  AlignedColumn | Provides access to a column in a aligned region or a sequence alignment |
| 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 |
| AllAtomPotential | |
| AllAtomPotentialOpts | Interaction statistics options |
| AminoAcidSet | Amino acid bit set |
| AtomGroup | |
| AtomGroupEntry | |
| AtomProp | |
| AtomSpec | |
| BinaryDataSink | |
| BinaryDataSource | |
| BinaryIStream< CONVERSIONTYPE > | |
| BinaryOStream< CONVERSIONTYPE > | |
| BlastError | |
| BlastHit | |
| BondSpec | |
| BondTable< ATOM > | |
| BondTableEntry< ATOM > | |
 Builder | Abstract builder interface |
 HeuristicBuilder | |
 RuleBasedBuilder | Use library of chemical compounds to derive bonds and clean-up structural problems |
| ChemClass | |
| Circle2 | |
| Classifier< impl::NullType > | |
| Classifier< int > | |
| Classifier< Real > | |
| ClassifierBase | Base class for classifiers |
| ContinuousClassifier | Classifier for real valued classes |
| IntegralClassifier | Classifier for integral classes |
| complexint16 | |
| complexint32_t | |
| complexint8 | |
| Compound | Knows about the atoms and bonds of a chemical compounds |
| CompoundLib | |
| ConnResEntry | |
| Conopology | |
| 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 |
| CRDReader | |
| Cuboid | Arbitrary oriented bounding cuboid |
| CuboidAxis | Cuboid axis defined by a normalized direction vector and a half extent |
| Database | SQLite database handle |
| Date | |
| Dihedral | Low level dihedral implementation |
| TorsionImpl | |
| 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 | |
| EntityIOPDBHandler | |
| EntityIOPDBHandler | |
| 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 | |
| CRDWriter | |
| ReducedPotentialImpl | |
| InteractionStatistics | |
| PackingPotential | Packing (solvent accessibility) potential |
| PackingStatistics | |
| Error | |
| InvalidatedPointer | |
| DatabaseError | |
| 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 |
| InvalidAlignment | |
| InvalidSequence | |
| FileNotFound | |
| FixedString< LENGTH > | String class that uses an array of static size to hold the characters |
| FormattedLine | |
| FragmentImpl | |
| GDTResult | |
| GenericPropContainerImpl | Base class for the implementation |
| AtomImpl | Atom implementation |
| ChainImpl | |
| ConnectorImpl | |
| EntityImpl | |
| ResidueImpl | |
| SequenceImpl | |
| GenericPropError | |
| GenProp | Struct to store info about GenericProperties parsed from the |
| GeomException | |
| DivideByZeroException | |
| OutOfRangeException | |
| HBond | |
| HHSearchHit | |
| HHSearchResult | |
| HitSummary | |
| Hyperbola2 | |
| If< false, T, F > | |
| If< true, T, F > | |
| IfNull< C, T, F > | |
| ImageFormatBase | |
| DAT | |
| DF3 | |
| DM3 | |
| DX | |
| MRC | |
| CCP4 | |
| Nanoscope | |
| PNG | |
| Situs | |
| Spider | |
| TIF | |
| JPK | |
| UndefinedImageFormat | |
| IndexBase< D > | |
| IndexBase< 1 > | |
| Index< 1 > | |
| IndexBase< 2 > | |
| Index< 2 > | |
| IndexBase< 3 > | |
| Index< 3 > | |
| IndexBase< 4 > | |
| Index< 4 > | |
| IndexBase< 5 > | |
| Index< 5 > | |
| IndexBase< 6 > | |
| Index< 6 > | |
| IndexBase< 7 > | |
| Index< 7 > | |
| IndexFind< C, T, I > | |
| IndexFind< C, impl::NullType, I > | |
| IndexIterator< D > | |
| 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 | |
| IsEqual< T1, T2 > | |
| IsEqual< T, T > | |
| iterator | |
| circular_iter< T > | |
| const_circular_iter< T > | |
| AtomHandleIter | |
| AtomViewIter | |
| ChainHandleIter | |
| pointer_it< T > | |
| ResidueHandleIter | |
| ResidueViewIter | |
| AminoAcidSetIterator | |
| AlignedColumnIterator | |
| SequenceListIterator< T, I > | |
| IterRange< I > | Adaptor to turn iterator into an iterator range |
| LengthOf< T1, T2, T3, T4, T5, T6, T7 > | |
