| VIEW::AddBackboneModel | AddBackboneModel class |
| VIEW::AddBallAndStickModel | AddBallAndStickModel class |
| VIEW::AddCartoonModel | AddCartoonModel class |
| AddHydrogenProcessor | Saturate atoms with hydrogen atoms |
| Addition< First, Second, DataType > | Addition class |
| PDB::AdditionalAtomInfo | A structure tracking the current values of all auxiliary information required to write ATOM or HETATM records |
| VIEW::AddLineModel | AddLineModel class |
| VIEW::AddSurfaceModel | AddSurfaceModel class |
| VIEW::AddVanDerWaalsModel | AddVanDerWaalsModel class |
| AmberBend | Amber bond stretch component |
| VIEW::AmberConfigurationDialog | Dialog for changing the options of the AMBER forcefield |
| AmberEvaluation | A class for energetic evaluators of docking results using an AMBER force field as scoring function |
| AmberFF | AMBER force field class |
| AmberFF::Default | Default values for AMBER options |
| AmberFF::Option | Option names |
| AmberNonBonded | Amber NonBonded (VdW + Electrostatic) component |
| AmberStretch | Amber bond stretch component |
| AmberTorsion | Amber bond stretch component |
| Peptides::AminoAcidDescriptor | This class represents one amino acid in the sequence |
| AnisotropyShiftProcessor | Shift assignment processor implementing Anisotropy |
| AromaticBondsPredicate | Predicate class for atoms bearing aromatic bonds |
| AromaticityProcessor | Processor method to detect aromaticity of AtomContainers |
| AssignBaseProcessor | Only used for deriving interface |
| AssignChargeProcessor | Assigns a charge to each atom |
| AssignRadiusProcessor | Assigns the radius to each atom |
| AssignShiftProcessor | Set a property called chemical_shift |
| AssignTypeNameProcessor | Assign type names to atoms |
| AssignTypeProcessor | Type assignment processor |
| Atom | Atom class |
| AtomBijection | Atom bijection |
| VIEW::AtomBondModelBaseProcessor | AtomBondModelBaseProcessor class |
| VIEW::AtomChargeColorProcessor | AtomChargeColorProcessor class |
| AtomContainer | Atom Container Base Class |
| AtomContainerIteratorTraits | Traits class for the AtomContainerIterators |
| VIEW::AtomDistanceColorProcessor | AtomDistanceColorProcessor class |
| AtomicPolarizabilities | This descriptor adds up the atomic polarizabilities for all atoms |
| AtomInformationContent | This descriptor is $n$ times MeanAtomInformationContent |
| AtomIteratorTraits | Traits class for the AtomIterators |
| AtomNamePredicate | Predicate for matching atom names |
| VIEW::AtomOverview | Dialog for creating labels for a selection of molecular objects |
| AtomTypePredicate | Predicate for matching atom types |
| AtomTyper | Base class for a programable Atom typer |
| AtomTypes | Force Field Atom Type Class |
| AtomVector | Atom vector class |
| AutoDeletable | Auto-deletable concept |
| AxialPredicate | Axial predicate |
| BackBonePredicate | Predicate indicating backbone atoms |
| BalabanIndexJ | The Balaban index J is topological index |
| VIEW::BALLThread | Baseclass for threads in BALL |
| BaseIterator< Container, DataType, Position, Traits > | Generic Iterator Class |
| BidirectionalIterator< Container, DataType, Position, Traits > | Mutable bidirectional iterator |
| BinaryFileAdaptor< T > | Helper class for data conversion |
| BinaryFunctor< FirstArgumentType, SecondArgumentType, ResultType > | Generic Binary Functor Class |
| BinaryPredicate< T1, T2 > | Generic Binary Predicate Class |
| BinaryProcessor< T1, T2 > | Generic Binary Processor Class |
| Bit | Bit Class |
| Bit::IllegalOperation | Exception thrown if a file could not be processed right |
| BitVector | Bit vector class |
| Bond | Bond class |
| Bond::NotBound | Not bound to two atoms |
| BondPolarizabilities | This descriptor is calculated by adding up the differences in atomic polarizabilities of the both participating atoms through all bonds |
| VIEW::BondProperties | Dialog for showing and changing the properties of the bonds of an atom |
| PDB::BookKeeping | This struct contains the number of records in a PDB file as required for the MASTER record |
| BoundingBoxProcessor | Bounding box creating processor |
| VIEW::Box | Box class |
| Bruker1DFile | Bruker 1D spectrum format |
| Bruker2DFile | Bruker 2D spectrum format |
| Exception::BufferOverflow | Buffer overflow exception |
| BuildBondsProcessor | Bond creation processor |
| BuildBondsProcessor::Default | Default values for options |
| BuildBondsProcessor::Option | Option names |
| BuriedPolar | Fresno buried polar component |
| BuriedPolar::Default | Default values for SLICK options |
| BuriedPolar::Option | Option names |
| VIEW::Camera | Camera with viewpoint, a look at point and an up-vector |
| CanonicalMD | A MD simulation in the canoncial ensemble |
| CanonicalMD::AuxFactors | Helper class containing auxiliary factors |
| Chain | Protein chain class |
| ChainBuilder | This class provides methods for analysis of the chains in a molecule |
| ChainIteratorTraits | Traits class for the various ChainIterators |
| ChainPredicate | Predicate for matching chains |
| ChargePredicate | Charge predicate |
| ChargeRuleProcessor | Charge Rule Processor |
| CharmmBend | Charmm bond stretch component |
| VIEW::CharmmConfigurationDialog | Dialog for changing the options of the CHARMM forcefield |
| CharmmEEF1 | Force Field Parameter Section for CHARMM EEF1 |
| CharmmEEF1::Data | ????? |
| CharmmEEF1::Values | ????? |
| CharmmFF | CHARMM force field class |
| CharmmFF::Default | Default values |
| CharmmFF::Option | Options names |
| CharmmImproperTorsion | Charmm improper torsion component |
| CharmmNonBonded | Charmm NonBonded component |
| CharmmStretch | Charmm bond stretch component |
| CharmmTorsion | CHARMM torsion component |
| ChemScoreMetal | ChemScore Metal component { Definition:} {BALL/MOLMEC/SLICK/chemScoreMetal.h} |
| CHPI | SLICK ringstacking component |
| CHPI::AromaticRing | A class for storing aromatic rings and information associated with them |
| CHPI::CHGroup | A class for storing aliphatic CH groups suitable for building CH- interactions with aromatic rings |
| ClaverieParameter | ClaverieParameter class |
| ClearChargeProcessor | Clears the charge on all atoms |
| ClearRadiusProcessor | Clears the radius of all atoms |
| ClearShiftProcessor | Clear assigned shift data of all atoms |
| Client | Client class |
| Client::InvalidClient | InvalidClient exception class |
| Client::NoPersistentObject | NoPersistentObject exception class |
| VIEW::ClippingDialog | Dialog for selcting which Representations are clipped by one clipping plane |
| VIEW::ClippingPlane | ClippingPlane |
| VIEW::ColorExtension2 | Base class for geometric objects that need two colors |
| VIEW::ColorHSV | ColorHSV class |
| VIEW::ColoringSettingsDialog | Dialog for the molecular model coloring settings |
