Chemical Data Processing Library C++ API - Version 1.4.0
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123456]
 CCDPL::Shape::AlignedColorTverskyScoreFunctor wrapping Shape::calcAlignedColorTverskyScore()
 CCDPL::Shape::AlignedShapeTverskyScoreFunctor wrapping Shape::calcAlignedShapeTverskyScore()
 CCDPL::Shape::AlignedTotalOverlapTverskyScoreFunctor wrapping Shape::calcAlignedTotalOverlapTverskyScore()
 CCDPL::Shape::AlignedTverskyComboScoreFunctor wrapping Shape::calcAlignedTverskyComboScore()
 CCDPL::Shape::AlignmentResultResult of a Gaussian-shape alignment between a reference and an aligned shape
 CCDPL::ConfGen::TorsionRule::AngleEntryOne preferred torsion angle for a rule, characterized by its value, the two tolerance bands and a score
 CCDPL::Base::AnySafe, type checked container for arbitrary data of variable type
 CCDPL::Util::Array< ValueType >Dynamic array class providing amortized constant time access to arbitrary elements
 ►CCDPL::Util::Array< MatchConstraint >
 CCDPL::Util::Array< MMFF94AngleBendingInteraction >
 CCDPL::Util::Array< MMFF94BondStretchingInteraction >
 CCDPL::Util::Array< MMFF94ElectrostaticInteraction >
 CCDPL::Util::Array< MMFF94OutOfPlaneBendingInteraction >
 CCDPL::Util::Array< MMFF94StretchBendInteraction >
 CCDPL::Util::Array< MMFF94TorsionInteraction >
 CCDPL::Util::Array< MMFF94VanDerWaalsInteraction >
 CCDPL::Util::Array< StereoDescriptor >
 ►CCDPL::Util::Array< StringDataBlockEntry >
 ►CCDPL::Util::Array< typename ValueType::SharedPointer >
 ►CCDPL::Util::Array< V >
 CCDPL::Chem::Atom2DCoordinatesCalculatorGenerates 2D coordinates for the atoms of a molecular graph using a layout algorithm that combines ring-system templates, chain extension, and substituent placement
 CCDPL::Chem::Atom3DCoordinatesFunctorHelper-functor for retrieving the 3D coordinates of an atom (via the Chem::AtomProperty::COORDINATES_3D property)
 CCDPL::Chem::AtomArray3DCoordinatesFunctorHelper-functor for retrieving the 3D coordinates of an atom from a separately-stored coordinates array, indexed by the atom's position in the underlying molecular graph
 CCDPL::Chem::AtomBondMappingData structure for the common storage of related atom to atom and bond to bond mappings
 CCDPL::Chem::AtomConformer3DCoordinatesFunctorHelper-functor for retrieving the 3D coordinates of an atom for a specific conformer (via the Chem::AtomProperty::CONFORMER_COORDINATES_3D conformer-array property)
 CCDPL::GRAIL::AtomDensityGridCalculatorCalculator that fills a spatial grid with combined per-atom density contributions
 CCDPL::Chem::AtomDictionaryA global dictionary for the lookup of data associated with the atom types defined in namespace Chem::AtomType
 CCDPL::MolProp::AtomHydrophobicityCalculatorImplementation of Greene's algorithm [CATA] for the calculation of atom hydrophobicities
 CCDPL::Descr::AutoCorrelation2DVectorCalculatorCalculation of the topological (2D) auto-correlation vector of a molecular graph
 CCDPL::Descr::AutoCorrelation3DVectorCalculator< T >Generic implementation of the 3D auto-correlation vector calculation for sequences of entities of arbitrary type
 ►CCDPL::Descr::AutoCorrelation3DVectorCalculator< Chem::Atom >
 ►CCDPL::Descr::AutoCorrelation3DVectorCalculator< Pharm::Feature >
 CCDPL::Chem::AutomorphismGroupSearchEnumerates the atom/bond automorphisms of a molecular graph
 CCDPL::Descr::BCUTDescriptorCalculatorCalculation of the BCUT (Burden-CAS-University-of-Texas) descriptor of a molecular graph
 CCDPL::Chem::BemisMurckoAnalyzerDecomposes a molecular graph into its Bemis-Murcko framework, ring systems, linkers and side chains
 CCDPL::Math::BFGSMinimizer< VA, VT, FVT >Implementation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) algorithm for solving unconstrained nonlinear optimization problems
 CCDPL::Math::BFGSMinimizer< QuaternionTransformation >
 CCDPL::GRAIL::BindingAffinityCalculatorPredicts the binding affinity of a ligand pose from its GRAIL descriptor vector
 ►CCDPL::Chem::BondContainerCommon interface for data structures that support a random access to stored Chem::Bond instances
 CCDPL::Chem::BondOrderCalculatorPerceives bond orders of a molecular graph from its 3D structure and atom connectivity
 CCDPL::Chem::PatternBasedTautomerizationRule::BondOrderChangeEncodes a single bond order change between two pattern atoms applied when the parent transformation pattern matches
 CCDPL::Chem::BondStereoFlagCalculatorCalculator that derives 2D wedge/hash bond stereo flags from atom 2D coordinates and stereochemical descriptors of a molecular graph
 CCDPL::Util::BronKerboschAlgorithmImplementation of the Bron-Kerbosch clique-detection algorithm [BKA]
 CCDPL::Vis::BrushSpecifies the fill pattern and fill color of shapes
 CCDPL::Descr::BulkSimilarityCalculator< DT, SVT >Calculator that performs a bulk pairwise comparison of a single query descriptor against a stored set of target descriptors using a configurable similarity function
 CCDPL::Descr::BurdenMatrixGeneratorCalculation of the Burden matrix of a molecular graph
 CCDPL::GRAIL::BuriednessGridCalculatorCalculator that fills a spatial grid with per-cell buriedness scores derived from GRAIL::BuriednessScore
 CCDPL::GRAIL::BuriednessScoreFunctor for the calculation of the buriedness of a 3D query position with respect to the surrounding atoms
 CCDPL::Vis::CairoPointer< T >A smart pointer managing the lifetime of allocated Cairo data structures
 CCDPL::Vis::CairoPointer< cairo_t >
 CCDPL::Vis::CairoPointerTraits< T >Traits class providing the reference-count management functions for a particular Cairo data type T
 CCDPL::Vis::CairoPointerTraits< cairo_pattern_t >Specialization of CairoPointerTraits for the object type cairo_pattern_t
 CCDPL::Vis::CairoPointerTraits< cairo_surface_t >Specialization of CairoPointerTraits for the object type cairo_surface_t
 CCDPL::Vis::CairoPointerTraits< cairo_t >Specialization of CairoPointerTraits for the object type cairo_t
 CCDPL::Chem::CanonicalNumberingCalculatorCalculation of canonical atom numberings for molecular graphs using McKay's algorithm
 CCDPL::Biomol::MMCIFData::CategoryA single mmCIF data category, holding an ordered list of data items (columns)
 CCDPL::Pharm::CationPiInteractionConstraintConstraint functor that tests whether an aromatic/cationic feature pair satisfies the geometric criteria for a cation-π interaction (center distance plus cation-to-ring-plane-normal angle)
 CCDPL::Chem::ChEMBLStandardizerImplementation of the ChEMBL structure preprocessing pipeline
 CCDPL::Chem::CIPConfigurationLabelerAssigns Cahn-Ingold-Prelog (CIP) configuration labels to stereogenic atoms and bonds of a molecular graph
 CCDPL::Chem::CIPPriorityCalculatorComputes a topological approximation of CIP (Cahn-Ingold-Prelog) priorities for the atoms of a molecular graph
 CCDPL::Descr::CircularFingerprintGeneratorGeneration of atom-centered circular substructure fingerprints in the spirit of SciTegic's Extended Connectivity Fingerprints (ECFP)
 CCDPL::Vis::ColorSpecifies a color in terms of its red, green and blue components and an alpha-channel for transparency
 CCDPL::Shape::ColorTanimotoScoreFunctor wrapping Shape::calcColorTanimotoScore()
 CCDPL::Shape::ColorTverskyScoreFunctor wrapping Shape::calcColorTverskyScore()
