  _fake_std_streams | |
| _TestInfo | |
| _XMLTestResult | |
 AlgorithmBase | Algorithm base class |
 ConstModIPAlgorithm | In-place modification const algorithm |
| ButterworthLowPassFilter | Butterworth Low Pass Filter |
 ButterworthHighPassFilter | Butterworth High Pass Filter |
| CrossCorrelate | |
| FermiHighPassFilter | Fermi High Pass Filter |
| FermiLowPassFilter | Fermi Low Pass Filter |
| FractionalShift | |
| GaussianHighPassFilter | Gaussian High Pass Filter |
| GaussianLowPassFilter | Gaussian Low Pass Filter |
| HighPassFilter | High Pass Filter |
| LowPassFilter | Low Pass Filter |
| Normalizer | |
| ImageStateConstModIPAlgorithm< FNC > | In-place modifying image state const visitor plus ip algorithm |
| ConstModOPAlgorithm | Out-of-place modification const algorithm |
| DFT | Computes Fourier Trasnform honoring the origin of the image |
| ImageStateConstModOPAlgorithm< FNC > | Out-of-place modifying image state const visitor plus op algorithm |
| ModIPAlgorithm | In-place modification algorithm |
| ImageStateModIPAlgorithm< FNC > | In-place modifying image state visitor plus ip algorithm |
| ImageStateMorphAlgorithm< FNC > | Morph visitor plus ip algorithm |
| ModOPAlgorithm | Out-of-place modification algorithm |
| Cartesian | |
| EllipticPolar | |
| Polar | |
| ImageStateModOPAlgorithm< FNC > | Out-of-place modifying image state visitor plus op algorithm |
 NonModAlgorithm | Non-modifying Algorithm, abstract base class |
 ImageStateNonModAlgorithm< FNC > | Non-modifying image state visitor plus non-mod algorithm |
| AlignedColumn | Provides access to a column in a aligned region or a sequence alignment |
| AlignedColumnIterator | |
| AlignedCuboid | Axis-aligned cuboid |
| AlignedPatch | |
| AlignedRegion | Region in a sequence alignment |
| AlignmentHandle | Representation of a multiple sequence alignemnt consisting of two or more sequences |
| AlignmentOpts | Options for local and global sequence alignment algorithms |
| AminoAcidSet | Amino acid bit set |
| AminoAcidSetIterator | |
| AnisotropicFilter | |
| AtomGroup | |
| AtomGroupEntry | |
| AtomProp | |
| AtomSpec | |
| AutoCorrelateFnc | |
| binary_dispatch_ip< FNC > | In-place binary dispatch |
| binary_dispatch_op< FNC > | Out-of-place binary dispatch |
| BinaryColExpr | |
| BinaryDataSink | |
| BinaryDataSource | |
| BinaryIStream< CONVERSIONTYPE > | |
| BinaryOStream< CONVERSIONTYPE > | |
| BlastError | |
| BlastHit | |
| BondLengthInfo | |
| BondSpec | |
| BondTable< ATOM > | |
| BondTableEntry< ATOM > | |
| Builder | |
| CADResult | |
| Checker | |
| ChemClass | |
| ChemType | |
| Circle2 | |
| circular_iter< T > | |
| ClashEvent | |
| ClashingDistances | List of reference atom-atom distances to detect clashes between non-bonded atoms |
| ClashingInfo | |
| cluster | |
| complexint16 | |
| complexint32 | |
| complexint8 | |
| Compound | Knows about the atoms and bonds of a chemical compounds |
| CompoundLibBase | |
| CompoundLib | |
| MinimalCompoundLib | |
| ConjFnc | |
| Conopology | |
| const_circular_iter< T > | |
| ConstData | Abstract base class for read-only data |
| ConstImageHandle | Read-only ImageHandle implementation |
| Data | Abstract base class for data |
| ImageHandle | Manage shared instances of images |
| NullData | Null data singleton |
| ConstGenericPropContainer< H > | |
| GenericPropContainer< H > | Base class for the handler classes |
| ConstGenericPropContainer< AtomBase > | |
| GenericPropContainer< AtomBase > | |
| AtomBase | Base class for AtomHandle and AtomView |
| AtomHandle | Handle to atom datatype |
