  geom | |
  Axis | |
 AlignedCuboid | Axis-aligned cuboid |
| Line2 | Line2 |
| Rectangle2 | |
| Polygon2 | |
| Ellipse2 | |
| Hyperbola2 | |
| Circle2 | |
| Line3 | Line3 |
| Plane | |
| Sphere | |
| CuboidAxis | Cuboid axis defined by a normalized direction vector and a half extent |
| Cuboid | Arbitrary oriented bounding cuboid |
| Rotation3 | |
| GeomException | |
| DivideByZeroException | |
| OutOfRangeException | |
| VectorAdditions | |
| Mat2 | |
| Mat3 | |
| Mat4 | |
| PointCloud | |
| PointCloudManager | |
| Quat | Unit quaternion |
| Transform | Basic and essential transformation class, including translation, rotation and center of rotation |
| Vec2 | |
| Vec3 | Three dimensional vector class, using Real precision |
| Vec3List | |
 Vec4 | |
| OpenMM | |
| ost | |
 bindings | |
| align_3dcomb | |
| blast | |
| AlignedPatch | |
| BlastHit | |
| BlastError | |
| cadscore | |
| CADResult | |
| clustalw | |
| dssp | |
| hbplus | |
| HBond | |
| hhblits | |
| HHblitsHit | |
| HHblitsHeader | |
| HHblits | |
| ialign | |
| iAlignResult | |
| kclust | |
| cluster | |
| lga | |
| GDTResult | |
| msms | |
| MsmsProcessError | |
| naccess | |
| tmtools | |
| MMAlignResult | |
| TMScoreResult | |
| utils | |
| TempDirWithFiles | |
| TMAlignResult | |
| conop | |
| cleanup | |
| AminoAcidSetIterator | |
| AminoAcidSet | Amino acid bit set |
| Date | |
| AtomSpec | |
| BondSpec | |
| Compound | Knows about the atoms and bonds of a chemical compounds |
| CompoundLib | |
| CompoundLibBase | |
| Conopology | |
| Diag | |
| DiagError | |
| Diagnostics | |
| HeuristicProcessor | |
| MinimalCompoundLib | |
| Checker | |
| Processor | |
| RingFinder | Class for finding rings in an entity |
| RuleBasedProcessor | |
| db | |
| LinearCharacterContainer | |
| LinearPositionContainer | |
| AssemblyInfo | |
| LinearIndexer | |
| PagedArray | |
| PreparedStatement | |
| DatabaseError | |
| RowSet | Row set iterator |
| Database | SQLite database handle |
| geom | |
| gfx | |
| img | |
| alg | |
| MirrorFnc | |
| ShiftFnc | |
| TransformFnc | |
| AnisotropicFilter | |
| AutoCorrelateFnc | |
| ConjFnc | |
| ExplicitConvoluteFnc | |
| ExplicitCorrelateFnc | |
| CrossCorrelate | |
| SliceFnc | |
| DFT | |
| DiscreteShrinkFnc | Shrink image by integral amount |
| FFTException | |
| FFTFnc | |
| LowPassFilter | Low Pass Filter |
| HighPassFilter | High Pass Filter |
| GaussianLowPassFilter | Gaussian Low Pass Filter |
| GaussianHighPassFilter | Gaussian High Pass Filter |
| FermiLowPassFilter | Fermi Low Pass Filter |
| FermiHighPassFilter | Fermi High Pass Filter |
| ButterworthLowPassFilter | Butterworth Low Pass Filter |
| ButterworthHighPassFilter | Butterworth High Pass Filter |
| FractionalShift | |
| GaussianFilterBase | Gaussian Filter |
| GaussianGradientMagnitudeFilterBase | First Derivative Gaussian Filter |
| GaussianLaplacianFilterBase | Gaussian Filter |
| HighestPeakSearch3DBase | |
| HistogramError | |
| HistogramBase | |
| LineAverageBase | Computes mean value of columns or lines |
| LineIterator | Line iterator generator |
| LocalSigmaThresholdBase | |
| MaskImageBase | |
| LinearNormalizer | Linear normalization |
| LinearRangeNormalizer | |
| LogNormalizer | Log normalization |
| LogRangeNormalizer | |
| TransmissionToODNormalizer | |
| Normalizer | |
| Polar | |
| EllipticPolar | |
| Cartesian | |
| PowerSpectrumFnc | |
| RandomizeFnc | |
| SmoothMaskImageBase | |
| StatBase | |
| StatAccumulator | |
| StatMinMaxBase | |
| CosFnc | |
| ExpFnc | |
| LogFnc | |
| Log10Fnc | |
| SinFnc | |
| SqrtFnc | |
| TanFnc | |
| PowFnc | |
| Transformation | Transformation base class |
| Rotate2D | Rotate in XY plane |
| Rotate2D90 | Rotate 90 degree CW in XY plane |