| VIEW::ColorMap | This class is used to implement a color Map that can be used to map a floating point value into a color |
| VIEW::ColorProcessor | Calculating colors for given GeometricObject instances |
| VIEW::ColorRGBA | ColorRGBA class |
| VIEW::ColorUnit | ColorUnit class |
| VIEW::ColorUnit::NotInHexFormat | NotInHexFormat Exception class |
| VIEW::ColorUnitHue | Value for the hue component of the class ColorHSV |
| Comparator< T > | Generic Comparator Class |
| ComposedEnergyProcessor | A class for composed energy calculations |
| Composite | Composite Class |
| CompositeIteratorTraits | Composite Iterator Traits This class is used in the implementation of the kernel iterators |
| VIEW::CompositeManager | Management of Composites |
| VIEW::CompositeMessage | CompositeMessage is the base class of all messages concerning the change of one Composite |
| VIEW::CompositeProperties | Dialog for showing and changing the properties of an Composite, e.g |
| Conformation4C1Predicate | Predicate for determining whether a sugar ring is in 4C1 conformation |
| ConformationSet | Data structure for conformation results |
| ConjugateGradientMinimizer | A minimizer for geometry optimization based on different conjugate gradient (CG) algorithms |
| ConjugateGradientMinimizer::Default | Defaults for all options |
| ConjugateGradientMinimizer::Option | Options names |
| ConnectedToPredicate | Predicate class for atoms being connected to a constellation defined by an expression |
| VIEW::ConnectionObject | Base class for all widgets and dialogs that handles communication through message posting |
| ConnectivityBase | Generic QSAR molecular connectivity descriptors class \ |
| Constant | Python constants namespace wrapper |
| ConstantFunction< constant_template > | Constant function class |
| ConstBidirectionalIterator< Container, DataType, Position, Traits > | Constant Bidirectional Iterator |
| ConstForwardIterator< Container, DataType, Position, Traits > | Generic non-mutable forward itterator |
| VIEW::ContourSurfaceDialog | Dialog for creating contour surfaces from RegularData3D |
| VIEW::ControlSelectionMessage | Used to inform MainControl of selection in MolecularControl (not the one of the checkboxes!) and the other way round |
| CosineTorsion | Cosine Torsion |
| VIEW::CreateRepresentationMessage | Notify the DisplayProperties dialog so that it creates a new Representation |
| CreateSpectrumProcessor | Processor creates peaklist_ |
| CubicFunction< Function, DataType > | CubicFunction class |
| VIEW::CustomColorProcessor | CustomColorProcessor colorizes every GeometricObject with the default color |
| VIEW::Dataset | Baseclass for datasets |
| VIEW::DatasetControl | DatasetControl is a widget to manage and manipulate arbitrary data types |
| VIEW::DatasetController | Controller base class for one type of Dataset A DatasetController provides all neccessary means to manage and manipulate a kind of data in the DatasetControl |
| VIEW::DatasetMessage | Message to notify about changes in a Dataset |
| DCDFile | DCD Trajectory file format |
| Density | This descriptor calculates the density of the molecule, by deviding the molecular weight by the van der Waals surface area |
| Descriptor | Generic QSAR molecular descriptor class |
| VIEW::DeselectControlsMessage | Message send by one GenericControl to notify all other GenericControl instances to deselect their QListView |
| Directory | Directory class |
| VIEW::Disc | Disc class |
| VIEW::DisplayProperties | Dialog for creating and changing representations for a selection of molecular objects |
| Division< First, Second, DataType > | Division class |
| Exception::DivisionByZero | Division by zero error |
| VIEW::DockDialog | Dialog for docking / redocking two systems |
| DockingAlgorithm | Interface class for docking algorithms |
| VIEW::DockingController | Class for docking two systems |
| VIEW::DockingFinishedMessage | Message to notify docking has finished |
| VIEW::DockingThread | Thread for Docking |
| VIEW::DockProgressDialog | Dialog for showing the progress during a docking calculation |
| DockResult | Result of a (re)docking calculation |
| DockResult::Compare_ | Nested class in DockResult |
| DockResult::Scoring_ | Nested class in DockResult |
| VIEW::DockResultController | Controller base class for one type of Dataset |
| VIEW::DockResultDialog | Dialog for showing the docking results |
| VIEW::DockResultDialog::Compare_ | Nested class in DockResultDialog |
| VIEW::DockWidget | Class for ModularWidget, which can be docked in the MainApplication window |
| DoubleBondsPredicate | Predicate for atoms bearing double bonds |
| VIEW::DownloadPDBFile | Dialog to search for and download structure files from the PDB data bank |
| DSN6File | DSN6 density map file format |
| VIEW::EditableScene | Extended 3D view for editing molecules |
| VIEW::EditFunctions | EditFunctions class |
| VIEW::EditOperationDialog | Dialog for storing the undo Operations of EditableScene |
| VIEW::EditSettings | EditSettings is a widget that will be inserted into the tab dialog Preferences |
| EFShiftProcessor | Shift assignment processor implementing the electric field effect |
| ElectrostaticPotentialCalculator | This class is used to compute the electrostatic potential for of a system |
| ElectrostaticPotentialCalculator::Default | Default values for the options in ElectrostaticPotentialCalculator::options |
| ElectrostaticPotentialCalculator::Option | Symbolic names for option keys |
| Element | Element class |
| VIEW::ElementColorProcessor | ElementColorProcessor class |
| ElementPredicate | Predicate for matching elements |
| Embeddable | Python Embedding Base Class |
| EnergeticEvaluation | Base class for energetic evaluators of docking results |
| EnergyMinimizer | EnergyMinimizer |
| EnergyMinimizer::Option | Option names |
| VIEW::EnergyMinimizerThread | Thread for EnergyMinimization |
| EnergyProcessor | Processor for energy calculations |
| Enumerator< Container, SiteIterator, Variant > | Enumerator class |
| EnumeratorIndex | EnumeratorIndex class |
| EnumeratorIndex::IncompatibleIndex | Exception for reporting incompatible EnumeratorIndex instances, i.e |
| Experiment< PeakListType > | Class describing a certain type of NMR experiment |
| Expression | Expression class |
| ExpressionParser | Expression Parser |
| ExpressionParser::SyntaxTree | SyntaxTree |
| ExpressionPredicate | ExpressionPredicate |
| ExpressionTree | Expression tree class |
| Factory< T > | Factory class |
| FalsePredicate | False predicate |
| FDPB | Finite Difference Poisson Boltzmann Solver |
| FDPB::Boundary | This struct contains symbols for the available boundary conditions |
| FDPB::ChargeDistribution | Constants to define the charge distribution methods |
| FDPB::Default | Default values for FDPB options |