| LengthOf< NullType, NullType, NullType, NullType, NullType, NullType, NullType > | |
| Line2 | Line2 |
| Line3 | Line3 |
| LineSlice | |
| Logger | |
| LogSink | |
| FileLogSink | |
| MultiLogSink | |
| StreamLogSink | |
| StreamLogSink | |
| LPaddedFloat | |
| LPaddedInt | |
| MAEReader | |
| MapIOHandler | |
| DF3MapIOHandler | |
| MapIODatHandler | |
| MapIODm3Handler | |
| MapIODxHandler | |
| MapIOMrcHandler | |
| MapIONanoscopeHandler | |
| MapIOPngHandler | |
| MapIOSitusHandler | |
| MapIOSpiHandler | |
| MapIOTiffHandler | |
| MapIOJpkHandler | |
| MapIOHandlerFactoryBase | |
| MapIOHandlerFactory< HANDLER > | |
| Mat2 | |
| Mat3 | |
| Mat4 | |
| ModelRepository | |
| MsmsProcessError | Custom exception that substitutes CalledProcessError |
| MultiClassifier< V, T1, T2, T3, T4, T5, T6, T7 > | Generic n-dimensional classifier |
| MultiClassifier< uint32_t, T1, T2, T3, T4, T5, T6, T7 > | |
| Histogram< T1, T2, T3, T4, T5, T6, T7 > | Histogram specialization for multi classifier |
| Node | |
| LogicOPNode | |
| SelNode | |
| NullFind< I > | |
| NullType | |
| NumberOfClasses< T > | |
| NumberOfClasses< impl::NullType > | |
| OstOptionParser | |
| PackingPotentialOpts | |
| PairToTupleConverter< T1, T2 > | Helper to convert between python tuple and std::pair |
| PDBReader | |
| PDBWriter | |
| Plane | |
| PodVector< T > | Vector container that treats its data as POD - even if it isn't in the strict sense |
| PointCloud | |
| PointCloudManager | |
| Polygon2 | |
| PreparedStatement | |
| Profile | |
| Prop | |
| PropertyError | |
| PtrObserver< T > | |
| Quat | Unit quaternion |
| Query | Selection Query |
| QueryError | |
| QueryErrorDesc | |
| QueryFlag | Query flags |
| QueryImpl | Query statement implementation |
| QueryLexer | |
| QueryState | Holds state used during query evaluation |
| QueryToken | |
| QueryViewWrapper | |
| Range | |
| Rectangle2 | |
| ReducedPotential | Reduced model statistical potential operating on the residue level |
| ReducedStatistics | |
| ReducedStatOptions | Aggregates the option for the reduced model statistics |
| RefMode | |
| 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 | |
| SerializeHelper< false, T > | |
| SerializeHelper< true, T > | |
| SerializeWriteHelper< false, T > | |
| SerializeWriteHelper< true, T > | |
| SpatialOrganizer< ITEM, VEC > | Spatial organizer |
| Sphere | |
| StarDataItem | |
| StarLoopDesc | |
| StarParser | Parser for the STAR file format |
| ChemdictParser | |
| ChemdictParser | |
| StringRef | Convenient datatype for referencing character data |
| LPadded | |
| RPadded | |
| SubstWeightMatrix | Position-independet substitution weight matrix |
| SuperposerSVD | Effiently superpose a bunch of models with the same number of atoms Choose either two EntityViews or two AtomViewLists |
| 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 | |
| TempDirWithFiles | |
| tiff_warning_handler_wrapper | |
| TMAlignResult | |
| TMScoreResult | |
| ConnResEntry::TorsionEntry | |
| TorsionHandle | Named torsion (dihedral) angle |
| TorsionPotential | Torsion potential |
| TorsionPotentialOpts | Torsion potential options |
| TorsionPotentialOptsSolis | Torsion potential options |
| TorsionPotentialSolis | Torsion potential |
| TorsionStatistics | Sequence dependent torsion statistics |
| TorsionStatisticsSolis | Sequence dependent torsion statistics |
| Transform | Basic and essential transformation class, including translation, rotation and center of rotation |
| TriMatrix< T > | Triangular matrix template |
| Units | |
| Vec2 | |
| Vec3 | Three dimensional vector class, using Real precision |
| Vec3List | |
| Vec4 | |
| VectorAdditions< Container > | |
| ViewAddFlag | Flags to control the behaviour when adding handles to views |
| WithinParam | |
1.8.1.1