| Scale | Apply scale |
| Translate | Apply translation |
| detail | |
| PasteFnc | |
| image_state | |
| dispatch | |
| unary_dispatch_ip | In-place unary dispatch |
| unary_dispatch_op | Out-of-place unary dispatch |
| binary_dispatch_ip | In-place binary dispatch |
| binary_dispatch_op | Out-of-place binary dispatch |
| DispatchException | |
| ImageStateImpl | |
| ImageStateNonModAlgorithm | Non-modifying image state visitor plus non-mod algorithm |
| ImageStateModIPAlgorithm | In-place modifying image state visitor plus ip algorithm |
| ImageStateConstModIPAlgorithm | In-place modifying image state const visitor plus ip algorithm |
| ImageStateModOPAlgorithm | Out-of-place modifying image state visitor plus op algorithm |
| ImageStateConstModOPAlgorithm | Out-of-place modifying image state const visitor plus op algorithm |
| ImageStateMorphAlgorithm | Morph visitor plus ip algorithm |
| ImageStateBase | |
| FrequencyDomain | |
| HalfFrequencyDomain | |
| SpatialDomain | |
| InvalidImageStateVisitor | ImageStateVisitor general exception |
| ImageStateNonModVisitorBase | Non-modifying image state visitor base class |
| ImageStateNonModVisitor | Non-modifying image state visitor |
| ImageStateModIPVisitorBase | In-place modifying image state visitor base class |
| ImageStateModIPVisitor | In-place modifying image state visitor |
| ImageStateConstModIPVisitorBase | In-place modifying image state const visitor base class |
| ImageStateConstModIPVisitor | In-place modifying image state visitor |
| ImageStateModOPVisitorBase | Out-of-place modifying image state visitor base class |
| ImageStateModOPVisitor | Out-of-place modifying image state visitor |
| ImageStateConstModOPVisitorBase | Out-of-place modifying image state const visitor base class |
| ImageStateConstModOPVisitor | Out-of-place modifying image state visitor |
| ImageStateMorphVisitorBase | Morphing image state visitor base class |
| ImageStateMorphVisitor | Morphing image state visitor |
| Index | |
| IndexIterator | |
| ValueHolder | |
| physics | |
| detail | |
| quantity | |
| multiply_dimensions | |
| divide_dimensions | |
| Scalar | |
| util | |
| CircleMask | |
| OpBase | |
| AndOp | |
| OrOp | |
| XorOp | |
| CompositeMask | |
| ConstData | Abstract base class for read-only data |
| Data | Abstract base class for data |
| AlgorithmBase | Algorithm base class |
| NonModAlgorithm | Non-modifying Algorithm, abstract base class |
| ModIPAlgorithm | In-place modification algorithm |
| ConstModIPAlgorithm | In-place modification const algorithm |
| ModOPAlgorithm | Out-of-place modification algorithm |
| ConstModOPAlgorithm | Out-of-place modification const algorithm |
| InvalidObserver | |
| DataObserver | Abstract base class of data observer |
| InvalidExtentException | |
| Extent | Defines lower and upper valid indices |
| ExtentIterator | Extent iterator |
| ExtentMask | |
| InvalidImageHandle | Exception thrown upon invalid image handle usage |
| ImageHandle | Manage shared instances of images |
| ConstImageHandle | Read-only ImageHandle implementation |
| ImageList | Manages a collection of images |
| InvertedMask | |
| MaskBase | |
| MaskVisitor | |
| NormalizeFnc | Abstract normalizer base class |
| NormalizerImpl | |
| NoOpNormalizer | |
| RangeHandler | |
| NullData | Null data singleton |
| Observable | Templated observable class |
| Peak | |
| Phase | Manages phases og Complex numbers |
| InvalidSampling | |
| PixelSampling | Helper class to handle pixel sampling |
| Point | Class encapsulating 1D to 3D point |
| PointList | List of points |
| PolygonMask | |
| Progress | |
| RasterImage | Generic raster image |
| Pixel | Single pixel spec |