| FDPB::DielectricSmoothing | Constants to define the dielectric smoothing methods |
| FDPB::FastAtomStruct | Compact internal datastructure for the administration of the atoms extracted from the system |
| FDPB::Option | Symbolic names for option keys |
| VIEW::FDPBDialog | Dialog for performing Finite Distance Poisson Bolzmann calculations |
| FermiBaseFunction | Sigmoidal base function |
| VIEW::FetchHTMLThread | Thread to fetch a file over TCP network traffic |
| VIEW::FieldLineCreator | FieldLineCreator class |
| VIEW::FieldLinesDialog | Dialog for creating field lines |
| File | File Class |
| File::CannotWrite | Exception CannotWrite A given file could not be written, either because its not open or it has a wrong open mode |
| Exception::FileNotFound | File not found |
| VIEW::FileObserver | Class for observing changes in a molecular file |
| FileSystem | File System Class This class is a wrapper around some very basic properties of the machine's file system properties |
| VIEW::ForceColorProcessor | Coloring by the forces, acting on atoms |
| ForceField | Force field class |
| ForceFieldComponent | Generic force field component class |
| ForceFieldEvaluation | Base class for energetic evaluators of docking results using a force field as scoring function |
| ForceFieldParameters | Force field parameter class |
| VIEW::ForceModel | ForceModel class |
| FormalCharge | This descriptor adds up the formal charges |
| ForwardIterator< Container, DataType, Position, Traits > | Generic mutable forward iterator class |
| Fragment | Fragment class |
| FragmentDB | FragmentDB - fragment database class |
| FragmentDB::BuildBondsProcessor | Bond creation processor |
| FragmentDB::NoFragmentNode | No fragment node found |
| FragmentDB::NormalizeNamesProcessor | Name normalization processor |
| FragmentDistanceCollector | Collects all MolecularFragments that are close enough to another molecular fragment |
| FragmentIteratorTraits | Traits class for the FragmentIterator |
| GAMESSDatFile | GAMESSDat file class |
| GAMESSDatFile::block | Nested class for the data blocks of the GAMESSFile * |
| GAMESSDatFile::State | State of the parser * |
| GAMESSLogFile | GAMESSLog file class |
| GAMESSLogFile::State | State of the parser * |
| Exception::GeneralException | General exception class |
| GeneralizedBornModel | Compute the electrostatics of a molecule in solution |
| VIEW::GenericControl | GenericControl is a widget to display the structure of Composite objects |
| GenericMolFile | Base class for all molecule file format classes |
| VIEW::GenericSelectionMessage | GenericSelectionMessage class |
| GeometricCenterProcessor | Calculates the geometric center of a given Composite object |
| VIEW::GeometricControl | GeometricControl is a widget to display the list of representations |
| GeometricFit | GeometricFit This class is derived from class DockingAlgorithm |
| GeometricFit::Option | Symbolic names for option keys |
| GeometricFit::Peak_ | Nested class Peak_ This class is needed for an efficient handling of all peaks corresponding to one orientation in a multiset |
| GeometricFit::RotationAngles_ | Nested class RotationAngles_ |
| VIEW::GeometricFitDialog | Dialog for options of the docking algorithm GeometricFit |
| VIEW::GeometricObject | GeometricObject class |
| VIEW::GeometricObjectSelectionMessage | GeometricObjectSelectionMessage class |
| VIEW::GLDisplayList | GLDisplayList class |
| VIEW::GLDisplayList::DisplayListRedeclaration | DisplayListRedeclaration exception class |
| VIEW::GLDisplayList::NestedDisplayList | NestedDisplayList exception class |
| VIEW::GLDisplayList::NoDisplayListAvailable | NoDisplayListAvailable exception class |
| Exception::GlobalExceptionHandler | Class handling uncaught exception globally |
| VIEW::GLRenderer | GLRenderer Renderer which provides hardware accelerated OPENGL rendering |
| VIEW::GLRenderer::WrongModes | WrongModes Exception class |
| Gradient | Gradient class |
| GraphEdge< Vertex, Edge, Face > | Generic GraphEdge Class |
| GraphFace< Vertex, Edge, Face > | Generic GraphFace Class |
| GraphTriangle< Vertex, Edge, Face > | Generic GraphTriangle Class |
| GraphVertex< Vertex, Edge, Face > | Generic GraphVertex Class |
| VIEW::GridVisualisation | GridVisualisation |
| VIEW::GridVisualizationDialog | Dialog for visualizing grids |
| HaighMallionShiftProcessor | Shift assignment processor implementing Haigh Mallion theory |
| HashFunction< T > | General Hash Function Template |
| HashGrid3< Item > | Three-dimensional Hash Grid Class |
| HashGridBox3< Item > | Grid Box Class |
| HashGridBox3< Item >::DataItem | ????? |
| HashGridBox3< Item >::NeighborBoxItem | ????? |
| HashMap< Key, T > | Generic Hash Map Class |
| HashMap< Key, T >::IllegalKey | IllegalKey exception |
| HashSet< Key > | Generic Hash Set Class |
| HashSet< Key >::IllegalKey | Illegal key exception |
| VIEW::HBondModelProcessor | HBondModelProcessor class |
| HBondProcessor | This processor computes all hydrogen bonds occuring between amino acids in the composite it is applied to |
| HBondShiftProcessor | Shift assignment processor implementing the effect of hydrogen bonds |
| VIEW::HelpViewer | DockWidget to show online help texts e.g |
| HINFile | HyperChem file class |
| VIEW::HotkeyTable | Class for storing Python hotkeys in a GUI table |
| HydrogenBond | Fresno Hydrogen Bond component |
| HydrogenBond::Default | Default values for SLICK options |
| HydrophobicVdWSurface | This descriptor calculates the sum of atomic SAS van der Waals surface areas of the molecule, of the hydrophobic atoms |
| Exception::IllegalPosition | Invalid Position |
| Exception::IllegalSelfOperation | Illegal self operation |
| Exception::IllegalTreeOperation | Illegal tree operation |
| Exception::IncompatibleIterators | Incompatible iterator |
| Exception::IndexOverflow | Index overflow |
| Exception::IndexUnderflow | Index underflow |
| INIFile | INIFile |
| INIFile::IteratorTraits_ | Interface for the LineIterator |
| INIFile::Section | A section within an INI file |
| InRingPredicate | Predicate for atoms being included in rings of a certain number |
| VIEW::InterpolateColorProcessor | Base class for ColorProcessors, that interpolate between two values |
| Exception::InvalidFormat | Invalid format |
| Exception::InvalidIterator | Invalid iterator |
| Exception::InvalidOption | Exception to be thrown if an invalid option is given |
| Exception::InvalidRange | Invalid range |
| Exception::InvalidSize | Invalid Size Throw this exception to indicate that a size was unexpected |
| IOSockStream | IOSocketStream |
| IOStreamSocket | IOStreamSocket |
| ISockStream | Input stream from a socket |
| JCAMPFile | JCAMP file class |
| JohnsonBoveyShiftProcessor | Shift assignment processor implementing Johnson Bovey theory |
