Index

_

__getitem__() (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) 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) 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_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), [1] AlignmentFromChainView() (in module ost.seq.alg) AlignmentFromSequenceList() (in module ost.seq) AlignmentFromString() (in module ost.io) AlignmentHandle (class in ost.seq) alignments (OligoLDDTScorer attribute), [1] (QSscorer property), [1] AlignmentToString() (in module ost.io) AlignToSEQRES() (in module ost.seq.alg) aln (AlignedPatch attribute) (HHblitsHit attribute) 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), [1] 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) 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) 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) Begin() (ToolOptionEnum method) best_score (QSscorer property), [1] 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_feasibility_check (IOProfile attribute) bond_order (MMCifInfoEntityBranchLink attribute) bond_specs (Compound attribute) bond_table (StereoChemicalProps attribute), [1] BondExists() (in module ost.mol) bonds (AtomHandle attribute) BondSpec (class in ost.conop) 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), [1] ca_entity (QSscoreEntity property), [1] 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) 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), [1] (OligoLDDTScorer attribute), [1] (QSscoreEntity attribute), [1] (QSscorer attribute), [1] 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) (ResidueHandle attribute) (ResidueView attribute) center_of_mass (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (ResidueHandle attribute) (ResidueView attribute) CenterOn() (Scene method) CenterSpatialOrigin() (ImageHandle method) central_atom (ResidueHandle attribute) central_normal (ResidueHandle attribute) chain (ResidueHandle attribute) (ResidueView attribute) chain_count (EntityHandle attribute) (EntityView attribute) chain_mapping (QSscorer property), [1] chain_mapping_scheme (QSscorer property), [1] chain_name (MMCifInfoStructRefSeq attribute) ChainHandle (class in ost.mol) chainintervals (MMCifInfoBioUnit attribute) 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 CheckStructure() (in module ost.mol.alg) chem_class (Compound attribute) (ResidueHandle attribute) chem_groups (QSscoreEntity property), [1] chem_mapping (OligoLDDTScorer attribute), [1] (QSscorer property), [1] chem_type (Compound attribute) (ResidueHandle 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) ClashingDistances (class in ost.mol.alg) ClashingDistances() (ClashingDistances method) ClashingInfo (class in ost.mol.alg) CleanlDDTReferences() built-in function CleanlDDTReferences() (in module ost.mol.alg) 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), [1] cluster (class in ost.bindings.kclust) cmm_frequency (Settings attribute) cname (lDDTLocalScore attribute), [1] 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) ConnectBranchLink() (MMCifInfoEntityBranchLink method) ConnectBranchLinks() (MMCifInfo method) ConopAction (class in ost.conop) Conservation() (in module ost.seq.alg) conserved_contacts (lDDTScorer attribute) conserved_dist (lDDTLocalScore attribute), [1] constrain_bonds (Settings attribute) constrain_hbonds (Settings attribute) ConstSequenceHandle (class in ost.seq) ConstSequenceList (class in ost.seq) ContactPredictionScoreResult (class in ost.seq.alg) contacts (QSscoreEntity property), [1] contacts_ca (QSscoreEntity property), [1] 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 CreateDistanceList() (in module ost.mol.alg) CreateDistanceListFromMultipleReferences() built-in function CreateDistanceListFromMultipleReferences() (in module ost.mol.alg) 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) 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) 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 DistanceRMSDTest() (in module ost.mol.alg) Distances (class in ost.seq.alg) DistRMSDFromTraj() (in module ost.mol.alg.trajectory_analysis) doi (MMCifInfoCitation attribute) domain (ImageHandle attribute) Dot() (in module ost.geom) DoubleClick() (Tool method) DRMSD() built-in function DRMSD() (in module ost.mol.alg)