| Size | Class encapsulating 1D to 3D size |
| SphericalMask | |
| io | |
| detail | |
| SerializeWriteHelper | |
| SerializeWriteHelper< false, T > | |
| SerializeWriteHelper< true, T > | |
| SerializeHelper | |
| SerializeHelper< false, T > | |
| SerializeHelper< true, T > | |
| tiff_warning_handler_wrapper | |
| complexint32 | |
| complexint16 | |
| complexint8 | |
| fmt | |
| LPadded | |
| RPadded | |
| LPaddedInt | |
| LPaddedFloat | |
| jpk_tags | |
| remote | |
| RemoteRepository | |
| repository | |
| ModelRepository | |
| BinaryDataSink | |
| BinaryDataSource | |
| ChemdictParser | |
| ClustalIOHandler | |
| Convert | |
| BinaryOStream | |
| BinaryIStream | |
| CRDReader | CHARMM coordinate file import |
| CRDWriter | CHARMM coordinate file export |
| EntityIOCRDHandler | |
| EntityIOHandler | Pure abstract base class for entity io handlers |
| EntityIOHandlerFactoryBase | Pure abstract base class for creation of a specfic entity io handle |
| EntityIOHandlerFactory | |
| MAEReader | |
| EntityIOMAEHandler | |
| EntityIOMMCIFHandler | |
| EntityIOPDBHandler | |
| PQRReader | CHARMM coordinate file import |
| PQRWriter | CHARMM coordinate file export |
| EntityIOPQRHandler | |
| EntityIOSDFHandler | |
| FastaIOHandler | |
| LineSlice | |
| FormattedLine | |
| HhmIOHandler | |
| ImageFormatBase | |
| UndefinedImageFormat | |
| DAT | |
| MapIODatHandler | |
| DF3 | |
| DF3MapIOHandler | |
| DM3 | |
| MapIODm3Handler | |
| DX | |
| MapIODxHandler | |
| MapIOHandler | |
| MapIOHandlerFactoryBase | |
| MapIOHandlerFactory | |
| IPL | |
| MapIOIPLHandler | |
| JPK | |
| MapIOJpkHandler | |
| MRC | |
| CCP4 | |
| MapIOMrcHandler | |
| Nanoscope | |
| MapIONanoscopeHandler | |
| PNG | |
| MapIOPngHandler | |
| Situs | |
| MapIOSitusHandler | |
| Spider | |
| MapIOSpiHandler | |
| TIF | |
| MapIOTiffHandler | |
| IOException | |
| IOUnknownFormatException | |
| IOFileAlreadyLoadedException | |
| IOManager | Central registry for input/output handlers |
| IOProfile | |
| IOProfileRegistry | |
| MMCifInfoStructDetails | |
| MMCifInfoTransOp | |
| MMCifInfoBioUnit | |
| MMCifInfoCitation | |
| MMCifInfoObsolete | Container class for information on obsolete entries |
| MMCifInfoRevisions | Container class for information on file revisions See Python doc |
| MMCifInfoStructRef | |
| MMCifInfoStructRefSeq | |
| MMCifInfoStructRefSeqDif | |
| MMCifInfo | Container class for additional information from MMCif files |
| MMCifReader | Reader for the mmcif file format |
| PDBReader | |
| PDBWriter | |
| SDFReader | |
| SDFWriter | |
| StarDataItem | |
| StarLoopDesc | |
| StarParser | Parser for the STAR file format |
| SurfaceIOHandler | |
| SurfaceIOHandlerFactoryBase | |
| SurfaceIOHandlerFactory | |
| SurfaceIOMSMSHandler | |
| PirIOHandler | |
| ProfileIOHandler | Pure abstract base class for profile io handlers |
| ProfileIOHandlerFactoryBase | Pure abstract base class for creation of a specfic io handler |
| ProfileIOHandlerFactory | |
| PromodIOHandler | |
| PssmIOHandler | |
| SequenceIOHandler | Pure abstract base class for entity io handlers |
| SequenceIOHandlerFactoryBase | Pure abstract base class for creation of a specfic alignment io handler |
| SequenceIOHandlerFactory | |
| IOProfiles | |
| mol | |
| alg | |
| hbond | |
| HBondableAtoms | |
| HBondDonor | |
| HBondAcceptor | |
| HBond | |
| helix_kinks | |
| qsscoring | |
| QSscoreError | QS scoring |
| QSscorer | |
| QSscoreEntity | |
| OligoLDDTScorer | Oligo-lDDT scores |
| MappedLDDTScorer | |
| _CachedRMSD | |
| structure_analysis | |
| superpose | |
| trajectory_analysis | |
| views | |
| NACCESSAccessibilityParam | |
| DSSPAccessibilityParam | |
| OverlapResult | |
| AdjacencyBitmap | |
| Contact | |