 CCDPL::Chem::CommonConnectedSubstructureSearchEnumerates all maximal common connected substructures shared between a query and a target molecular graph
 CCDPL::Math::CommonType< T1, T2 >Trait that resolves the common arithmetic type of T1 and T2 via std::common_type
 CCDPL::Math::ComplexTraits< T >Common operations and type aliases for complex arithmetic types
 ►CCDPL::Math::ComplexTraits< std::complex< T > >
 CCDPL::Util::CompressionAlgoTraits< CompAlgo >Traits-style template selecting the boost::iostreams compression/decompression filters that implement a given Util::CompressionAlgo. Specialized for each supported algorithm
 CCDPL::Util::CompressionAlgoTraits< BZIP2 >Util::CompressionAlgoTraits specialization for the bzip2 algorithm
 CCDPL::Util::CompressionAlgoTraits< GZIP >Util::CompressionAlgoTraits specialization for the gzip algorithm
 CCDPL::ConfGen::ConformerGeneratorHigh-level driver for the generation of low-energy conformer ensembles of molecular graphs
 CCDPL::ConfGen::ConformerGeneratorSettingsBundle of configuration parameters for conformer ensemble generation via class ConfGen::ConformerGenerator
 ►CCDPL::Base::ControlParameterContainerBase class providing methods for the storage and lookup of control-parameter values
 CCDPL::Descr::CosineSimilarityFunctor class for calculating Cosine Similarities [WCOS] of bitsets and vectors
 CCDPL::Base::DataFormatProvides meta-information about a particular data storage format
 CCDPL::Base::DataInputHandler< T >Factory interface providing methods for the creation of Base::DataReader instances handling a particular object type and storage format
 ►CCDPL::Base::DataInputHandler< Chem::Molecule >
 ►CCDPL::Base::DataInputHandler< Pharmacophore >
 ►CCDPL::Base::DataInputHandler< typename ReaderImpl::DataType >
 CCDPL::Base::DataIOManager< T >Singleton class that serves as a global registry for Base::DataInputHandler and Base::DataOutputHandler implementation instances
 CCDPL::Base::DataOutputHandler< T >Factory interface providing methods for the creation of Base::DataWriter instances handling a particular object type and storage format
 ►CCDPL::Base::DataOutputHandler< Chem::MolecularGraph >
 ►CCDPL::Base::DataOutputHandler< typename WriterImpl::DataType >
 CCDPL::Descr::PathFingerprintGenerator::DefAtomDescriptorFunctorThe default functor for the generation of atom descriptors
 CCDPL::Chem::HashCodeCalculator::DefAtomHashSeedFunctorThe default functor for the generation of atom hash seeds
 CCDPL::Descr::CircularFingerprintGenerator::DefAtomIdentifierFunctorThe functor for the generation of ECFP atom identifiers
 CCDPL::Util::ObjectPool< T >::DefaultConstructorDefault object factory which creates new instances of ObjectType via new
 CCDPL::Util::ObjectStack< T >::DefaultConstructorDefault object factory which creates new instances of ObjectType via new
 CCDPL::Util::ObjectPool< T >::DefaultDestructorDefault object destructor which destroys instances of ObjectType via delete
 CCDPL::Descr::PathFingerprintGenerator::DefBondDescriptorFunctorThe default functor for the generation of bond descriptors
 CCDPL::Chem::HashCodeCalculator::DefBondHashSeedFunctorThe default functor for the generation of bond hash seeds
 CCDPL::Descr::CircularFingerprintGenerator::DefBondIdentifierFunctorThe default functor for the generation of bond identifiers
 CCDPL::Util::Dereferencer< ArgType, ResType >Unary functor for the dereferenciation of pointers without null pointer checking
 CCDPL::ConfGen::DGConstraintGeneratorConstructs geometric constraints (distance, planarity, volume) for distance-geometry-based 3D structure generation
 ►CCDPL::ConfGen::DGConstraintGeneratorSettingsBundle of configuration parameters for distance-geometry constraint generation via class ConfGen::DGConstraintGenerator
 ►CCDPL::Util::DGCoordinatesGeneratorBase< Dim, T, Derived >Serves as foundation for subclasses that perform coordinates generation based on distance-geometry
 ►CCDPL::Util::DGCoordinatesGeneratorBase< 3, T, DGCoordinatesGenerator< 3, T > >
 ►CCDPL::Util::DGCoordinatesGeneratorBase< Dim, T, DGCoordinatesGenerator< Dim, T > >
 CCDPL::ConfGen::DGStructureGeneratorDistance-geometry-based generation of raw 3D structures for molecular graphs
 CCDPL::Descr::DiceSimilarityFunctor class for calculating the Dice Similarity [GSIM] of bitsets
 CCDPL::Math::DirectAssignmentProxy< C >Proxy that converts an assignment to a Math container into the corresponding direct-assignment call on the container (assign / plusAssign / minusAssign) bypassing alias detection
 CCDPL::Util::DGCoordinatesGeneratorBase< Dim, T, Derived >::DistanceConstraintA constraint that pins the distance between two points to the interval [lb, ub]
 CCDPL::ForceField::ElasticPotentialStores parameters for an elastic potential (harmonic distance restraint) between a pair of atoms
 CCDPL::Shape::FastGaussianShapeAlignment::ShapeData::Element
 CCDPL::Shape::GaussianShape::ElementData structure representing a single sphere of the Gaussian shape, characterized by a position, radius, hardness and color
 ►CCDPL::Chem::Entity3DContainerCommon interface for data structures that support a random access to stored Chem::Entity3D instances
 CCDPL::Chem::Entity3DCoordinatesFunctorHelper-functor for retrieving the 3D coordinates of an Chem::Entity3D object (via the Chem::Entity3DProperty::COORDINATES_3D property)
 CCDPL::Biomol::ResidueDictionary::EntryA single residue dictionary entry
 CCDPL::Chem::AtomDictionary::EntryA single dictionary entry describing the properties of an (atom type, isotope) pair
 CCDPL::ForceField::MMFF94AngleBendingParameterTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94AromaticAtomTypeDefinitionTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94AtomTypePropertyTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94BondChargeIncrementTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94BondStretchingParameterTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94BondStretchingRuleParameterTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94DefaultStretchBendParameterTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94FormalAtomChargeDefinitionTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94OutOfPlaneBendingParameterTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94PartialBondChargeIncrementTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94PrimaryToParameterAtomTypeMap::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94StretchBendParameterTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94SymbolicAtomTypePatternTable::EntryA single atom type pattern record
 CCDPL::ForceField::MMFF94TorsionParameterTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::MMFF94VanDerWaalsParameterTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::ForceField::UFFAtomTypePropertyTable::EntryData structure for the storage of values associated with a single table entry
 CCDPL::Descr::EuclideanDistanceFunctor class for calculating the Euclidean Distance [CITB] between bitsets and vectors
 CCDPL::Descr::EuclideanSimilarityFunctor class for calculating the Euclidean Similarity [GSIM] of bitsets
 ►Cstd::exceptionSTL class
 CCDPL::Chem::FragmentGenerator::ExcludePatternA pattern descriptor specifying bonds that shall not be cleaved