| KCFFile | KEGG KCF file class |
| Kekuliser | Class to transform bonds with type "aromatic" to conjugated single and double bonds |
| KernelPredicate< T > | Kernel predicate class |
| VIEW::Label | Label class |
| VIEW::LabelDialog | Dialog for creating labels for a selection of molecular objects |
| VIEW::LabelModel | LabelModel class |
| LennardJones | Lennard Jones parameter section |
| VIEW::LightSettings | Dialog for setting the lighting, which is added to the Preferences |
| VIEW::LightSource | Light source is mainly used for Renderer classes (e.g |
| Limits< T > | Numeric limits class |
| VIEW::Line | Line class |
| LinearBaseFunction | Linear base function |
| LineBasedFile | A class for the convenient parsing of line-based file formats |
| LineSearch | Basic line search class |
| Lipophilic | Fresno lipophilic component |
| Lipophilic::Default | Default values for SLICK options |
| Lipophilic::Option | Option names |
| List< Value > | Extended list object |
| VIEW::LogEvent | Event class used for thread safe output to logview |
| LogStream | Log Stream Class |
| LogStreamBuf | Stream buffer used by LogStream |
| VIEW::LogView | LogView class |
| VIEW::MainControl | MainControl is the main administration unit for a program and must be used by all applications |
| VIEW::MainControlPreferences | MainControlPreferences is a widget that will be inserted into the tab dialog Preferences |
| VIEW::MaterialSettings | Dialog for setting the Material, which is added to the Preferences |
| MD5Hash | MD5 hash of a string |
| VIEW::MDSimulationThread | Thread for MDSimulation |
| MeanAtomInformationContent | Atom information content (mean) |
| VIEW::Mesh | Mesh class |
| VIEW::MeshBuffer | Wrapper class to draw BALLView Mesh instances with OpenGL vertex buffer objects |
| VIEW::Message | General Message class |
| VIEW::MessageEvent | A QT Event, that can contain a VIEW message |
| MicroCanonicalMD | Microcanonical MD: A class for doing molecular dynamics simulations according to the principle of a microcanonical ensemble (NVE), i.e., the total energy of the system is kept constant |
| MicroCanonicalMD::AuxFactors | A local auxiliary class |
| VIEW::MinimizationDialog | Dialog for performing energy minimisations |
| MMFF94 | MMFF94 force field class |
| MMFF94::Default | Default values for MMFF94 options |
| MMFF94::Option | Option names |
| MMFF94AtomType | Class to store the values of an atom type from MMFFPROP.PAR |
| MMFF94AtomTypeEquivalences | MMFF94 equivalences for atom types (see MMFFDEF.PAR) |
| MMFF94AtomTypes | MMFF94 parameters for atom types (see MMFFPROP.PAR) |
| MMFF94BendParameters | MMFF94 parameters for bond bending (see MMFFANG.PAR) |
| MMFF94ChargeProcessor | Assign MMFF94 Charges |
| VIEW::MMFF94ConfigurationDialog | Dialog for changing the options of the MMFF94 forcefield |
| MMFF94ESParameters | MMFF94 parameters for partial charges for electrostatics (see MMFFCHG.PAR MMFFPBCI.PAR) |
| MMFF94NonBonded | MMFF94 NonBonded (VdW + Electrostatic) component |
| MMFF94OutOfPlaneBend | MMFF94 Out of plane component |
| MMFF94ParametersBase | MMFF94 component parameters base class |
| MMFF94PlaneParameters | MMFF94 parameters for out of plane bending (see MMFFOOR.PAR) |
| MMFF94StretchBend | MMFF94 bond stretch component |
| MMFF94StretchBend::Bend | See MMFFANG.PAR |
| MMFF94StretchBendParameters | MMFF94 parameters for stretch-bend interactions (see MMFFSTBN.PAR) |
| MMFF94StretchParameters | MMFF94 parameters for bond stretching (see MMFFBOND.PAR) |
| MMFF94Torsion | MMFF94 bond stretch component |
| MMFF94Torsion::Torsion | See MMFFTOR.PAR |
| MMFF94TorsionParameters | MMFF94 parameters for torsions (see MMFFTOR.PAR) |
| MMFF94VDWParameters | MMFF94 parameters for VDW (see MMFFVDW.PAR) |
| VIEW::ModelInformation | ModelInformation class |
| VIEW::ModelProcessor | Base class for all model processors |
| VIEW::ModelSettingsDialog | Dialog for the molecular model settings, it is inserted into the Preferences |
| VIEW::ModifyRepresentationDialog | Dialog for coloring of surfaces The surfaces can be colored by a given color, or from the values, contained in a RegularData3D grid |
| VIEW::ModularWidget | ModularWidget is a base class for widely independent widget that realize one feature domain |
| MOL2File | SYBYL MOL2 file class |
| VIEW::MolecularControl | MolecularControl is a widget to display the molecular structure of Composite objects |
| MolecularDynamics | Molecular Dynamics base class |
| MolecularDynamics::Option | Local classes for option names and default option values for all MD(sub)classes |
| VIEW::MolecularDynamicsDialog | Dialog for performing MD simulations |
| VIEW::MolecularFileDialog | Dialog for opening molecular data files |
| MolecularInformation | MolecularInformation class |
| VIEW::MolecularStructure | MolecularStructure provides means to modify molecular structures and do several calculations |
| VIEW::MolecularTaskMessage | Message to perform specific tasks for molecular items |
| MolecularWeight | This descriptor calculates the molecular weight |
| Molecule | Molecule class |
| MoleculeAssembler | Class, providing methods for the assembly of a structure diagram |
| MoleculeIteratorTraits | MoleculeIteratorTratis_ |
| MoleculeObjectCreator | MoleculeObjectCreator class |
| MoleculePredicate | Predicate for matching molecules |
| MOLFile | MDL MOL file class |
| MOLFile::Property | String constants used for named properties |
| VIEW::MultiColorExtension | Base class for geometric objects that need multiple colors |
| VIEW::MultiLine | A line with multiple vertices and colors |
| MutableConstant< DataType > | Constant function class |
| MutablePower< Function, DataType > | MutablePower class |
| NamedProperty | Named Property Class |
| NegativePolarVdWSurface | This descriptor calculates the sum of atomic SAS van der Waals surface areas of the molecule, where the partial charge of the atom is negative and the atom is a polar atom |
| NegativeVdWSurface | This descriptor calculates the sum of atomic SAS van der Waals surface areas of the molecule, where the atoms have a negative partial charge |
| VIEW::NetworkPreferences | NeworkPreferences is a widget that will be inserted into the tab dialog Preferences |
| VIEW::NewSelectionMessage | Send by MainControl to Control objects to sync selection |
| NMRAtomData | NMRAtomData This structure includes all information for one atom delivered by a NMR-Star-File |
| NMRStarFile | |
| NodeItem< Node, Edge > | The node type in a molecular graph |
| NonpolarSolvation | SLICK nonpolar solvation component |
| NotificationTarget< NotificationSource > | Notification Target Class |
| Exception::NotImplemented | Not implemented exception |
| NucleicAcid | Nucleic acid class |
| NucleicAcidIteratorTraits | NucleicAcidIteratorTraits |