| LDT | |
| DistanceMatrix | |
| UniqueAtomIdentifier | Contains the infomation needed to uniquely identify an atom in a structure |
| Domain | |
| Domains | |
| BondLengthInfo | |
| ClashEvent | |
| ClashingInfo | |
| StereoChemicalBondViolation | |
| StereoChemicalAngleViolation | |
| StereoChemistryInfo | |
| ClashingDistances | List of reference atom-atom distances to detect clashes between non-bonded atoms |
| StereoChemicalParams | List of stereo chemical parameters (Bonds and angles) |
| FindMemParam | |
| StereoChemicalProps | |
| lDDTSettings | |
| lDDTLocalScore | |
| lDDTScorer | |
| MolckSettings | |
| PDBize | |
| SecStructureSegment | Consecutive secondary structure element |
| SimilarityMatrix | |
| SuperpositionResult | Stores the number of cycles and the two final EntityViews (in case IterativeSuperposition was applied), the root mean square deviation of the two superposed objects and the transformation matrix (geom::Mat4) to superpose input1 onto input2 |
| MeanSquareMinimizer | |
| impl | |
| tok | |
| AtomGroupEntry | |
| AtomGroup | |
| AtomImpl | Atom implementation |
| AtomProp | |
| ChainImpl | |
| ConnectorImpl | |
| Dihedral | Low level dihedral implementation |
| EntityImpl | |
| FragmentImpl | |
| pointer_it | |
| WithinParam | |
| StringOrRegexParam | |
| Node | |
| LogicOPNode | |
| SelNode | |
| QueryToken | |
| QueryLexer | |
| SelStmt | |
| SelItem | |
| GenProp | Struct to store info about GenericProperties parsed from the |
| QueryImpl | Query statement implementation |
| ResidueImpl | |
| SurfaceImpl | |
| TorsionImpl | |
| mm | |
| antechamber | |
| impl | |
| IndexBase | |
| HydrogenConstructor | |
| TerminiConstructor | |
| BlockModifier | |
| BuildingBlock | |
| DensityForce | |
| DensityForceImpl | |
| CalcDensityForceKernel | |
| GromacsData | |
| CHARMMData | |
| MMPreprocessor | |
| FFReader | |
| ResidueNames | |
| Forcefield | |
| GromacsPositionRuleEvaluator | |
| GromacsHydrogenConstructor | |
| GromacsBlockModifier | |
| HeuristicHydrogenConstructor | |
| HeuristicBlockModifier | |
| Index | |
| Index< 1 > | |
| Index< 2 > | |
| Index< 3 > | |
| Index< 4 > | |
| Index< 5 > | |
| Index< 6 > | |
| Index< 7 > | |
| IndexIterator | |
| Interaction | |
| Modeller | |
| Observer | |
| TrajObserver | |
| TrajWriter | |
| ReferenceDensityKernelFactory | |
| ReferenceCalcDensityForceKernel | |
| TerminiExceptions | |
| Settings | |
| Simulation | |
| StateExtractor | |
| Steep | |
| SystemCreator | |
| Topology | |
| TopologyCreator | |
| AtomBase | Base class for AtomHandle and AtomView |
| AtomHandle | Handle to atom datatype |
| AtomView | Definition of AtomView |
| BondHandle | Chemical bond |
| BondTableEntry | |
| BondTable | |
| Builder | |
| ChainBase | Base class for ChainHandle and ChainView |
| ChainHandle | Linear chain of residues |
| ChainView | Definition of ChainView |
| ChemClass | |
| ChemType | |
| CoordFrame | |
| CoordGroupHandle | Coordinate group, for trajectories and such |
| CoordSource | Coordinate source |
| EditorBase | Base class for entity editors |
| EntityBase | Definition of EntityBase |
| EntityHandle | Protein or molecule |
| EntityObserver | |
| EntityPropertyMapper | |
| EntityView | Definition of EntityView |
| EntityVisitor | EntityVisitor interface |
| EntityViewVisitor | EntityViewVisitor interface |
| ICSEditor | Editor for internal molecule coordinates |
| InMemCoordSource | In-memory coordinate source |
| NotConnectedError | Error to indicate that two atoms that are supposed to be connected are not |
| Prop | |
| PropertyError | |
| QueryFlag | Query flags |
| Query | Selection Query |
| QueryErrorDesc | |
| QueryError | |
| QueryState | Holds state used during query evaluation |