 ►CCDPL::Math::Expression< E >CRTP base class for all numeric expression types in the Math namespace (Barton-Nackman idiom)
 CCDPL::Shape::FastGaussianShapeAlignmentHigh-level driver for the fast alignment of Gaussian shapes against a set of reference shapes
 ►CCDPL::Pharm::FeatureDistanceConstraintConstraint functor that accepts a pair of features whose 3D-position distance lies within a configured [min, max] interval
 ►CCDPL::Pharm::FeatureGeneratorAbstract base class for generators that perceive one type of pharmacophore feature (e.g. an aromatic ring or H-bond donor) and append the perceived features to a Pharm::Pharmacophore
 CCDPL::Pharm::FeatureGeometryMatchFunctorMatch functor that quantifies the goodness of the spatial orientation match between two pharmacophore features, applying type-specific tolerances for H-bond donor/acceptor, halogen-bond donor/acceptor and aromatic features
 ►CCDPL::Pharm::FeatureInteractionScoreAbstract base class for scoring functors that quantify the strength of a directional pharmacophore-feature interaction (e.g. H-bond, ionic, π-π stacking) between two Pharm::Feature instances
 CCDPL::GRAIL::FeatureInteractionScoreGridCalculatorCalculator that fills a spatial grid with per-cell feature-interaction scores against a set of target pharmacophore features
 CCDPL::Pharm::FeaturePairDistanceMatchFunctorMatch functor that tests whether two feature pairs share a compatible inter-feature distance, with the compatibility relation switched between query-mode (asymmetric) and non-query-mode (symmetric)
 CCDPL::Pharm::FeaturePositionMatchFunctorMatch functor that quantifies the goodness of the 3D-position match between two pharmacophore features by comparing their separation against the configured per-feature tolerance
 CCDPL::Pharm::FeatureTypeMatchFunctorMatch functor that accepts a feature pair when both features share the same Pharm::FeatureType identifier
 CCDPL::Util::FileRemoverRAII helper that deletes a file when the FileRemover instance goes out of scope (unless released beforehand). Useful for guaranteeing the cleanup of temporary files
 CCDPL::Pharm::FileScreeningHitCollectorHit-callback functor for use with Pharm::ScreeningProcessor that writes each accepted hit molecule (optionally aligned and annotated with score/database properties) to a Base::DataWriter sink
 CCDPL::Vis::FontSpecifies a font for drawing text
 ►CCDPL::Vis::FontMetricsInterface providing methods for querying information about the metrics of a font
 CCDPL::ConfGen::FragmentAssemblerDriver for the fragment-based generation of 3D starting conformers
 CCDPL::ConfGen::FragmentAssemblerSettingsBundle of configuration parameters for fragment conformer assembly via class ConfGen::FragmentAssembler
 CCDPL::Chem::FragmentGenerator::FragmentationRuleA single fragmentation rule, consisting of a bond substructure match pattern and a numeric rule ID
 CCDPL::ConfGen::FragmentConformerGeneratorDriver for the generation of low-energy conformer ensembles for single molecular fragments (chain, small ring system or macrocycle)
 CCDPL::ConfGen::FragmentConformerGeneratorSettingsBundle of configuration parameters for fragment conformer ensemble generation via class ConfGen::FragmentConformerGenerator
 ►CCDPL::Chem::FragmentGeneratorGeneric rule-based molecule fragmentation engine that splits a molecular graph along bonds matching user-defined fragmentation rules
 CCDPL::ConfGen::FragmentLibraryData structure representing a library of pre-generated molecular fragment conformer ensembles
 CCDPL::ConfGen::FragmentLibraryEntryData structure representing a single entry of a conformer generation fragment library
 CCDPL::ConfGen::FragmentLibraryGeneratorDriver for populating a ConfGen::FragmentLibrary with conformers of canonicalized molecular fragments
 CCDPL::Chem::FragmentGenerator::FragmentLinkRecords the connectivity between two fragments produced by a single bond cleavage
 CCDPL::ConfGen::FragmentConformerGeneratorSettings::FragmentSettingsPer-fragment-class settings (separate parameters for chain, small ring system and macrocycle fragments)
 CCDPL::Shape::GaussianShapeAlignmentHigh-level driver for the alignment of Gaussian shapes against a set of reference shapes
 ►CCDPL::Shape::GaussianShapeAlignmentStartGeneratorAbstract base class for generators of starting transformations used to seed Gaussian-shape overlap optimization
 CCDPL::Shape::GaussianShapeFunctionFunction representation of a Gaussian shape, used to evaluate the shape's density, volume, surface area and related quantities at arbitrary 3D positions
 CCDPL::Shape::GaussianShapeFunctionAlignmentDriver for the alignment of one Shape::GaussianShapeFunction (the aligned shape) against a fixed reference Shape::GaussianShapeFunction
 CCDPL::Shape::GaussianShapeGeneratorGenerates Shape::GaussianShape instances from molecular graphs
 ►CCDPL::Shape::GaussianShapeOverlapFunctionAbstract base class for functions evaluating the overlap between two Gaussian shape functions
 CCDPL::GRAIL::GeneralizedBellAtomDensityFunctor for the evaluation of the generalized-bell atom density contribution of an atom at a query position
 CCDPL::ForceField::GradientVectorTraits< GV >Generic primary traits template providing zero-initialization for a 3D gradient vector container of type GV
 CCDPL::ForceField::GradientVectorTraits< Math::VectorArray< V > >ForceField::GradientVectorTraits specialization for containers of type Math::VectorArray
 CCDPL::ForceField::GradientVectorTraits< std::vector< V > >ForceField::GradientVectorTraits specialization for containers of type std::vector
 CCDPL::GRAIL::GRAILDataSetGeneratorGenerator that pre-computes the per-cell interaction-score grids and the atom-density grid used by GRAIL scoring of ligand poses against a target environment
 CCDPL::GRAIL::GRAILDescriptorCalculatorCalculation of GRAIL descriptors for protein-ligand complexes
 CCDPL::GRAIL::GRAILXDescriptorCalculatorCalculation of the extended GRAIL-X descriptor for protein-ligand complexes
 ►CCDPL::Vis::GraphicsPrimitive2DThe abstract base class of all 2D graphics primitives
 CCDPL::Chem::CompleteRingSet::Node::GreaterCmpFunc
 CCDPL::Math::GridBinary1Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::GridBinary1 instantiation Binary <E1, E2, F>
 ►CCDPL::Math::GridBooleanBinaryFunctor< G1, G2 >Base class for binary functors that take two grid expressions and return a bool result (Math::GridEquality)
 CCDPL::Math::GridCoordinatesMatrixTransformTraits< MatrixType >Reusable transformation traits used by Math::RegularSpatialGrid when the coordinate transform is a 4x4 matrix
 ►CCDPL::Math::GridCoordinatesMatrixTransformTraits< BoundedMatrix< T, 4, 4 > >
 ►CCDPL::Math::GridCoordinatesMatrixTransformTraits< CMatrix< T, 4, 4 > >
 CCDPL::Math::GridCoordinatesTransformTraits< T >Primary traits template for grid-coordinate transformations of type T (left unspecialized; specialize for new transform types)
 CCDPL::Math::GridScalarUnaryFunctor< M >Base class for unary functors that take a grid expression and return a scalar result (Math::GridElementSum)
 ►CCDPL::Math::GridScalarUnaryFunctor< G >
 ►CCDPL::Math::GridTemporaryTraits< G >Selects a concrete temporary grid type compatible with the grid expression G