| Nucleotide | Nucleotide class |
| NucleotideIteratorTraits | NucleotideIteratorTraits |
| NucleotidePredicate | Predicate indicating nucleotide atoms |
| Exception::NullPointer | Null pointer argument is invalid |
| NumberOfAromaticAtoms | This descriptor counts the number of aromatic atoms, a atom is aromatic if it participates a aromatic bond |
| NumberOfAromaticBonds | This descriptor counts the number of aromatic bonds |
| NumberOfAtoms | This descriptor counts the number of aromatic atoms |
| NumberOfBonds | This descriptor counts the number of bonds of the molecule |
| NumberOfBondsPredicate | Predicate class for atoms bearing a certain number of bonds |
| NumberOfBoron | This descriptor counts the number of boron |
| NumberOfBromine | This descriptor counts the number of bromine |
| NumberOfCarbon | This descriptor counts the number of carbon |
| NumberOfChlorine | This descriptor counts the number of chlorine |
| NumberOfDoubleBonds | This descriptor counts the number of double bonds of the molecule |
| NumberOfFlourine | This descriptor counts the number of flourine |
| NumberOfHeavyAtoms | This descriptor counts the heavy atoms, heavy atoms are atoms with an atomic number strictly greater than 1 (all but hydrgen) |
| NumberOfHeavyBonds | This descriptor counts the number of heavy bonds, a bond is heavy if both participating atoms are heavy |
| NumberOfHydrogen | This descriptor counts the number of hydrogen |
| NumberOfHydrogenBondAcceptors | This descriptor returns the number of hydrogen bonds acceptor atoms |
| NumberOfHydrogenBondDonors | This descriptor returns the number of the hydrogen bond donors of the molecule |
| NumberOfHydrophobicAtoms | This descriptor return the number of hydrophobic atoms |
| NumberOfIodine | This descriptor counts the number of iodine |
| NumberOfNitrogen | This descriptor counts the number of nitrogen |
| NumberOfOxygen | This descriptor counts the number of oxygen |
| NumberOfPhosphorus | This descriptor counts the number of phosphorus |
| NumberOfRotatableBonds | This descriptor counts the number of rotatable bonds, a bond ia rotatble if it is heavy, not in a ring and not bounds lone atoms like halogens |
| NumberOfRotatableSingleBonds | This descriptor counts the number of single bonds which are rotatable |
| NumberOfSingleBonds | This descriptor counts the number of single bonds of the molecule |
| NumberOfSulfur | This descriptor counts the number of sulfur |
| NumberOfTripleBonds | This descriptor counts the number of triple bonds of the molecule |
| NumericalIntegrator< Function, DataType > | Numerical integrator class |
| Object | Generic object class |
| ObjectCreator | ObjectCreator class |
| VIEW::OccupancyColorProcessor | Coloring by the occupancy of atoms from a PDBFile |
| VIEW::OpenBruker1DFile | Interface to select and open spectra stored in the bruker file format |
| VIEW::OpenBruker2DFile | Interface to select and open spectra stored in the bruker file format |
| Options | Options class |
| OSockStream | Output stream from a socket |
| Exception::OutOfGrid | Out of grid error |
| Exception::OutOfMemory | Out of memory |
| Exception::OutOfRange | Out of range |
| Pair6_12InteractionEnergyProcessor | Processor for the computation of the van-der-Waals interaction energy of a molecule with its surrounding |
| Pair6_12InteractionEnergyProcessor::Default | Default values for interaction energy calculations |
| Pair6_12InteractionEnergyProcessor::Option | Symbolic names for option keys |
| Pair6_12RDFIntegrator | 6-12 pair potential integrator |
| Pair6_12RDFIntegrator::Option | Symbolic names for option keys |
| PairExpInteractionEnergyProcessor | Processor for the computation of the van-derWaals interaction energy of a molecule |
| PairExpInteractionEnergyProcessor::Default | Default values for interaction energy calculations |
| PairExpInteractionEnergyProcessor::Option | Symbolic names for option keys |
| PairExpRDFIntegrator | 6-exp pair potential integrator |
| PairExpRDFIntegrator::Option | Symbolic names for option keys |
| Parameters | General Parameter class |
| ParameterSection | General Parameter Section Class |
| ParsedFunction< arg > | ParsedFunction |
| VIEW::ParsedFunctionDialog | Dialog to visualise a parsed function |
| Exception::ParseError | Parse Error |
| PartialChargeBase | Generic QSAR molecular partial charge descriptor class \ |
| PartialChargeProcessor | Generic |
| Path | Data path management class |
| PCMCavFreeEnergyProcessor | Processor for the computation of the cavitation free energy |
| PCMCavFreeEnergyProcessor::Default | Default values for cavitation free energy calculations |
| PCMCavFreeEnergyProcessor::Option | Symbolic names for option keys |
| PDBAtom | Atom class with additional attributes |
| PDBAtomIteratorTraits | Traits class for the PDBAtomIterator |
| PDBFile | PDB file class |
| PDBFile::Default | Default values for PDBFile options |
| PDBFile::Option | Symbolic names for option keys |
| PDBInfo | PDB information class |
| PDBRecords | PDB record class |
| Peak< PositionType > | Generic Peak Class |
| PeakList< PT > | A generic peak list for spectra of arbitrary dimension |
| Peptides::PeptideBuilder | Build a Peptide from a sequence and the corresponing angles |
| VIEW::PeptideDialog | Dialog for building peptides |
| PeriodicBoundary | Periodic boundary class for force field simulations |
| PeriodicBoundary::Default | Default values |
| PersistenceManager | Persistence manager class |
| PersistentObject | The persistent object |
| PiecewiseFunction | Piecewise function object |
| PiecewisePolynomial | Piecewise polynomial curve object |
| PierottiCavFreeEnergyProcessor | Processor for the computation of the cavitation free energy |
| PierottiCavFreeEnergyProcessor::Default | Default values for cavitation free anergy calculations |
| PierottiCavFreeEnergyProcessor::Option | Symbolic names for option keys |
| VIEW::Point | Point class |
| PolarSolvation | SLICK polar solvation component \ { Definition:} {BALL/SCORING/COMPONENTS/polarSolvation.h} |
| PolarVdWSurface | This descriptor calculates the sum of atomic SAS van der Waals surface areas of the molecule, of the polar atoms |
| PositivePolarVdWSurface | This descriptor calculates the sum of atomic SAS van der Waals surface areas of the molecule, where the partial charge of the atom is positive and the atom is a polar atom |
| PositiveVdWSurface | This descriptor calculates the sum of atomic SAS van der Waals surface areas of the molecule, where the atoms have a positive partial charge |
| Exception::Postcondition | Postcondition failed |
| Potential1210 | Potential1210 |
| VIEW::POVRenderer | POVRenderer class |
| PreciseTime | Time class |
| Exception::Precondition | Precondition failed |