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), [1] ent_to_cm_1 (QSscorer property), [1] ent_to_cm_2 (QSscorer property), [1] Entity (class in ost.gfx) entity (CoordGroupHandle attribute) EntityHandle (class in ost.mol) EntityToPDBStr() (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), [1] 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_release (MMCifInfoRevisions attribute) fix_elements (RuleBasedProcessor attribute) fix_heavy_atoms (Settings attribute) FixTransform() (XCSEditor method) 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) FromCRF() (ContextProfileDB 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_ha (TMScoreResult attribute) gdt_ts (TMScoreResult attribute) GDTResult (class in ost.bindings.lga) generate_disulfid_bonds (Settings attribute) GenericPropertyContainer (class in ost) geometric_center (ChainView 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), [1] 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) GetAngles() (BuildingBlock method) (QSscoreEntity method), [1] 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) GetAtomList() (ChainHandle method) (CoordGroupHandle method) (EntityHandle method) (EntityView method) (ResidueHandle method) (ResidueView method) GetAtomName() (UniqueAtomIdentifier method), [1] GetAtomPos() (CoordFrame method) (CoordGroupHandle method) GetAtoms() (BuildingBlock method) (Interaction method) GetAtomType() (Forcefield method) GetAttachedView() (ConstSequenceHandle method) GetAuthorList() (MMCifInfoCitation method) GetAverage() (Distances method) GetAverageOffset() (ClashingInfo method) GetAverageScore() (ProfileHandle method) GetAvgZscoreAngles() (StereoChemistryInfo method) GetAvgZscoreBonds() (StereoChemistryInfo method) GetAxis() (QSscoreEntity method), [1] GetB() (Ellipse2 method) GetBadAngleCount() (StereoChemistryInfo method) GetBadBondCount() (StereoChemistryInfo method) GetBins() (Histogram method), [1] GetBioUnits() (MMCifInfo method) GetBlockModifier() (Forcefield method) GetBlocksize() (DiscreteShrink method) GetBond() (Forcefield method) GetBondCount() (AtomHandle method) (EntityView method) (StereoChemistryInfo method) GetBondLength() (StereoChemicalBondViolation method) GetBondList() (AtomHandle method) (EntityView method) GetBondOrder() (MMCifInfoEntityBranchLink method) GetBondPartners() (AtomHandle method) GetBonds() (BuildingBlock method) GetBondViolationList() (StereoChemistryInfo method) GetBookPublisher() (MMCifInfoCitation method) GetBookPublisherCity() (MMCifInfoCitation method) GetBoolProp() (GenericPropertyContainer method) GetBoundingBox() (Ellipse2 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) GetCentralNormal() (ResidueHandle method) GetChain() (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), [1] GetChainNames() (LinearIndexer method) GetCharacter() (LinearCharacterContainer method) GetCharacters() (LinearCharacterContainer method) GetCharge() (AtomHandle method) (BuildingBlock method) (Topology method) GetCharges() (BuildingBlock method) (Topology method) GetChemType() (ResidueHandle method) GetCircumference() (Circle2 method) GetCitations() (MMCifInfo method) GetCitationType() (MMCifInfoCitation method) GetClashCount() (ClashingInfo method) 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), [1] 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) 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) GetFirstAtom() (ClashEvent method) (StereoChemicalAngleViolation method) (StereoChemicalBondViolation method) GetFirstNonGap() (ConstSequenceHandle method) GetFirstRelease() (MMCifInfoRevisions 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) (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) GetHeader() (lDDTLocalScore method), [1] 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) GetlDDTPerResidueStats() built-in function GetlDDTPerResidueStats() (in module ost.mol.alg) GetLength() (AlignedRegion method) (AlignmentHandle method) GetLimit() (ButterworthHighPassFilter method) (ButterworthLowPassFilter method) (FermiHighPassFilter method) (FermiLowPassFilter method) (GaussianHighPassFilter method) (GaussianLowPassFilter method) (HighPassFilter method) (LowPassFilter method) GetLJ() (Forcefield method), [1] GetLJPairIndex() (Topology method) GetLJPairIndices() (Topology method) GetLJPairParameters() (Topology method) GetLowerLimit() (ToolOptionFloat method) (ToolOptionInt method) GetMainArea() (Perspective method) GetMajor() (MMCifInfoRevisions method) GetMass() (AtomHandle method) (BuildingBlock method) (ChainView