 CCDPL::Math::GridUnaryTraits< E, F >Traits selecting the expression-template node and its result type for the Math::GridUnary instantiation <E, F>
 CCDPL::Descr::HammingDistanceFunctor class for calculating the Hamming Distance [WHAM, CITB] between bitsets
 CCDPL::Chem::HashCodeCalculatorComputes a 64-bit hash code that identifies a molecular graph up to a configurable set of atom and bond properties
 CCDPL::Base::LookupKey::HashFuncFunctor class implementing the generation of hash codes for LookupKey instances
 CCDPL::MolProp::HBondAcceptorAtomTyperImplements the perception of H-bond acceptor atom types (see namespace MolProp::HBondAcceptorAtomType)
 CCDPL::MolProp::HBondDonorAtomTyperImplements the perception of H-bond donor atom types (see namespace MolProp::HBondDonorAtomType)
 CCDPL::Pharm::HBondingInteractionConstraintConstraint functor that tests whether a Pharm::Feature pair satisfies geometric H-bond criteria (H-bond length plus acceptor-H-donor and H-bond direction to acceptor vector angles)
 CCDPL::Biomol::HierarchyViewData structure providing a hierarchical view on biological macromolecules
 CCDPL::Chem::Hydrogen3DCoordinatesCalculatorGenerates 3D coordinates for the hydrogen atoms of a molecular graph from the existing positions of their heavy atom neighbors
 ►CCDPL::Vis::ImageWriterAbstract base class for writers that render Chem::MolecularGraph or Chem::Reaction instances into a raster/vector image via an internal Cairo surface
 Cstd::integral_constant< bool, !(std::is_nothrow_move_constructible< T >::value &&sizeof(T)<=sizeof(Storage::stack) &&std::alignment_of< T >::value<=std::alignment_of< Storage::StackStorageT >::value)>
 ►CCDPL::Pharm::InteractionAnalyzerAnalyzer that detects pairwise interactions between features of two Pharm::FeatureContainer instances based on user-registered per-feature-type-pair interaction constraint functions
 CCDPL::Pharm::InteractionConstraintConnectorComposite feature-interaction constraint that combines two underlying constraint functions via a logical conjunction or disjunction
 CCDPL::Pharm::InteractionPharmacophoreGeneratorDriver that generates an interaction pharmacophore by perceiving a core pharmacophore on a ligand, an environment pharmacophore on the surrounding pocket residues, analyzing the inter-feature interactions and emitting features representing the detected interactions (optionally with exclusion volumes)
 ►Cstd::ios_baseSTL class
 ►Cstd::is_arithmetic
 CCDPL::Biomol::MMCIFData::ItemA single data item (column) of an mmCIF category, holding an ordered list of string values
 ►Cboost::iterator_facade
 CCDPL::Math::KabschAlgorithm< T >Implementation of the Kabsch algorithm [KABA]
 CCDPL::Math::KabschAlgorithm< double >
 CCDPL::Math::KabschAlgorithm< typename V::ValueType >
 CCDPL::Math::KabschAlgorithm< ValueType >
 CCDPL::Chem::KekuleStructureCalculatorAssigns an alternating single/double bond pattern (Kekulé structure) to the previously undefined bonds of a molecular graph (typically used to convert aromatic-bond annotations into explicit single/double bonds)
 CCDPL::Descr::KuvekPocketDescriptorCalculatorImplements the algorithm devised by Kuvek et al. [KBPD] for the calculation of receptor binding pocket shape and surface electrostatics descriptors
 CCDPL::Chem::CanonicalNumberingCalculator::AtomNode::LessCmpFunc
 CCDPL::Chem::CanonicalNumberingCalculator::Edge::LessCmpFunc
 CCDPL::Chem::CIPPriorityCalculator::AtomNode::LessCmpFunc
 CCDPL::Chem::SmallestSetOfSmallestRings::PathMessage::LessCmpFunc
 ►CCDPL::Vis::Line2DSpecifies a line segment in 2D space
 CCDPL::MolProp::LogSCalculatorCalculation of the aqueous solubility ( \( \log S \)) of molecular graphs using the atom-contribution method of Hou, Xia, Zhang and Xu
 CCDPL::Base::LookupKeyUnique lookup key for control-parameter and property values
 CCDPL::Math::LowerTag selecting the lower-triangular view (entries strictly above the diagonal read as zero) for Math::TriangularAdapter
 CCDPL::Descr::MACCSFingerprintGeneratorGeneration of 166 bit MACCS key fingerprints
 CCDPL::Descr::ManhattanDistanceFunctor class for calculating the Manhattan Distance [MADI] between bitsets and vectors
 CCDPL::Descr::ManhattanSimilarityFunctor class for calculating the Manhattan Similarity [GSIM] of bitsets
 CCDPL::Util::Map< Key, Value, AllowDefValues, KeyCompFunc >A unique sorted associative container that maps keys to values
 ►CCDPL::Util::Map< std::size_t, Color >
 CCDPL::Util::Map< std::size_t, double >
 ►CCDPL::Util::Map< unsigned int, double, true >
 ►CCDPL::Util::Map< unsigned int, std::size_t, true >
 CCDPL::Util::MapDefaultValue< ValueType, Allow >Helper supplying the default value returned by Util::Map when a queried key is absent
 CCDPL::Util::MapDefaultValue< ValueType, false >Util::MapDefaultValue specialization for the case in which default values are not allowed
 CCDPL::Chem::MatchConstraintDescribes a single attribute-comparison constraint between a query and a target object used by molecular graph matching algorithms
 CCDPL::Chem::MatchExpression< ObjType1, ObjType2 >Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms
 ►CCDPL::Chem::MatchExpression< Atom, MolecularGraph >
 ►CCDPL::Chem::MatchExpression< Bond, MolecularGraph >
 ►CCDPL::Chem::MatchExpression< MolecularGraph >
 ►CCDPL::Chem::MatchExpression< ObjType, void >Generic boolean expression interface for the implementation of query/target object equivalence tests in molecular graph matching algorithms
 ►CCDPL::Chem::MatchExpression< ObjType1, void >
 ►CCDPL::Chem::MatchExpression< Reaction >
 CCDPL::Vis::MaterialDefines material properties of Vis::Object3D instances
 CCDPL::Math::Matrix1VectorBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Matrix1VectorBinary instantiation <E1, E2, F>
 CCDPL::Math::Matrix2VectorBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Matrix2VectorBinary instantiation <E1, E2, F>
 CCDPL::Math::MatrixBinary1Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::MatrixBinary1 instantiation <E1, E2, F>
 CCDPL::Math::MatrixBinary2Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::MatrixBinary2 instantiation <E1, E2, F>
 ►CCDPL::Math::MatrixBinaryFunctor< M1, M2 >Base class for binary functors that take two matrix expressions and return a matrix element scalar result (Math::MatrixProduct)
 ►CCDPL::Math::MatrixBooleanBinaryFunctor< M1, M2 >Base class for binary functors that take two matrix expressions and return a bool result (Math::MatrixEquality)
 ►CCDPL::Math::MatrixScalarRealUnaryFunctor< M >Base class for unary functors that take a matrix expression and return a real-valued scalar (Math::MatrixNorm1, Math::MatrixNormFrobenius, Math::MatrixNormInfinity)
 ►CCDPL::Math::MatrixScalarUnaryFunctor< M >Base class for unary functors that take a matrix expression and return a scalar result (Math::MatrixElementSum, Math::MatrixTrace)
 ►CCDPL::Math::MatrixTemporaryTraits< M >Selects a concrete temporary matrix type compatible with the matrix expression M
 CCDPL::Math::MatrixUnaryTraits< E, F >Traits selecting the expression-template node and its result type for the Math::MatrixUnary instantiation <E, F>
 ►CCDPL::Math::MatrixVectorBinaryFunctor< M, V >Base class for binary functors that take a matrix expression and a vector expression and return a vector element scalar result (Math::MatrixVectorProduct, Math::VectorMatrixProduct)