| VIEW::Preferences | Preferences is a dialog for other preference pages to be inserted |
| VIEW::PreferencesEntry | Base class for a dialog or a Preferences page |
| VIEW::PreferencesEntry::ExtendedPreferencesObject | Base class for the more sophisticated GUI elements in a dialog, to support reading and (re)storing their state |
| PrincipalMomentOfInertia | This descriptor returns the principle moment of inertia calculated from the filed coordinates! |
| PrincipalMomentOfInertiaX | This descripor adds up the x-axis component of the principal moment of inertia over all atoms, calculated from the filed coordinates! |
| PrincipalMomentOfInertiaY | This descriptor adds up the y-axis component of the principal moment of inertia over all atoms, calculated from the filed coordinates! |
| PrincipalMomentOfInertiaZ | This descriptor adds up the z-axis component of the principal moment of interia over all atoms, calculated from the filed coordinates! |
| Processor | Global Types and Enums for Processors |
| Product< First, Second, DataType > | Multiplication class |
| PropertyManager | Property Manager class |
| Protein | Protein Class |
| ProteinIteratorTraits | ProteinIteratorTraits |
| ProteinPredicate | Predicate for matching proteins |
| PTE_ | Periodic Table of Elements Class |
| VIEW::PTEDialog | Dialog for choosing the element type for the edit mode of scene |
| VIEW::PubChemDialog | Dialog for querying PubChem and generating structures from a SMILES string |
| PyColorRGBAVector | Equivalent for a STL::vector of ColorRGBA in Python |
| PyCompositeList | Equivalent for a STL::List of Composite Pointers in Python |
| PyDatasetVector | Equivalent for a STL::Vector of Dataset Pointers in Python |
| PyIndexList | Equivalent for an STL::List of numbers/indices in Python |
| PyInterpreter | Embedded Python interpreter |
| VIEW::PythonHighlighter | Class for syntax highlighting of Python code |
| VIEW::PythonSettings | Dialog for setting the Python preferences |
| VIEW::PyWidget | Python Widget This class is a Window for a Python interpreter interface |
| VIEW::QColorTable | Class for storing colors in a GUI table |
| VIEW::QuadMesh | QuadMesh class |
| QuadraticAngleBend | QuadraticAngleBend |
| QuadraticBondStretch | QuadraticBondStretch |
| QuadraticImproperTorsion | QuadraticImproperTorsion |
| Quadruple< T1, T2, T3, T4 > | Quadruple Class |
| RadialDistributionFunction | Radial distribution function |
| RadiusRuleProcessor | Radius Rule Processor |
| RandomAccessIterator< Container, DataType, Position, Traits > | Random Access Iterator Class |
| RandomCoilShiftProcessor | Random coil shift assignment processor |
| RandomEvaluation | A basis class for energetic evaluators of docking results |
| RandomNumberGenerator | The following code is taken (and adapted to BALL's C++ interface) from the code provided at |
| RDFIntegrator | Integrator class for radial distribution functions |
| RDFParameter | Parametersection for radial distribution function ????? |
| RDFSection | Helper class for RDFParameter |
| Reciprocal< Function, DataType > | Reciprocal class |
| ReconstructFragmentProcessor | ReconstructFragmentProcessor |
| ReducedSurface | Generic ReducedSurface Class |
| VIEW::RegisterHelpSystemMessage | Register a QObject to a URL in the documentation This message is send by ModularWidget::registerForHelpSystem and should probably not be used otherwise |
| VIEW::RegularData1DWidget | Widget used to display one-dimensional data |
| VIEW::RegularData2DWidget | Widget used to display two-dimensional data |
| VIEW::RegularData3DController | Controller base class for one type of Dataset |
| RegularExpression | Regular expression class |
| ReissCavFreeEnergyProcessor | Processor for the computation of the cavitation free energy |
| ReissCavFreeEnergyProcessor::Default | Default values for cavitation free anergy calculations |
| ReissCavFreeEnergyProcessor::Option | Symbolic names for option keys |
| RelHydrophobicVdWSurface | This descriptor returns the fraction of the atomic SAS van der Waals surface, where the atoms are hydrophobic |
| RelNegativePartialCharge | This descriptor returns the fraction of negative partial charges, which is calculated by deviding the most negative partial charge value by the sum of negative partial charges |
| RelNegativePolarVdWSurface | This descriptor returns the fraction of the atomic SAS van der Waals surface, where the partial charge is negative and the atoms are polar |
| RelNegativeVdWSurface | This descriptor returns the fraction of the atomic SAS van der Waals surface, where the partial charge is negative |
| RelNumberOfRotatableBonds | This descriptor returns the fraction of rotatble bonds |
| RelNumberOfRotatableSingleBonds | This descriptor counts the fraction of the rotatble single bonds |
| RelPolarVdWSurface | This descriptor returns the fraction of the atomic SAS van der Waals surface, where the atoms are polar |
| RelPositivePartialCharge | This descriptor returns the fraction of positive partial charges, which is calculated by deviding the biggest partial charges value by the sum of positive partial charges |
| RelPositivePolarVdWSurface | This descriptor returns the fraction of the atomic SAS van der Waals surface, where the partial charge is positive and the atoms are polar |
| RelPositiveVdWSurface | This descriptor returns the fraction of the atomic SAS van der Waals surface, where the partial charge is positive |
| VIEW::Renderer | Renderer is just a generic base class |
| VIEW::Representation | Representation A Representation is a collection of geometric objects for a group of composites and a given model, for example a surface |
| VIEW::RepresentationManager | RepresentationManager manages the graphical Representation objects and all GeometricObject |
| VIEW::RepresentationMessage | Base class for all messages concerning a Representation |
| Residue | Residue class |
| ResidueChecker | Residue Consistency Checker |
| ResidueIDPredicate | Predicate for matching residues IDs |
| ResidueIteratorTraits | ResidueIteratorTraits |
| VIEW::ResidueNameColorProcessor | ResidueNameColorProcessor is derived from the class ColorProcessor |
| VIEW::ResidueNumberColorProcessor | ColorProcessor for coloring by the numbers of the Residue 's |
| ResiduePredicate | Predicate for matching residues |
| ResidueRotamerSet | Residue Rotamer Set |
| ResidueTorsions | Parameter class containing all proper torsions occuring in a residue |
| ResidueTorsions::Data | Strcuture containing the names of the residue and the atoms for a torsion |
| VIEW::ResidueTypeColorProcessor | Coloring by the type of a Residue |
| ResourceEntry | Resource entry class |
| ResourceFile | Resource file class |
| RingAnalyser | Class, providing methods for the analysis of the structure of ringsystems |
