view1 (SuperpositionResult attribute) view2 (SuperpositionResult attribute) ViewAddFlag (class in ost.mol) ViewsFromAlignment() (in module ost.seq) ViewsFromSequences() (in module ost.seq) volume (MMCifInfoCitation attribute)

W

w (Vec4 attribute) weighted_lddt (OligoLDDTScorer property) weights (ContactWeightMatrix attribute) (PairSubstWeightMatrix attribute)

width (FindMemParam attribute) (Rectangle2 attribute) WrappedMMAlign() (in module ost.bindings) WrappedTMAlign() (in module ost.bindings), [1]

X

x (Vec2 attribute) (Vec3 attribute) (Vec4 attribute)

XCSEditor (class in ost.mol)

Y

y (Vec2 attribute) (Vec3 attribute) (Vec4 attribute)

year (MMCifInfoCitation attribute)

Z

z (Vec3 attribute) (Vec4 attribute)

zero_occ_treatment (Processor attribute) Zip() (Table method)