 CCDPL::Chem::MaxCommonAtomSubstructureSearchComputes the maximum common atom substructure between a query and a target molecular graph by reducing the problem to maximum-clique enumeration on an association (modular product) graph
 CCDPL::Chem::MaxCommonBondSubstructureSearchComputes the maximum common bond substructure between a query and a target molecular graph by reducing the problem to maximum-clique enumeration on a bond-based association graph
 CCDPL::GRAIL::FeatureInteractionScoreGridCalculator::MaxScoreFunctorScore-combination functor returning the maximum (infinity norm) of the per-feature scores
 CCDPL::MolProp::MHMOPiChargeCalculatorCalculator that uses a Modified Hückel Molecular Orbital (MHMO) treatment to compute π-electron densities, π-charges, π-bond orders and the total π-electron energy of a molecular graph
 CCDPL::Math::MinimizerVariableArrayTraits< A >Traits template that adapts arbitrary variable-array types to the linear-algebra operations required by minimizer implementations (dot, norm2, axpy, clear, assign, multiply, sub)
 CCDPL::Math::MinimizerVariableArrayTraits< std::vector< V > >Math::MinimizerVariableArrayTraits specialization for std::vector storage of fixed-size vectors
 CCDPL::Math::MinimizerVariableArrayTraits< VA >
 CCDPL::Math::MinimizerVariableArrayTraits< VectorArray< V > >Math::MinimizerVariableArrayTraits specialization for Math::VectorArray storage (a sequence of fixed-size vectors)
 CCDPL::Math::MLRModel< T >Performs Multiple Linear Regression [WLIREG] on a set of data points \( (y_i, \vec{X}_i) \)
 CCDPL::Biomol::MMCIFDataData structure for the storage of imported MMCIF data (see [MMCIF])
 CCDPL::ForceField::MMFF94AngleBendingInteractionStores parameters for a single MMFF94 angle-bending interaction defined over an atom triplet
 CCDPL::ForceField::MMFF94AngleBendingInteractionParameterizerDetects and parameterizes the MMFF94 angle-bending interactions of a molecular graph
 CCDPL::ForceField::MMFF94AngleBendingParameterTableData structure for the storage and lookup of MMFF94 angle-bending interaction parameters
 CCDPL::ForceField::MMFF94AromaticAtomTypeDefinitionTableData structure for the storage and lookup of MMFF94 aromatic atom type definitions
 CCDPL::ForceField::MMFF94AtomTypePropertyTableData structure for the storage and lookup of structural and chemical property data associated with numeric MMFF94 atom types
 CCDPL::ForceField::MMFF94AtomTyperAssigns MMFF94 symbolic and numeric atom types to the atoms of a molecular graph
 CCDPL::ForceField::MMFF94BondChargeIncrementTableData structure for the storage and lookup of MMFF94 bond charge increments
 CCDPL::ForceField::MMFF94BondStretchingInteractionStores parameters for a single MMFF94 bond-stretching interaction between two bonded atoms
 CCDPL::ForceField::MMFF94BondStretchingInteractionParameterizerDetects and parameterizes the MMFF94 bond-stretching interactions of a molecular graph
 CCDPL::ForceField::MMFF94BondStretchingParameterTableData structure for the storage and lookup of MMFF94 bond-stretching interaction parameters
 CCDPL::ForceField::MMFF94BondStretchingRuleParameterTableData structure for the storage and lookup of MMFF94 bond-stretching interaction fallback parameters
 CCDPL::ForceField::MMFF94BondTyperAssigns MMFF94 bond type indices to the bonds of a molecular graph
 CCDPL::ForceField::MMFF94ChargeCalculatorCalculator for the MMFF94 partial atomic charges of a molecular graph
 CCDPL::ForceField::MMFF94DefaultStretchBendParameterTableData structure for the storage and lookup of MMFF94 stretch-bend interaction fallback parameters
 CCDPL::ForceField::MMFF94ElectrostaticInteractionStores parameters for a single MMFF94 electrostatic interaction between two non-bonded atoms
 CCDPL::ForceField::MMFF94ElectrostaticInteractionParameterizerDetects and parameterizes the MMFF94 electrostatic interactions of a molecular graph
 CCDPL::ForceField::MMFF94EnergyCalculator< ValueType >Calculates the total MMFF94 force field energy for a set of atom 3D coordinates
 CCDPL::ForceField::MMFF94FormalAtomChargeDefinitionTableData structure for the storage and lookup of formal charge definitions used by the MMFF94 charge model
 CCDPL::ForceField::MMFF94GradientCalculator< ValueType >Calculates the total MMFF94 force field energy and its gradient for a set of atom 3D coordinates
 CCDPL::ForceField::MMFF94HeavyToHydrogenAtomTypeMapData structure for the storage and lookup of heavy-to-hydrogen symbolic MMFF94 atom type mappings
 CCDPL::ForceField::MMFF94InteractionDataContainer holding the full set of MMFF94 interaction parameter records for a molecular graph
 CCDPL::ForceField::MMFF94InteractionParameterizerHighly configurable implementation of the complete workflow for molecular graph MMFF94 interaction perception and parameterization
 CCDPL::ForceField::MMFF94OutOfPlaneBendingInteractionStores parameters for a single MMFF94 out-of-plane bending interaction at a trigonal center
 CCDPL::ForceField::MMFF94OutOfPlaneBendingInteractionParameterizerDetects and parameterizes the MMFF94 out-of-plane bending interactions of a molecular graph
 CCDPL::ForceField::MMFF94OutOfPlaneBendingParameterTableData structure for the storage and lookup of MMFF94 out-of-plane bending interaction force constants
 CCDPL::ForceField::MMFF94PartialBondChargeIncrementTableData structure for the storage and lookup of MMFF94 per-atom partial bond charge increment and formal charge adjustment factors
 CCDPL::ForceField::MMFF94PrimaryToParameterAtomTypeMapData structure for the storage and lookup of primary numeric MMFF94 atom type to fallback parameter atom type list mappings
 CCDPL::ForceField::MMFF94StretchBendInteractionStores paramters for a single MMFF94 stretch-bend coupling interaction
 CCDPL::ForceField::MMFF94StretchBendInteractionParameterizerDetects and parameterizes the MMFF94 stretch-bend interactions of a molecular graph
 CCDPL::ForceField::MMFF94StretchBendParameterTableData structure for the storage and lookup of MMFF94 stretch-bend interaction parameters
 CCDPL::ForceField::MMFF94SymbolicAtomTypePatternTableData structure storing SMARTS substructure patterns used to assign symbolic MMFF94 atom types during atom typing
 CCDPL::ForceField::MMFF94SymbolicToNumericAtomTypeMapLookup table mapping each symbolic MMFF94 atom type to its corresponding numeric MMFF94 atom type
 CCDPL::ForceField::MMFF94TorsionInteractionStores parameters for a single MMFF94 torsion interaction over an atom quadruplet i-j-k-l
 CCDPL::ForceField::MMFF94TorsionInteractionParameterizerDetects and parameterizes the MMFF94 torsion interactions of a molecular graph
 CCDPL::ForceField::MMFF94TorsionParameterTableData structure for the storage and lookup of MMFF94 torsion interaction parameters
 CCDPL::ForceField::MMFF94VanDerWaalsInteractionStores parameters for a single MMFF94 Van der Waals interaction between two non-bonded atoms
 CCDPL::ForceField::MMFF94VanDerWaalsInteractionParameterizerDetects and parameterizes the MMFF94 Van der Waals interactions of a molecular graph
 CCDPL::ForceField::MMFF94VanDerWaalsParameterTableData structure for the storage and lookup of MMFF94 interaction parameters