| AtomView | Definition of AtomView |
| ConstGenericPropContainer< BondHandle > | |
| GenericPropContainer< BondHandle > | |
| BondHandle | Chemical bond |
| ConstGenericPropContainer< ChainBase > | |
| GenericPropContainer< ChainBase > | |
| ChainBase | Base class for ChainHandle and ChainView |
| ChainHandle | Linear chain of residues |
| ChainView | Definition of ChainView |
| ConstGenericPropContainer< ConstSequenceHandle > | |
| ConstSequenceHandle | Immutable sequence |
| ConstGenericPropContainer< EntityBase > | |
| GenericPropContainer< EntityBase > | |
| EntityBase | Definition of EntityBase |
| EntityHandle | Protein or molecule |
| EntityView | Definition of EntityView |
| ConstGenericPropContainer< ResidueBase > | |
| GenericPropContainer< ResidueBase > | |
| ResidueBase | Base class for ResidueHandle and ResidueView |
| ResidueHandle | Residue handle |
| ResidueView | Residue view |
| ConstGenericPropContainer< SequenceHandle > | |
| GenericPropContainer< SequenceHandle > | |
| SequenceHandle | Mutable sequence handle |
| ConstSequenceList | List of immutable sequences |
| Convert< CONVERSIONTYPE, VALUETYPE > | |
| CoordGroupHandle | Coordinate group, for trajectories and such |
| CoordSource | Coordinate source |
| InMemCoordSource | In-memory coordinate source |
| CosFnc | |
| CRDReader | CHARMM coordinate file import |
| Cuboid | Arbitrary oriented bounding cuboid |
| CuboidAxis | Cuboid axis defined by a normalized direction vector and a half extent |
| Database | SQLite database handle |
| DataObserver | Abstract base class of data observer |
| Date | |
| Diag | |
| Diagnostics | |
| Dihedral | Low level dihedral implementation |
| TorsionImpl | |
| DiscreteShrinkFnc | Shrink image by integral amount |
| divide_dimensions< D1, D2 > | |
| EditorBase | Base class for entity editors |
| ICSEditor | Editor for internal molecule coordinates |
| XCSEditor | External coordinate system editor |
| EleImpl | |
| Ellipse2 | |
| EntityIOHandler | Pure abstract base class for entity io handlers |
| EntityIOCRDHandler | |
| EntityIOCRDHandler | |
| EntityIOMAEHandler | |
| EntityIOMAEHandler | |
| EntityIOMMCIFHandler | |
| EntityIOMMCIFHandler | |
| EntityIOPDBHandler | |
| EntityIOPDBHandler | |
| EntityIOPQRHandler | |
| EntityIOPQRHandler | |
| EntityIOSDFHandler | |
| EntityIOSDFHandler | |
| EntityIOHandlerFactoryBase | Pure abstract base class for creation of a specfic entity io handle |
| EntityIOHandlerFactory< HANDLER > | |
| EntityIOHandlerFactory< HANDLER > | |
| EntityObserver | |
| EntityPropertyMapper | |
| EntityViewVisitor | EntityViewVisitor interface |
| SDFWriter | |
| SDFWriter | |
| EntityVisitor | EntityVisitor interface |
| CRDWriter | CHARMM coordinate file export |
| CRDWriter | CHARMM coordinate file export |
| PQRWriter | CHARMM coordinate file export |
| PQRWriter | CHARMM coordinate file export |
| Error | |
| InvalidatedPointer | |
| DiagError | |
| DatabaseError | |
| GenericPropError | |
| FFTException | |
| HistogramError | |
| DispatchException | |
| InvalidImageStateVisitor | ImageStateVisitor general exception |
| InvalidExtentException | |
| InvalidImageHandle | Exception thrown upon invalid image handle usage |
| InvalidObserver | |
| InvalidSampling | |
| InfoError | |
| IntegrityError | |
| InvalidHandle | Signals access of member functions of invalid handles |
| IOException | |
| IOFileAlreadyLoadedException | |
| IOUnknownFormatException | |
| NotConnectedError | Error to indicate that two atoms that are supposed to be connected are not |
| PropertyError | |
| QueryError | |
| InvalidAlignment | |