method) (EntityHandle method) (EntityView method) (Forcefield method) (MMCifInfoStructDetails 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) 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) 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), [1] (Table method) (Tool method) GetNames() (Interaction method) (ProfileDB method) GetNormal() (Plane method) GetNormStdDev() (Distances method) GetNTerModifier() (Forcefield method) GetNum() (MMCifInfoRevisions method) (ResNum 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), [1] GetOneLetterCode() (ConstSequenceHandle 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) GetP() (Plane method) GetPageFirst() (MMCifInfoCitation method) GetPageLast() (MMCifInfoCitation 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), [1] GetPhiTorsion() (ResidueHandle method) GetPixelSampling() (ImageHandle method) GetPlatform() (in module ost.settings) GetPos() (AlignmentHandle method) (AtomHandle method) (ConstSequenceHandle method) GetPosition() (LinearPositionContainer method) GetPositions() (EntityHandle method) (LinearPositionContainer method) (Simulation method) GetPotentialEnergy() (Simulation method) GetProb() (HMMData method) GetProfile() (ProfileDB method) GetPropAsString() (GenericPropertyContainer method) GetPsiTorsion() (ResidueHandle method) GetPublishedIn() (MMCifInfoCitation method) GetPubMed() (MMCifInfoCitation method) GetQObject() (ContextMenu method) (in module ost.gui) (PanelManager method) (SceneWin method) GetQualifiedAtomName() (UniqueAtomIdentifier method), [1] GetQualifiedName() (AtomHandle method) GetRadius() (AtomHandle method) (Circle2 method) (Sphere method) GetRandomNumberSeed() (BrownianIntegrator method) (LangevinIntegrator method) (VariableLangevinIntegrator method) GetReal() (ImageHandle method) GetReplacedPDBID() (MMCifInfoObsolete 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), [1] GetResNum() (UniqueAtomIdentifier method), [1] GetResolution() (MMCifInfo method) GetRevisions() (MMCifInfo method) GetRMSD() (CoordFrame method) GetRowCount() (AlignedColumn method) GetRTC() (Scene method) GetScore() (ContactPredictionScoreResult method) (ProfileColumn method) GetSecondAtom() (ClashEvent method) (StereoChemicalAngleViolation method) (StereoChemicalBondViolation method) GetSequence() (AlignmentHandle 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) GetWeightedStdDev() (Distances method) GetWidth() (Rectangle2 method) GetYear() (MMCifInfoCitation method) global_dist_list (lDDTScorer attribute) global_score (lDDTScorer attribute) (QSscorer property), [1] globalAA (CADResult attribute) GlobalAlign() (in module ost.seq.alg) GlobalRDMap (built-in class) (class in ost.mol.alg) 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), [1] HasAltAtomGroup() (ResidueHandle method) HasAltAtoms() (ResidueHandle method) HasAttachedView() (ConstSequenceHandle method) HasCol() (Table method) HasException() (TerminiExceptions method) hash_code (AtomHandle attribute) (AtomView 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) 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), [1] inchi (Compound attribute), [1] 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) Interaction (class in ost.mol.mm) Intersection() (in module ost.mol) IntersectionPoint() (in module ost.geom) Invert() (in module ost.geom) (SurfaceHandle method) IOProfile (class in ost.io) is_assessed (lDDTLocalScore attribute), [1] is_hetatom (AtomHandle attribute) is_leaving (AtomSpec attribute) is_ligand (ResidueHandle 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) is_valid (lDDTScorer attribute) (QSscoreEntity attribute), [1] 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) IsNonCanonical() (ChemType method) IsNucleotide() (ChemType method) IsNucleotideLinking() (ChemClass method) IsOligosaccharide() (ChainHandle method) IsOnLine() (in module ost.geom) IsParametrized() (Interaction method) IsPeptideLinking() (ChemClass method) (ResidueHandle method) IsPlatformAvailable() (Simulation static method) IsPolymer() (ChainHandle method) IsPolynucleotide() (ChainHandle method) IsPolypeptide() (ChainHandle method) IsPolysaccharide() (ChainHandle method) IsResidueSelected() (Query method) IsSaccharide() (ChemType method) IsSpatial() (ImageHandle method) IsValid() (AtomHandle method) (ChainHandle method) (ChainView method) (CoordGroupHandle method) (EntityHandle method) (EntityView method) (ImageHandle method) (ResidueHandle method) IsWater() (ChemType method) IterativeSuperposeSVD() (in module ost.mol.alg)