 CCDPL::Descr::MolecularComplexityCalculatorCalculation of the molecular complexity of a molecular graph after Hendrickson, Huang and Toczko
 CCDPL::Descr::MoleculeAutoCorr2DDescriptorCalculatorCalculation of a topological (2D) auto-correlation descriptor of a molecular graph partitioned by specific atom types
 CCDPL::Descr::MoleculeAutoCorr3DDescriptorCalculatorCalculation of a 3D auto-correlation descriptor of a molecular graph partitioned by specific atom types
 CCDPL::Descr::MoleculeRDFDescriptorCalculatorCalculation of an RDF descriptor of a molecular graph partitioned by specific atom types
 CCDPL::Chem::MorganNumberingCalculatorComputes a canonical atom numbering of a molecular graph using a modified Morgan algorithm
 ►CCDPL::Chem::MultiConfMoleculeInputProcessorAbstract base interface for processors that detect and assemble multi-conformer molecules from a stream of successive single-conformer input molecules
 CCDPL::Util::MultiMap< Key, Value, AllowDefValues, KeyCompFunc >A multiple sorted associative container that maps keys to values
 ►CCDPL::Util::MultiMap< const Atom *, const Atom *, true >
 ►CCDPL::Util::MultiMap< const Bond *, const Bond *, true >
 ►CCDPL::Util::MultiMap< const Entity3D *, const Entity3D *, true >
 ►CCDPL::Util::MultiMap< const Feature *, const Feature *, true >
 CCDPL::Util::MultiMapDefaultValue< ValueType, Allow >Helper supplying the default value returned by Util::MultiMap when a queried key is absent
 CCDPL::Util::MultiMapDefaultValue< ValueType, false >Util::MultiMapDefaultValue specialization for the case in which default values are not allowed
 CCDPL::Chem::MultiSubstructureSearchEvaluates a boolean expression over multiple substructure queries against a target molecular graph
 CCDPL::Chem::Atom2DCoordinatesCalculator::LGNode::NodeLayoutInfo
 ►CCDPL::Descr::NPointPharmacophoreFingerprintGeneratorAbstract base for N-point pharmacophore fingerprint generators
 CCDPL::Util::NullCheckDereferencer< ArgType, ResType >Unary functor for the dereferenciation of pointers with null pointer checking
 CCDPL::Util::ObjectPool< T >Data structure that caches instances of type T up to a user specified amount
 CCDPL::Util::ObjectPool< BasicAtom >
 CCDPL::Util::ObjectPool< BasicBond >
 CCDPL::Util::ObjectPool< BasicFeature >
 CCDPL::Util::ObjectPool< BasicMolecule >
 CCDPL::Util::ObjectPool< Cell >
 CCDPL::Util::ObjectPool< Edge >
 CCDPL::Util::ObjectPool< Math::Vector3DArray >
 CCDPL::Util::ObjectPool< PathMessage >
 CCDPL::Util::ObjectPool< StructureData >
 CCDPL::Util::ObjectPool< SubstructDescriptor >
 CCDPL::Util::ObjectStack< T >Reusable object pool with stack-like borrow/return semantics
 CCDPL::Util::ObjectStack< AGEdge >
 CCDPL::Util::ObjectStack< AGNode >
 CCDPL::Util::ObjectStack< AtomBondMapping >
 CCDPL::Util::ObjectStack< AtomNode >
 CCDPL::Util::ObjectStack< ClipPathPrimitive2D >
 CCDPL::Util::ObjectStack< Edge >
 CCDPL::Util::ObjectStack< GaussianShapeFunction >
 CCDPL::Util::ObjectStack< IndexArray >
 CCDPL::Util::ObjectStack< LGEdge >
 CCDPL::Util::ObjectStack< LinePrimitive2D >
 CCDPL::Util::ObjectStack< LineSegmentListPrimitive2D >
 CCDPL::Util::ObjectStack< PathPrimitive2D >
 CCDPL::Util::ObjectStack< PointListPrimitive2D >
 CCDPL::Util::ObjectStack< PolygonPrimitive2D >
 CCDPL::Util::ObjectStack< PolylinePrimitive2D >
 CCDPL::Util::ObjectStack< RingInfo >
 CCDPL::Util::ObjectStack< RingSysNode >
 CCDPL::Util::ObjectStack< State >
 CCDPL::Util::ObjectStack< StructureView2D >
 CCDPL::Util::ObjectStack< TextLabelPrimitive2D >
 CCDPL::Util::ObjectStack< Util::BitSet >
 CCDPL::Util::ObjectStack< Util::STPairArray >
 CCDPL::Pharm::OrthogonalPiPiInteractionConstraintConstraint functor that tests whether an aromatic feature pair satisfies the geometric criteria for an orthogonal (T-shaped) π-π interaction (horizontal/vertical center separations plus ring-normal angle)
 CCDPL::Pharm::ParallelPiPiInteractionConstraintConstraint functor that tests whether an aromatic feature pair satisfies the geometric criteria for a parallel (sandwich/displaced) π-π interaction (vertical/horizontal center separations plus ring-normal angle)
 ►CCDPL::Vis::Path2DProvides a container for painting operations, enabling arbitrary graphical shapes to be constructed and reused
 CCDPL::Vis::Path2DConverterProvides an interface for classes that implement the conversion of Vis::Path2D objects into rendering backend specific path descriptions or drawing operations
 CCDPL::Descr::PathFingerprintGeneratorGeneration of Daylight-style path fingerprints of molecular graphs
 CCDPL::Chem::PatternAtomTyper::PatternStores a single substructure query molecular graph, its atom label value, its priority and match-handling flags
 CCDPL::Chem::SubstructureHistogramCalculator::PatternStores a single substructure query molecular graph, its histogram ID, its priority and match-handling flags
 CCDPL::Chem::PatternAtomTyperAssigns numeric labels to specific atoms of a molecular graph that are described by substructure patterns
 CCDPL::Biomol::PDBDataData structure for the storage of data records found in PDB formatted data [PDB]
 CCDPL::Vis::PenSpecifies how to draw lines and outlines of shapes
 CCDPL::MolProp::PEOESigmaChargeCalculatorCalculator that uses the Partial Equalization of Orbital Electronegativities (PEOE) method of Gasteiger and Marsili to compute σ atomic charges and electronegativities of a molecular graph
 CCDPL::Descr::PharmacophoreAutoCorr3DDescriptorCalculatorCalculation of a 3D auto-correlation descriptor of a pharmacophore partitioned by specific feature types
 ►CCDPL::Pharm::PharmacophoreFitScoreScoring functor that quantifies how well a candidate set of features fits a reference pharmacophore, combining feature-match count, per-feature position deviation and geometry-match contributions
 ►CCDPL::Pharm::PharmacophoreGeneratorBase class for pharmacophore generators that orchestrate per-feature-type Pharm::FeatureGenerator instances to produce the features of a Pharm::Pharmacophore from a Chem::MolecularGraph
 CCDPL::Descr::PharmacophoreRDFDescriptorCalculatorCalculation of an RDF descriptor of a pharmacophore partitioned by specific feature types
 CCDPL::Chem::CIPPriorityCalculator::AtomNode::PriorityGreaterCmpFunc
 CCDPL::Chem::CIPPriorityCalculator::AtomNode::PriorityLessCmpFunc
 ►CCDPL::Base::PropertyContainerBase class providing methods for the storage and lookup of object properties
 CCDPL::Util::PropertyValue< T >Unary functor that retrieves the value of a given property from the Base::PropertyContainer instance provided as argument
 CCDPL::Util::PropertyValueProduct< ResType, PropertyValueType >Binary functor that calculates the product of two property values retrieved from a pair of Base::PropertyContainer instances passed as argument
 CCDPL::Chem::ProtonationStateStandardizerAdjusts the protonation state of a molecule (atom formal charges and bonded hydrogen counts) according to one of several pre-defined objectives
 CCDPL::Descr::PubChemFingerprintGeneratorGeneration of 881 bit PubChem fingerprints
 CCDPL::Vis::QtObjectFactoryProvides methods for the creation of QFont, QColor, QPen and QBrush objects from Font, Color, Pen and Brush instances
 CCDPL::Math::QuaternionBinary1Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::QuaternionBinary1 instantiation <E1, E2, F>