| RingClusterer | Class, providing a method for agglomerative clustering of single rings to ringsystems |
| RingFinder | Helper class for all predicates that need ring information |
| RingPerceptionProcessor | Processor, which marks all atoms and bonds in a ring structure with the Composite Property "InRing" |
| RingPerceptionProcessor::Default | Default options for the ring perception |
| RingPerceptionProcessor::Option | Option names |
| RMSDMinimizer | RMSD minimizer class |
| RombergIntegrator< Function, DataType > | A numerical integration of a BALL-Function using a Romberg integration scheme |
| Rotamer | Rotamer class |
| RotamerLibrary | Rotamer Library Class |
| RotationalEntropyLoss | SLICK rotational entropy loss contrbution { Definition:} {BALL/SCORING/COMPONENTS/rotationalEntropyLoss.h} |
| RotationalEntropyLoss::Default | Default values for SLICK options |
| RotationalEntropyLoss::Option | Option names |
| RSComputer | Generic RSComputer Class |
| RSConstructor | Class, performing the prefabication of ringsystems (i.e. providing them with relative 2D-coordinates) |
| RSEdge | Generic RSEdge Class |
| RSFace | Generic RSFace Class |
| RSVertex | Generic RSVertex Class |
| RuleEvaluator | Rule evaluator class |
| RuleProcessor | Rule Processor class |
| VIEW::RunGAMESSDialog | |
| SampleCondition | SampleConditions |
| SASEdge | Generic SASEdge Class |
| SASFace | Generic SASFace Class |
| SASTriangulator | Generic SASTriangulator Class |
| SASVertex | Generic SASVertex Class |
| VIEW::Scene | Scene is the main visualization widget that shows the graphical Representation 's |
| VIEW::SceneMessage | SceneMessage is the message class that is responsible for changing the content of the Scene |
| ScoringBaseFunction | Define the interface for the base function |
| ScoringTypes | Define the interface for the base function |
| SCWRLRotamerFile | Reads Dunbrack/SCWRL rotamer library files |
| SDFile | MDL SD file class |
| SDGenerator | The main class, provides methods for analysis of the input |
| SecondaryStructure | Secondary structure class |
| VIEW::SecondaryStructureColorProcessor | Coloring by the secondary structure, a Composite is in |
| SecondaryStructureIteratorTraits | SecondaryStructureIteratorTraits |
| SecondaryStructurePredicate | Predicate for matching secondary structures |
| SecondaryStructureProcessor | Secondary structure extraction from 3D structure |
| Selectable | Selectable Concept |
| SelectedPredicate | Selection predicate |
| Selector | Atom Selection from Regular Expression |
| VIEW::Server | Server class |
| VIEW::Server::NotCompositeObject | NotCompositeObject Exception class |
| VIEW::ServerPreferences | Preferences tab for the Server |
| SESComputer | Generic SESComputer Class |
| SESEdge | Generic SESEdge Class |
| SESFace | Generic SESFace Class |
| SESSingularityCleaner | Generic SESComputer Class |
| SESTriangulator | Generic SESTriangulator Class |
| SESVertex | Generic SESVertex Class |
| VIEW::SetCamera | Dialog to set the camera to a given value |
| VIEW::SetClippingPlane | Dialog to set a clipping plane to a given value |
| ShiftedLVMMMinimizer | Shifted limited-memory variable metric methods minimizer |
| ShiftedLVMMMinimizer::Option | Symbolic names for option keys |
| ShiftModel | A class representing a complete parameterized NMR shift model |
| ShiftModule | A single contribution of a NMR shift model |
| ShiftReferenceElement | ShiftReferenceElement |
| ShiftReferenceSet | ShiftReferenceSet |
| VIEW::ShowDisplayPropertiesMessage | Notify the DisplayProperties dialog to show itself |
| SimpleBase | QSAR molecular simple descriptors base class, this class implements some methods to calculate simple descriptors |
| VIEW::SimpleBox | SimpleBox class |
| SimpleExperiment1D | Simple 1D NMR experiment class |
| VIEW::SimulationThread | Baseclass for threads, which perform a simulation |
| SingleBondsPredicate | Predicate class for atoms bearing single bonds |
| SizeOfSSSR | This descriptor returns the number of rings in the SSSR |
| Exception::SizeUnderflow | Size underflow |
| SLICKEnergy | SLICKEnergy scoring function { Definition:} {BALL/SCORING/FUNCTIONS/slickEnergy.h} |
| SLICKEnergy::Default | Default values for SLICKEnergy options |
| SLICKEnergy::Option | Option names |
| SLICKScore | SLICKEnergy scoring function { Definition:} {BALL/SCORING/FUNCTIONS/slickScore.h} |
| SLICKScore::Default | Default values for SLICKEnergy options |
| SLICKScore::Option | Option names |
| SmartsMatcher::RecStruct_ | Wrapper class which is used as an interface in the matching code to the pool |
| SmartsMatcher::RecStructCore_ | Core structure of the recursive matching algorithm for the object pool |
| SmartsMatcher::RecStructPool_ | Class which does the pool operations of the RecStructCore_ pool |
| SmartsParser | SMARTS Parser |
| SmartsParser::SPAtom | Smarts Parser Atom class |
| SmartsParser::SPAtom::Property | Property struct of smarts parser atom |
| SmartsParser::SPAtom::PropertyValue | Possible types of the properties |
| SmartsParser::SPBond | Bond representation of the smarts parser |
| SmartsParser::SPEdge | Edge representation of the smarts parser graph |
| SmartsParser::SPNode | Representation of a node in the smarts parser graph |
| SmartsParser::State | Parser state (used by the parser itself) |
| SMARTSPredicate | Predicate for using smarts |
| SnapShot | SnapShot class, containing the actual data of one single snapshot |
| SnapShotManager | Snapshot management e.g |
| SnapShotManager::Default | Local class for handling default values for the options |
| SnapShotManager::Option | Local class for handling options |
| VIEW::SnapshotVisualisationDialog | Dialog to visualise SnapShot instances |
| SockAddr | Socket addresses |
| SocketBuf | Socket buffer class |
| SockInetAddr | INET socket address |
| SockInetBuf | INET socket buffer |
| SolventAccessibleSurface | Generic SolventAccessibleSurface Class |
| SolventAtomDescriptor | This struct contains the information for one atom type of the solvent |
| SolventDescriptor | Solvent Description |
| SolventExcludedSurface | Generic SolventExcludedSurface Class |
| SolventParameter | Parameter section for the solvent description |
| SolventPredicate | Predicate indicating solvent atoms |
| Sp2HybridizedPredicate | Predicate indicating sp2 hybridized atoms |
| Sp3HybridizedPredicate | Predicate indicating sp3 hybridized atoms |
| Spectrum< DataT, PeakT, PositionT > | A generic NMR spectrum class |
| VIEW::Sphere | Sphere class |
| SpHybridizedPredicate | Predicate indicating sp hybridized atoms |
| SquareFunction< Function, DataType > | SquareFunction class |
| VIEW::Stage | A Stage has a Camera, LightSources and a background color |
| VIEW::StageSettings | Dialog for the Stage setup |
| SteepestDescentMinimizer | A minimizer for geometry optimization based on steepest descent steps |