| QueryViewWrapper | |
| ResidueBase | Base class for ResidueHandle and ResidueView |
| ResidueHandle | Residue handle |
| ResNum | |
| ResidueView | Residue view |
| SecStructure | Secondary structure types as defined by DSSP. For convenience, the enum values match the characters used in the DSP file format |
| SpatialOrganizer | Spatial organizer |
| SurfaceHandle | |
| SurfaceVertex | |
| SurfaceTri | |
| TorsionHandle | Named torsion (dihedral) angle |
| ViewAddFlag | Flags to control the behaviour when adding handles to views |
| XCSEditor | External coordinate system editor |
| ost_startup | |
| OstOptionParser | |
| seq | |
| alg | |
| mat | |
| renumber | |
| AlignmentOpts | Options for local and global sequence alignment algorithms |
| ContactPredictionScoreResult | |
| ContactWeightMatrix | Matrix to weight pairs of amino-acids |
| Distances | Container for a pair wise distance for each structure. Each structure is identified by its index in the originally used alignment |
| DistanceMap | |
| InsDel | Get insertions and deletions of an alignment |
| PairSubstWeightMatrix | Position-independet pair substitution weight matrix |
| RefMode | |
| SubstWeightMatrix | Position-independet substitution weight matrix |
| VarianceMap | Container for variances for each entry in a distance map. Main functionality: Get/Set, Min, Max, ExportXXX Get/Set and GetSize taken from TriMatrix |
| Dist2Mean | Container for distances to mean for N structures. Main functionality: Get/Set, ExportXXX |
| impl | |
| SequenceImpl | |
| SequenceListImpl | |
| SequenceListIterator | |
| AlignedColumn | Provides access to a column in a aligned region or a sequence alignment |
| AlignedColumnIterator | |
| AlignedRegion | Region in a sequence alignment |
| AlignmentHandle | Representation of a multiple sequence alignemnt consisting of two or more sequences |
| InvalidSequence | |
| InvalidAlignment | |
| ProfileColumn | Defines profile of 20 frequencies for one residue |
| ProfileHandle | Provides a profile for a sequence |
| ProfileDB | Contains a DB of profiles (identified by a unique name (String)) |
| ConstSequenceHandle | Immutable sequence |
| SequenceHandle | Mutable sequence handle |
| ConstSequenceList | List of immutable sequences |
| SequenceList | List of sequences |
| settings | |
| FileNotFound | |
| stutil | |
| table | |
| BinaryColExpr | |
| TableCol | |
| TableRow | |
| Table | |
| table_selector | |
| TableSelector | |
| testutils | |
| xmlrunner | |
| _TestInfo | |
| _XMLTestResult | |
| XMLTestRunner | |
| _fake_std_streams | |
 XMLTestRunnerTest | |
 NullStream | |
| PairToTupleConverter | Helper to convert between python tuple and std::pair |
| VectorToListConverter | Helper to convert between python list tuple and std::vecot |
| FixedString | String class that uses an array of static size to hold the characters |
| GenericPropError | |
| GenericPropContainerImpl | Base class for the implementation |
| ConstGenericPropContainer | |
| GenericPropContainer | Base class for the handler classes |
| IntegrityError | |
| InvalidHandle | Signals access of member functions of invalid handles |
| Logger | |
| LogSink | |
| StreamLogSink | |
| StringLogSink | |
| FileLogSink | |
| MultiLogSink | |
| Error | |
| PodVector | Vector container that treats its data as POD - even if it isn't in the strict sense |
| Profile | |
| Range | |
| StringRef | Convenient datatype for referencing character data |
| TriMatrix | Triangular matrix template |
| Units | |
| test_image | |
| value_holder_test | |
| circular_iter | |
| const_circular_iter | |
| InvalidatedPointer | |
| PtrObserver | |
| types | Structure |
| types | Structure |
1.8.5