 CCDPL::Math::QuaternionBinary2Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::QuaternionBinary2 instantiation <E1, E2, F>
 ►CCDPL::Math::QuaternionBinaryFunctor< Q1, Q2 >Base class for per-component binary functors that take two quaternion expressions and produce a quaternion result (Math::QuaternionProduct)
 ►CCDPL::Math::QuaternionBooleanBinaryFunctor< Q1, Q2 >Base class for binary functors that take two quaternion expressions and return a bool result (Math::QuaternionEquality)
 ►CCDPL::Math::QuaternionScalarRealUnaryFunctor< Q >Base class for unary functors that take a quaternion expression and return a real-valued scalar (Math::QuaternionNorm, Math::QuaternionNorm2)
 ►CCDPL::Math::QuaternionScalarUnaryFunctor< Q >Base class for unary functors that take a quaternion expression and return a scalar result (Math::QuaternionElementSum)
 ►CCDPL::Math::QuaternionTemporaryTraits< Q >Selects a concrete temporary quaternion type compatible with the quaternion expression Q
 CCDPL::Math::QuaternionTemporaryTraits< const VectorQuaternionAdapter< V > >Math::QuaternionTemporaryTraits specialization selecting Math::Quaternion as the temporary type for a const Math::VectorQuaternionAdapter view
 CCDPL::Math::QuaternionTemporaryTraits< VectorQuaternionAdapter< V > >Math::QuaternionTemporaryTraits specialization selecting Math::Quaternion as the temporary type for a Math::VectorQuaternionAdapter view
 CCDPL::Math::QuaternionUnary1Traits< E, F >Traits selecting the expression-template node and its result type for the Math::QuaternionUnary1 instantiation <E, F>
 CCDPL::Math::QuaternionUnary2Traits< E, F >Traits selecting the expression-template node and its result type for the Math::QuaternionUnary2 instantiation <E, F>
 ►CCDPL::Math::QuaternionUnaryFunctor< Q >Base class for per-component unary functors that take a quaternion expression and produce a quaternion result via applyC1 / applyC2 / applyC3 / applyC4 (Math::QuaternionUnreal, Math::QuaternionConjugate)
 ►CCDPL::Math::QuaternionVectorBinaryFunctor< Q, V >Base class for binary functors that take a quaternion expression and a vector expression and return a vector element scalar (Math::QuaternionVectorRotation)
 CCDPL::Math::QuaternionVectorBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::QuaternionVectorBinary instantiation <E1, E2, F>
 CCDPL::Math::Range< S >Half-open index range \( [start, stop) \) used for slicing vector and matrix expressions
 CCDPL::Math::Range< SizeType >
 CCDPL::Descr::RDFCodeCalculator< T >Generic implementation of the radial distribution function (RDF) code calculation for sequences of entities of arbitrary type
 ►CCDPL::Descr::RDFCodeCalculator< Chem::Atom >
 ►CCDPL::Descr::RDFCodeCalculator< Pharm::Feature >
 CCDPL::Chem::ReactionSubstructureSearchReaction-level analogue of Chem::SubstructureSearch that locates atom/bond mappings of a query reaction pattern in a target reaction
 CCDPL::Chem::ReactorApplies a Chem::Reaction template to the reactant components of a target Chem::Reaction to generate the corresponding product molecules
 CCDPL::Vis::Rectangle2DSpecifies an axis aligned rectangular area in 2D space
 CCDPL::Shape::ReferenceColorTverskyScoreFunctor wrapping Shape::calcReferenceColorTverskyScore()
 CCDPL::Shape::ReferenceShapeTverskyScoreFunctor wrapping Shape::calcReferenceShapeTverskyScore()
 CCDPL::Shape::ReferenceTotalOverlapTverskyScoreFunctor wrapping Shape::calcReferenceTotalOverlapTverskyScore()
 CCDPL::Shape::ReferenceTverskyComboScoreFunctor wrapping Shape::calcReferenceTverskyComboScore()
 ►CCDPL::Vis::Renderer2DInterface providing methods for low level 2D drawing operations
 CCDPL::Biomol::ResidueDictionaryGlobal dictionary for the lookup of meta-data associated with the residues in biological macromolecules
 CCDPL::Chem::ResonanceStructureGeneratorEnumerates the resonance structures of a molecular graph by redistributing π-electrons across the resonance-active bonds
 CCDPL::Shape::GaussianShapeFunctionAlignment::ResultA single alignment result: rigid-body transformation plus shape and color overlap values
 CCDPL::ConfGen::RMSDConformerSelectorGreedy RMSD-based conformer-diversity filter
 ►CCDPL::Math::Scalar13QuaternionTernaryFunctor< T1, Q, T2 >Base class for per-component ternary functors that take a scalar T1 (lhs), a quaternion expression, and a scalar T2 (Math::ScalarQuaternionDivision)
 CCDPL::Math::Scalar13QuaternionTernaryTraits< E1, E2, E3, F >Traits selecting the expression-template node and its result type for the Math::Scalar13QuaternionTernary instantiation <E1, E2, E3, F>
 CCDPL::Math::Scalar1GridBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar1GridBinary instantiation <E1, E2, F>
 CCDPL::Math::Scalar1MatrixBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar1MatrixBinary instantiation <E1, E2, F>
 CCDPL::Math::Scalar1QuaternionBinary1Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar1QuaternionBinary1 instantiation <E1, E2, F>
 CCDPL::Math::Scalar1QuaternionBinary2Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar1QuaternionBinary2 instantiation <E1, E2, F>
 ►CCDPL::Math::Scalar1QuaternionBinaryFunctor< T, Q >Base class for per-component binary functors that take a scalar T (lhs) and a quaternion expression (Math::Scalar1QuaternionAddition, Math::Scalar1QuaternionSubtraction)
 CCDPL::Math::Scalar1VectorBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar1VectorBinary instantiation <E1, E2, F>
 CCDPL::Math::Scalar2GridBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar2GridBinary instantiation <E1, E2, F>
 CCDPL::Math::Scalar2MatrixBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar2MatrixBinary instantiation <E1, E2, F>
 CCDPL::Math::Scalar2QuaternionBinary1Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar2QuaternionBinary1 instantiation <E1, E2, F>
 CCDPL::Math::Scalar2QuaternionBinary2Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar2QuaternionBinary2 instantiation <E1, E2, F>
 ►CCDPL::Math::Scalar2QuaternionBinaryFunctor< Q, T >Base class for per-component binary functors that take a quaternion expression (lhs) and a scalar T (Math::Scalar2QuaternionAddition, Math::Scalar2QuaternionSubtraction, Math::QuaternionInverse)
 CCDPL::Math::Scalar2VectorBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::Scalar2VectorBinary instantiation <E1, E2, F>
 ►CCDPL::Math::Scalar3GridBooleanTernaryFunctor< G1, G2, T >Base class for ternary functors that take two grid expressions plus a tolerance scalar and return a bool result (Math::GridToleranceEquality)
 ►CCDPL::Math::Scalar3MatrixBooleanTernaryFunctor< M1, M2, T >Base class for ternary functors that take two matrix expressions plus a tolerance scalar and return a bool result (Math::MatrixToleranceEquality)
 ►CCDPL::Math::Scalar3QuaternionBooleanTernaryFunctor< Q1, Q2, T >Base class for ternary functors that take two quaternion expressions plus a tolerance scalar and return a bool result (Math::QuaternionToleranceEquality)
 ►CCDPL::Math::Scalar3QuaternionTernaryFunctor< Q1, Q2, T >Base class for per-component ternary functors that take two quaternion expressions plus a scalar (Math::QuaternionDivision)
 CCDPL::Math::Scalar3QuaternionTernaryTraits< E1, E2, E3, F >Traits selecting the expression-template node and its result type for the Math::Scalar3QuaternionTernary instantiation <E1, E2, E3, F>