| InvalidSequence | |
| ExpFnc | |
| ExplicitConvoluteFnc | |
| ExplicitCorrelateFnc | |
| Extent | Defines lower and upper valid indices |
| ExtentMask | |
| ExtentIterator | Extent iterator |
| FFTFnc | |
| FileNotFound | |
| FixedString< LENGTH > | String class that uses an array of static size to hold the characters |
| fnc_add_ip< T1, D1, T2, D2 > | |
| fnc_div_ip< T1, D1, T2, D2 > | |
| fnc_mul_ip< T1, D1, T2, D2 > | |
| fnc_paste_ip< T1, D1, T2, D2 > | |
| fnc_sub_ip< T1, D1, T2, D2 > | |
| FormattedLine | |
| FragmentImpl | |
| FrequencyDomain | |
| GaussianFilterBase | Gaussian Filter |
| GaussianGradientMagnitudeFilterBase | First Derivative Gaussian Filter |
| GaussianLaplacianFilterBase | Gaussian Filter |
| GDTResult | |
| GenericPropContainerImpl | Base class for the implementation |
| AtomImpl | Atom implementation |
| ChainImpl | |
| ConnectorImpl | |
| EntityImpl | |
| ResidueImpl | |
| SequenceImpl | |
| GenProp | Struct to store info about GenericProperties parsed from the |
| GeomException | |
| DivideByZeroException | |
| OutOfRangeException | |
| HalfFrequencyDomain | |
| HBond | |
| HighestPeakSearch3DBase | |
| HistogramBase | |
| Hyperbola2 | |
| ImageFormatBase | |
| DAT | |
| DAT | |
| DF3 | |
| DF3 | |
| DM3 | |
| DM3 | |
| DX | |
| DX | |
| IPL | |
| IPL | |
| MRC | |
| CCP4 | |
| CCP4 | |
| MRC | |
| Nanoscope | |
| Nanoscope | |
| PNG | |
| PNG | |
| Situs | |
| Situs | |
| Spider | |
| Spider | |
| TIF | |
| JPK | |
| JPK | |
| TIF | |
| UndefinedImageFormat | |
| UndefinedImageFormat | |
| ImageList | Manages a collection of images |
| ImageStateBase | |
| ImageStateImpl< T, D > | |
| ImageStateConstModIPVisitorBase | In-place modifying image state const visitor base class |
| ImageStateConstModIPAlgorithm< FNC > | In-place modifying image state const visitor plus ip algorithm |
| ImageStateConstModIPVisitor< FNC > | In-place modifying image state visitor |
| ImageStateConstModOPVisitorBase | Out-of-place modifying image state const visitor base class |
| ImageStateConstModOPAlgorithm< FNC > | Out-of-place modifying image state const visitor plus op algorithm |
| ImageStateConstModOPVisitor< FNC > | Out-of-place modifying image state visitor |
| ImageStateModIPVisitorBase | In-place modifying image state visitor base class |
| ImageStateModIPAlgorithm< FNC > | In-place modifying image state visitor plus ip algorithm |
| ImageStateModIPVisitor< FNC > | In-place modifying image state visitor |
| ImageStateModOPVisitorBase | Out-of-place modifying image state visitor base class |
| ImageStateModOPAlgorithm< FNC > | Out-of-place modifying image state visitor plus op algorithm |
| ImageStateModOPVisitor< FNC > | Out-of-place modifying image state visitor |
| ImageStateMorphVisitorBase | Morphing image state visitor base class |
| ImageStateMorphAlgorithm< FNC > | Morph visitor plus ip algorithm |
| ImageStateMorphVisitor< FNC > | Morphing image state visitor |
| ImageStateNonModVisitorBase | Non-modifying image state visitor base class |
| ImageStateNonModAlgorithm< FNC > | Non-modifying image state visitor plus non-mod algorithm |
| ImageStateNonModVisitor< FNC > | Non-modifying image state visitor |
| Index | |
| IndexIterator | |
| InfoConstVisitor | |
| InfoGroup | |
| InfoHandle | Main info handle |
| InfoImpl | |
| InfoItem | |
| InfoPath | Encapsulates path to info groups and items |
| InfoSet | |
| InfoVisitor | |
| VerboseInfoVisitor | |
| InsDel | Get insertions and deletions of an alignment |
| IOManager | Central registry for input/output handlers |
| IOProfile | |
| IOProfileRegistry | |