| StrangLBFGSMinimizer | Limited-memory BFGS minimizer based on the Strang recurrence |
| StrangLBFGSMinimizer::Option | Symbolic names for option keys |
| String | Extended String class |
| StringHashMap< Value > | StringHashMap |
| StructureMapper | Structure mapping class |
| Substring | A substring class |
| Substring::InvalidSubstring | Exception thrown if an invalid substring is accessed |
| Substring::UnboundSubstring | Exception thrown if an unbound substring is accessed |
| Subtraction< First, Second, DataType > | Subtraction class |
| SurfaceBase | Generic QSAR molecular surface descriptors class \ |
| SurfaceProcessor | SurfaceProcessor |
| System | System class |
| TAngle< T > | Generic Angle Class |
| TBox3< T > | Generic three-dimensional Box |
| TCircle3< T > | Generic Circle in Three-Dimensional Space |
| TContour< T > | This class is intended to create and store ContourLines belonging to the same data-set |
| TContourLine< T > | This class is intended to store a single contour line generated from a RegularData2D - class |
| TContourSurface< T > | This class contains a contour surface |
| TContourSurface< T >::Cube | A cube in the grid |
| TCPTransfer | Class for TCPTransfers |
| TCPTransfer::TransferFailed | TransferFailed exception |
| VIEW::TemperatureFactorColorProcessor | Coloring by the temperature factor of atoms from a PDBFile |
| Templates | Force Field Residue Template Class |
| VIEW::TestFramework | Class for recording mouse and keyboard inputs, storing them in a line based file and replaying them |
| TextPersistenceManager | Text-format-based persistence manager |
| TFFT1D< ComplexTraits > | A class to perform Fast Fourier Transforms and inverse Fast Fourier Transforms on regularly spaced one dimensional data |
| TFFT2D< ComplexTraits > | A class to perform Fast Fourier Transforms and inverse Fast Fourier Transforms on regularly spaced two dimensional data |
| TFFT3D< ComplexTraits > | A class to perform Fast Fourier Transforms and inverse Fast Fourier Transforms on regularly spaced three dimensional data |
| Timer | Timer Class |
| TimeStamp | Time stamp concept |
| TLine3< T > | Generic Line in Three-Dimensional Space |
| TMatrix4x4< T > | Generic 4x4 Matrix Class |
| Exception::TooManyBonds | Exception to be thrown if too many bonds for one atom |
| Exception::TooManyErrors | Exception to be thrown if too many errors occur, e.g. in ForceField |
| TotalNegativePartialCharge | This descriptor adds up all negative partial charges over all atoms |
| TotalPositivePartialCharge | This descriptor adds up all positive partial charges over all atoms |
| TPlane3< T > | Threedimensional plane |
| TQuaternion< T > | Generic Quaternion Class |
| VIEW::TrajectoryController | Controller base class for one type of Dataset |
| TrajectoryFile | Trajectory file format for MD simulation |
| TransformationManager | This class handles automatic file transformation methods |
| TransformationProcessor | Transformation applicator |
| TranslationProcessor | Translation processor |
| VIEW::TreeWidget | Base class for all control widgets |
| TRegularData1D< ValueType > | A class to store regularaly spaced data |
| TRegularData1D< ValueType >::BlockValueType | The block data type for reading and writing binary data |
| TRegularData2D< ValueType > | Two-dimensional grid class |
| TRegularData2D< ValueType >::BlockValueType | The block data type for reading and writing binary data |
| TRegularData2D< ValueType >::IndexType | The index type used to refer to a specific element in the grid (x-, and y-index) |
| TRegularData3D< ValueType > | Three-dimensional grid class |
| TRegularData3D< ValueType >::BlockValueType | The block data type for reading and writing binary data |
| TRegularData3D< ValueType >::IndexType | The index type used to refer to a specific element in the grid (x-, y-, and z-index) |
| Triangle | Generic TriangleEdge Class |
| TriangleEdge | Generic TriangleEdge Class |
| TrianglePoint | Generic TriangleEdge Class |
| TriangulatedSAS | Generic TriangulatedSAS Class |
| TriangulatedSES | Generic TriangulatedSES Class |
| TriangulatedSphere | Generic TriangulatedSphere Class |
| TriangulatedSurface | Generic TriangulatedSurface Class |
| Triple< T1, T2, T3 > | Triple Class |
| TripleBondsPredicate | Predicate class for atoms bearing triple bonds |
| TRRFile | TRR Trajectory file format |
| TRRFile::TRRHeader | The header for each coordinate set stored in the TRR file |
| TruePredicate | Default predicate |
| TSimpleBox3< T > | Generic three-dimensional Box |
| TSphere3< T > | Generic Sphere Class |
| TSurface< T > | Generic Three-dimensional Surface class |
| VIEW::Tube | Tube class |
| TVector2< T > | Generic Two-Dimensional Vector |
| TVector3< T > | Generic Three-Dimensional Vector |
| TVector4< T > | Generic Four-Dimensional Vector |
| VIEW::TwoColoredLine | TwoColoredLine class |
| VIEW::TwoColoredTube | TwoColoredTube class |
| TypenameRuleProcessor | Typename Rule Processor |
| TypeRuleProcessor | Type Rule Processor |
| UCK | Unique Chemical Key |
| UhligCavFreeEnergyProcessor | Processor for the computation of the cavitation free energy |
| UhligCavFreeEnergyProcessor::Default | Default values for cavitation free energy calculations |
| UhligCavFreeEnergyProcessor::Option | Symbolic names for option keys |
| UnaryFunctor< ArgumentType, ResultType > | Generic Unary Functor Class |
| UnaryPredicate< T > | Generic Unary Predicate Class |
| UnaryProcessor< T > | Generic Unary Processor Class |
| VanDerWaals | SLICK van-der-Waals Component based on AmberNonBonded \ { Definition:} {BALL/SCORING/COMPONENTS/vanDerWaals.h} |
| VdWSurface | This descriptor calculates the van der Waals surface area of the molecule |
| VdWVolume | This descriptor calculates the van der Waals volume of the molecule |
| VIEW::VectorGridController | Controller base class for one type of Dataset |
| VersionInfo | Version information class |
| VIEW::Vertex | Vertex is a base class for all GeometricObject 's that have a single vertex |
| VIEW::Vertex2 | Vertex2 is a base class for all GeometricObject 's that have two vertices |
| VertexAdjacency | The vertex adjacency is calculated using the formula \( 1 + m \), where $m$ is the number of heavy bonds |
| VertexAdjacencyEquality | The vertex adjacency equality si calculateed using the formula: \(-(1-f) (1-f) - f f \), where $f$ is defined as: \( f = {(n^2 -2m)}{n^2}\), where $n$ is the number of heavy atoms and $m$ is the number of heavy bonds |
| Visitor< Host > | |
| VIEW::VRMLRenderer | VRMLRenderer class |
| XDRPersistenceManager | XDR-format-based persistence manager |
| XYZFile | XYZ file class |
| ZagrebIndex | This descriptor returns the Zagreb Index, which is calculated as: $ d_i^2$, over all heavy atoms |