J

join_spread_atom_records (IOProfile attribute)

K

kClust() (in module ost.bindings.kclust)

keep_ff_specific_naming (Settings attribute) kill_electrostatics (Settings attribute)

L

label (lDDTSettings attribute) LangevinIntegrator (class in ost.mol.mm) lddt_mdl (OligoLDDTScorer property), [1] lddt_ref (OligoLDDTScorer property), [1] lddt_scorer (MappedLDDTScorer attribute), [1] LDDTHA() built-in function LDDTHA() (in module ost.mol.alg) lDDTLocalScore (built-in class) (class in ost.mol.alg) lDDTScorer (class in ost.mol.alg) lDDTSettings (class in ost.mol.alg) Length() (in module ost.geom) Length2() (in module ost.geom) 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_lddt (lDDTLocalScore attribute), [1] local_scores (lDDTScorer attribute) localAA (CADResult attribute) LocalAlign() (in module ost.seq.alg) LocalDistDiffTest() built-in function, [1], [2], [3] LocalDistDiffTest() (in module ost.mol.alg), [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)

M

MainArea (class in ost.gui) map_nonstd_res (MolckSettings attribute) MapNonStandardResidues() (in module ost.mol.alg) mapped_lddt_scorers (OligoLDDTScorer property), [1] mapped_residues (QSscorer property), [1] MappedLDDTScorer (class in ost.mol.alg.qsscoring), [1] mass (AtomHandle attribute) (ChainHandle attribute) (ChainView attribute) (EntityHandle 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), [1] max_mappings_extensive (QSscorer attribute), [1] MaxIdx() (Table method) MaxRow() (Table method) mdl (OligoLDDTScorer attribute), [1] 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) 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 (lDDTScorer attribute) model_chain_name (MappedLDDTScorer attribute), [1] model_details (MMCifInfoStructDetails attribute) 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.helix_kinks ost.mol.alg.qsscoring, [1] 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) name (AtomHandle attribute) (AtomSpec attribute) (ChainHandle attribute) (ChainView attribute) (ConstSequenceHandle attribute) (Entity attribute) (ResidueHandle attribute) (ResidueView attribute) ncycles (SuperpositionResult attribute) neff (HMMData attribute) (ProfileHandle attribute) neff_d (HMMData attribute)

neff_i (HMMData attribute) next (ResidueHandle attribute) no_hetatms (IOProfile attribute) nonbonded_cutoff (Settings attribute) nonbonded_method (Settings attribute) nonbonded_table (StereoChemicalProps attribute), [1] normal (Plane attribute) Normal (SurfaceVertex attribute) Normalise() (ConstSequenceHandle method) Normalize() (in module ost.geom) 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), [1] oligo_lddt_scorer (OligoLDDTScorer property), [1] OligoLDDTScorer (class in ost.mol.alg.qsscoring), [1] 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) order (BondSpec attribute) origin (Line2 attribute) (Line3 attribute) (Plane attribute) (Sphere attribute) original_name (QSscoreEntity attribute), [1] 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.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.helix_kinks module ost.mol.alg.qsscoring module, [1] 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_VAX_DATA (ost.io.Endianess attribute)

P

p (Plane attribute) page_first (MMCifInfoCitation attribute) page_last (MMCifInfoCitation attribute) 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) 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) pdb_id (MMCifInfoObsolete attribute) PDBStrToEntity() (in module ost.io) penalize_extra_chains (OligoLDDTScorer attribute), [1] peptide_bonds (Processor attribute) peptide_linking (ResidueHandle attribute) Percentiles() (Table method) periodic_box_extent (Settings attribute) Perspective (class in ost.gui) phi_torsion (ResidueHandle 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) PopLogSink() (in module ost)

PopVerbosityLevel() (in module ost) pos (AtomHandle attribute) (FindMemParam attribute) Position (SurfaceVertex attribute) positions (EntityHandle attribute) PredictContacts() (in module ost.seq.alg) PreparelDDTGlobalRDMap() built-in function PreparelDDTGlobalRDMap() (in module ost.mol.alg) prev (ResidueHandle attribute) PrintAllDistances() (ClashingDistances method) PrintAllParameters() (StereoChemicalParams method) PrintGlobalRDMap() built-in function PrintGlobalRDMap() (in module ost.mol.alg) PrintlDDTPerResidueStats() built-in function PrintlDDTPerResidueStats() (in module ost.mol.alg) PrintParameters() (lDDTSettings method) PrintPerResidueStats() (lDDTScorer method) PrintResidueRDMap() built-in function PrintResidueRDMap() (in module ost.mol.alg) prob (HHblitsHit attribute) Process() (Processor method) Processor (class in ost.conop) ProfileColumn (class in ost.seq) ProfileDB (class in ost.seq) ProfileHandle (class in ost.seq) Prune() (EditorBase method) psi_torsion (ResidueHandle 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_ent_1 (QSscorer attribute), [1] qs_ent_2 (QSscorer attribute), [1] QSscoreEntity (class in ost.mol.alg.qsscoring), [1] QSscoreError, [1] QSscorer (class in ost.mol.alg.qsscoring), [1] quack_mode (IOProfile attribute)