| IOProfiles | |
| Line2 | Line2 |
| Line3 | Line3 |
| LineAverageBase | Computes mean value of columns or lines |
| LineIterator | Line iterator generator |
| LineSlice | |
| LocalSigmaThresholdBase | |
| Log10Fnc | |
| LogFnc | |
| Logger | |
| LogSink | |
| FileLogSink | |
| MultiLogSink | |
| StreamLogSink | |
| StreamLogSink | |
| StringLogSink | |
| LPaddedFloat | |
| LPaddedInt | |
| MAEReader | |
| MapIOHandler | |
| DF3MapIOHandler | |
| DF3MapIOHandler | |
| MapIODatHandler | |
| MapIODatHandler | |
| MapIODm3Handler | |
| MapIODm3Handler | |
| MapIODxHandler | |
| MapIODxHandler | |
| MapIOIPLHandler | |
| MapIOIPLHandler | |
| MapIOMrcHandler | |
| MapIOMrcHandler | |
| MapIONanoscopeHandler | |
| MapIONanoscopeHandler | |
| MapIOPngHandler | |
| MapIOPngHandler | |
| MapIOSitusHandler | |
| MapIOSitusHandler | |
| MapIOSpiHandler | |
| MapIOSpiHandler | |
| MapIOTiffHandler | |
| MapIOJpkHandler | |
| MapIOJpkHandler | |
| MapIOTiffHandler | |
| MapIOHandlerFactoryBase | |
| MapIOHandlerFactory< HANDLER > | |
| MapIOHandlerFactory< HANDLER > | |
| MaskBase | |
| CircleMask | |
| CompositeMask | |
| ExtentMask | |
| InvertedMask | |
| PolygonMask | |
| SphericalMask | |
| MaskImageBase | |
| MaskVisitor | |
| Mat2 | |
| Mat3 | |
| Mat4 | |
| MeanSquareMinimizer | |
| MirrorFnc | |
| MMAlignResult | |
| MMCifInfo | Container class for additional information from MMCif files |
| MMCifInfoBioUnit | |
| MMCifInfoCitation | |
| MMCifInfoObsolete | Container class for information on obsolete entries |
| MMCifInfoRevisions | Container class for information on file revisions (database_pdb_rev) |
| MMCifInfoStructDetails | |
| MMCifInfoStructRef | |
| MMCifInfoStructRefSeq | |
| MMCifInfoStructRefSeqDif | |
| MMCifInfoTransOp | |
| ModelRepository | |
| MsmsProcessError | |
| multiply_dimensions< D1, D2 > | |
| Node | |
| LogicOPNode | |
| SelNode | |
| NormalizeFnc | Abstract normalizer base class |
| NormalizerImpl | |
| LinearNormalizer | Linear normalization |
| LinearRangeNormalizer | |
| LogNormalizer | Log normalization |
| LogRangeNormalizer | |
| TransmissionToODNormalizer | |
| NoOpNormalizer | |
| XMLTestRunnerTest.NullStream | |
| Observable | Templated observable class |
| OpBase | |
| AndOp | |
| OrOp | |
| XorOp | |
| OstOptionParser | |
| PairToTupleConverter< T1, T2 > | Helper to convert between python tuple and std::pair |
| PasteFnc | |
| PDBize | |
| PDBReader | |
| PDBWriter | |
| Phase | Manages phases og Complex numbers |
| RasterImage::Pixel | Single pixel spec |
| PixelSampling | Helper class to handle pixel sampling |
| Plane | |
| PodVector< T > | Vector container that treats its data as POD - even if it isn't in the strict sense |
| Point | Class encapsulating 1D to 3D point |
| Peak | |
| PointCloud | |
| PointCloudManager | |
| pointer_it< T > | |
| PointList | List of points |
| Polygon2 | |
| PowerSpectrumFnc | |
| PowFnc | |
| PQRReader | CHARMM coordinate file import |
| PreparedStatement | |
| Processor | |
| HeuristicProcessor | |
| RuleBasedProcessor | |
| Profile | |
| Progress | |
| Prop | |
| PtrObserver< T > | |
| quantity< Dimensions > | |
| quantity< detail::scalar_dimension > | |
| Scalar | |
| Quat | Unit quaternion |
| Query | Selection Query |
| QueryErrorDesc | |
| QueryFlag | Query flags |
| QueryImpl | Query statement implementation |
| QueryLexer | |
| QueryState | Holds state used during query evaluation |
| QueryToken | |
| QueryViewWrapper | |
| RandomizeFnc | |
| Range | |
| RangeHandler | |
| LinearRangeNormalizer | |
| LogRangeNormalizer | |
| RasterImage | Generic raster image |