qualified_name (AtomHandle attribute) quality_problems (lDDTLocalScore attribute), [1] 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) ReadGromacsForcefield() (FFReader method) ReadITP() (FFReader method) ReadResidueDatabase() (FFReader method) ReadStereoChemicalPropsFile() (in module ost.io) Rectangle2 (class in ost.geom) ref (OligoLDDTScorer attribute), [1] reference_chain_name (MappedLDDTScorer attribute), [1] reference_properties (Settings attribute) references (lDDTScorer 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) RemoveAtoms() (in module ost.mol.alg) RemoveChain() (EntityView method) RemoveCol() (Table method) removed_chains (QSscoreEntity attribute), [1] 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) RequestRedraw() (Scene method) res_num_alignment (QSscorer attribute), [1]

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) (class in ost.mol.alg) 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 (SuperpositionResult attribute) rmsd_below_five (TMScoreResult attribute) rmsd_common (TMScoreResult attribute) RMSD_Matrix_From_Traj() (in module ost.mol.alg.trajectory_analysis) rmsd_superposed_atoms (SuperpositionResult attribute) rname (lDDTLocalScore attribute), [1] rnum (lDDTLocalScore attribute), [1] (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), [1] sc_lddt_scorers (OligoLDDTScorer property), [1] Scene (class in ost.gfx) SceneWin (class in ost.gui) score (AlignedPatch attribute) (HHblitsHit attribute) Search() (HHblits method) SearchColNames() (Table method) searched_hmms (HHblitsHeader attribute) sec_structure (ResidueHandle 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) 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) 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() (MMCifInfoEntityBranchLink method) SetBookPublisher() (MMCifInfoCitation method) SetBookPublisherCity() (MMCifInfoCitation method) SetBoolProp() (GenericPropertyContainer method) SetCAS() (MMCifInfoCitation method) SetCASPFlag() (MMCifInfoStructDetails method) SetCenter() (Circle2 method) SetCentralAtom() (ResidueHandle 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) SetDefaultCompoundLib() (in module ost.testutils) 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) 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), [1] (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), [1] SetT() (FermiHighPassFilter method) (FermiLowPassFilter method) SetTemperature() (BrownianIntegrator method) (LangevinIntegrator method) (VariableLangevinIntegrator method) Settings (class in ost.mol.mm) settings (lDDTScorer attribute) (MappedLDDTScorer attribute), [1] (OligoLDDTScorer attribute), [1] 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) 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] 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) 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) (class in ost.mol.alg) StereoChemistryInfo (class in ost.mol.alg) StreamLogSink (class in ost) strict_hydrogens (IOProfile attribute) (RuleBasedProcessor attribute) strict_interactions (Settings attribute) string (Query attribute) StringFromChainType() (in module ost.mol) struct_details (MMCifInfo attribute) struct_refs (MMCifInfo attribute) Sum() (Table method) Superpose() (in module ost.mol.alg) SuperposeFrames() (in module ost.mol.alg), [1] SuperposeSVD() (in module ost.mol.alg) superposition (QSscorer property), [1] 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), [1] symm_2 (QSscorer property), [1]

T

Table (class in ost.table) Take() (ConstSequenceList method) 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 (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) 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), [1] (lDDTSettings method) (MolckSettings method) (Table method) total_contacts (lDDTScorer attribute) total_dist (lDDTLocalScore attribute), [1] 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 (Scene attribute) (TMScoreResult attribute) transformation (SuperpositionResult attribute) 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) (class in ost.mol.alg) 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) use_dispersion_correction (Settings attribute)

V

valid (AtomHandle attribute) (ChainHandle attribute) (ChainView attribute) (EntityHandle attribute) (EntityView attribute) (Query attribute) (ResidueHandle attribute) ValidateSEQRESAlignment() (in module ost.seq.alg) 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) 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), [1] weights (ContactWeightMatrix attribute) (PairSubstWeightMatrix attribute)

width (FindMemParam attribute) (Rectangle2 attribute) 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)