| Rectangle2 | |
| RefMode | |
| RemoteRepository | |
| ResNum | |
| RingFinder | Class for finding rings in an entity |
| Rotation3 | |
| RowSet< R > | Row set iterator |
| SDFReader | |
| SecStructure | Secondary structure types as defined by DSSP. For convenience, the enum values match the characters used in the DSP file format |
| SecStructureSegment | Consecutive secondary structure element |
| SelItem | |
| SelStmt | |
| SequenceIOHandler | Pure abstract base class for entity io handlers |
| ClustalIOHandler | |
| ClustalIOHandler | |
| FastaIOHandler | |
| FastaIOHandler | |
| PirIOHandler | |
| PirIOHandler | |
| PromodIOHandler | |
| PromodIOHandler | |
| SequenceIOHandlerFactoryBase | Pure abstract base class for creation of a specfic alignment io handler |
| SequenceIOHandlerFactory< HANDLER > | |
| SequenceIOHandlerFactory< HANDLER > | |
| SequenceList | List of sequences |
| SequenceListImpl | |
| SequenceListIterator< T, I > | |
| SerializeHelper< false, T > | |
| SerializeHelper< true, T > | |
| SerializeWriteHelper< false, T > | |
| SerializeWriteHelper< true, T > | |
| ShiftFnc | |
| SinFnc | |
| Size | Class encapsulating 1D to 3D size |
| SliceFnc | |
| SmoothMaskImageBase | |
| SpatialDomain | |
| SpatialOrganizer< ITEM, VEC > | Spatial organizer |
| Sphere | |
| SqrtFnc | |
| StarDataItem | |
| StarLoopDesc | |
| StarParser | Parser for the STAR file format |
| ChemdictParser | |
| ChemdictParser | |
| MMCifReader | Reader for the mmcif file format |
| MMCifReader | Reader for the mmcif file format |
| StatAccumulator< MAX_MOMENT > | |
| StatBase | |
| StatMinMaxBase | |
| StereoChemicalAngleViolation | |
| StereoChemicalBondViolation | |
| StereoChemicalParams | List of stereo chemical parameters (Bonds and angles) |
| StereoChemistryInfo | |
| StringOrRegexParam | |
| StringRef | Convenient datatype for referencing character data |
| LPadded | |
| RPadded | |
| SubstWeightMatrix | Position-independet substitution weight matrix |
| 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 |
| SurfaceHandle | |
| SurfaceImpl | |
| SurfaceIOHandler | |
| SurfaceIOMSMSHandler | |
| SurfaceIOMSMSHandler | |
| SurfaceIOHandlerFactoryBase | |
| SurfaceIOHandlerFactory< HANDLER > | |
| SurfaceIOHandlerFactory< HANDLER > | |
| SurfaceTri | |
| SurfaceVertex | |
| Table | |
| TableCol | |
| TableRow | |
| TableSelector | |
| TanFnc | |
| TempDirWithFiles | |
| tiff_warning_handler_wrapper | |
| TMAlignResult | |
| TMScoreResult | |
| TorsionHandle | Named torsion (dihedral) angle |
| Transform | Basic and essential transformation class, including translation, rotation and center of rotation |
| Transformation | Transformation base class |
| Rotate2D | Rotate in XY plane |
| Rotate2D90 | Rotate 90 degree CW in XY plane |
| Scale | Apply scale |
| Translate | Apply translation |
| TransformFnc | |
| TriMatrix< T > | Triangular matrix template |
| types | Structure |
| types | Structure |
| unary_dispatch_ip< FNC > | In-place unary dispatch |
| unary_dispatch_op< FNC > | Out-of-place unary dispatch |
| UniqueAtomIdentifier | Contains the infomation needed to uniquely identify an atom in a structure |
| Units | |
| ValueHolder< V > | |
| Vec2 | |
| Vec3 | Three dimensional vector class, using Real precision |
| Vec3List | |
| CoordFrame | |
| Vec4 | |
| VectorAdditions< Container > | |
| VectorToListConverter< T > | Helper to convert between python list tuple and std::vecot |
| ViewAddFlag | Flags to control the behaviour when adding handles to views |
| WithinParam | |
| XMLTestRunner | |
| XMLTestRunnerTest | |
1.8.1.1