 ►CCDPL::Math::Scalar3VectorBooleanTernaryFunctor< V1, V2, T >Base class for ternary functors that take two vectors and a scalar tolerance and return a boolean (Math::VectorToleranceEquality)
 CCDPL::Math::ScalarAbsImpl< Signed >Helper class template for retrieving the absolute value of scalar arithmetic types
 CCDPL::Math::ScalarAbsImpl< false >Specialization of Math::ScalarAbsImpl for unsigned types
 ►CCDPL::Math::ScalarBinaryAssignmentFunctor< T1, T2 >Base class for binary in-place assignment functors of the form F::apply(T1, const T2&)
 ►CCDPL::Math::ScalarBinaryFunctor< T1, T2 >Base class for binary scalar functors of the form F::apply(const T1&, const T2&) returning a Math::CommonType result
 ►CCDPL::Math::ScalarRealUnaryFunctor< T >Base class for unary scalar functors that return the real part of T (Math::ScalarReal, Math::ScalarImaginary)
 ►CCDPL::Math::ScalarTraits< T >Common operations and type aliases for scalar arithmetic types
 ►CCDPL::Math::ScalarUnaryFunctor< T >Base class for unary scalar functors of the form F::apply(const T&) returning a T result
 CCDPL::GRAIL::FeatureInteractionScoreGridCalculator::ScoreSumFunctorScore-combination functor returning the sum of the per-feature scores
 ►CCDPL::Pharm::ScreeningDBAccessorAbstract base class for accessors that read the data stored in pharmacophore screening databases
 ►CCDPL::Pharm::ScreeningDBCreatorAbstract base class for creators that build optimized pharmacophore screening databases
 CCDPL::Pharm::ScreeningProcessorHigh-level driver for pharmacophore-based screening of a Pharm::ScreeningDBAccessor-backed database against a query feature container, reporting alignment hits via a user-supplied callback
 CCDPL::Shape::ScreeningProcessorHigh-level driver for shape-based virtual screening of molecular databases
 CCDPL::Shape::ScreeningSettingsBundle of configuration parameters for Shape::ScreeningProcessor
 CCDPL::Pharm::ScreeningProcessor::SearchHitData structure representing a single alignment hit produced by the screening processor, bundling the source pharmacophore/molecule, the alignment transformation and the source-database indices
 ►CCDPL::Vis::Shape3DThe abstract base of all classes describing the geometric shape of 3D objects
 ►CCDPL::Vis::Shape3DVisitorThe base of all Vis::Shape3D visitor implementations [VPTN]
 CCDPL::Shape::ShapeTanimotoScoreFunctor wrapping Shape::calcShapeTanimotoScore()
 CCDPL::Shape::ShapeTverskyScoreFunctor wrapping Shape::calcShapeTverskyScore()
 CCDPL::Vis::SizeSpecificationSpecifies the value and type of a size attribute and defines how the value may change during processing steps
 CCDPL::Math::Slice< S, D >Index slice ( \( start, stride, size \)) used for strided slicing of vector and matrix expressions
 CCDPL::Math::Slice< SizeType, DifferenceType >
 CCDPL::Math::SparseContainerElement< C, K >Proxy that exposes a single (key, value) entry of a sparse container as a writable reference
 CCDPL::Chem::SpatialEntityAlignment< T >Computes a spatial alignment between two sets of entities (with 3D coordinates) by composing topological entity matching with Kabsch-style 3D superposition
 ►CCDPL::Chem::SpatialEntityAlignment< Feature >
 CCDPL::Chem::StereoDescriptorData structure for the storage and retrieval of stereochemical information about atoms and bonds
 CCDPL::Chem::StereoisomerGeneratorEnumerates the stereoisomers of a molecular graph by flipping the configurations of selected atom and bond stereocenters
 ►CStreamType
 CCDPL::Chem::StringDataBlockEntryRepresents a data item consisting of a header and a data payload
 CCDPL::Chem::ResonanceStructureGenerator::StructureDataHolds the per-atom formal charges and per-bond orders that define a single resonance structure
 CCDPL::ConfGen::StructureGeneratorHigh-level driver for the generation of a single low-energy 3D structure from a molecular graph
 CCDPL::ConfGen::StructureGeneratorSettingsBundle of configuration parameters for single 3D structure generation via class ConfGen::StructureGenerator
 CCDPL::Chem::SubstructureEditorPattern-driven editor that rewrites matched substructures of a Chem::Molecule using a result template, with optional exclude patterns guarding sites that must not be touched
 CCDPL::Chem::SubstructureHistogramCalculatorCounts occurrences of registered substructure patterns in a molecular graph, emitting the per-pattern hit counts into a user-supplied histogram container
 CCDPL::Chem::SubstructureSearchSubgraph-isomorphism search of a query molecular graph against a target molecular graph, implemented after the VF2 algorithm
 CCDPL::Chem::SurfaceAtomExtractorExtracts the solvent-accessible surface atoms of a set of atoms
 CCDPL::Chem::SymmetryClassCalculator::AtomNode::SVMNumberCmpFunc
 CCDPL::Chem::SymmetryClassCalculator::AtomNode::SymClassCmpFunc
 CCDPL::Chem::SymmetryClassCalculatorPerceives topological-symmetry classes of the atoms in a molecular graph
 CCDPL::Shape::TanimotoComboScoreFunctor wrapping Shape::calcTanimotoComboScore()
 CCDPL::Descr::TanimotoSimilarityFunctor class for calculating Tanimoto Similarities [CITB] of bitsets and vectors
 ►CCDPL::Chem::TautomerGeneratorEnumerates the tautomers of a molecular graph by iteratively applying a configurable set of Chem::TautomerizationRule instances and reporting each accepted tautomer to a user-supplied callback
 ►CCDPL::Chem::TautomerizationRuleAbstract base class for all tautomerization rule implementations used by the Chem::TautomerGenerator
 CCDPL::Chem::TautomerScoreFunctor for the calculation of a heuristic stability score of a tautomeric form represented as a molecular graph
 CCDPL::Chem::TopologicalEntityAlignment< T >Computes a topological alignment between two sets of entities by reducing the alignment problem to a maximum-common-subgraph search on a compatibility graph
 CCDPL::Chem::TopologicalEntityAlignment< Feature >
 ►CCDPL::ConfGen::TorsionCategoryRepresents a node of a hierarchical torsion library
 CCDPL::ConfGen::TorsionDriverDriver for the systematic enumeration of conformers obtained by rotating around rotatable bonds of a molecular graph, using preferred torsion angles taken from configured ConfGen::TorsionLibrary instances
 CCDPL::ConfGen::TorsionDriverSettingsBundle of configuration parameters for systematic conformer enumeration via class ConfGen::TorsionDriver
 CCDPL::ConfGen::TorsionRuleData structure for the representation of single torsion library rules
 CCDPL::ConfGen::TorsionRuleMatchA single match of a ConfGen::TorsionRule against a rotatable bond: the rule, the bond and the four atoms that span the torsion
 CCDPL::ConfGen::TorsionRuleMatcherFinds torsion rules from a ConfGen::TorsionLibrary instance that match a given rotatable bond
 CCDPL::Shape::TotalOverlapTanimotoScoreFunctor wrapping Shape::calcTotalOverlapTanimotoScore()
 CCDPL::Shape::TotalOverlapTverskyScoreFunctor wrapping Shape::calcTotalOverlapTverskyScore()
 CCDPL::MolProp::TPSACalculatorCalculation of the topological polar surface area (TPSA) of molecular graphs based on fragment contributions
 CCDPL::Shape::TverskyComboScoreFunctor wrapping Shape::calcTverskyComboScore()
 CCDPL::Descr::TverskySimilarityFunctor class for calculating the Tversky Similarity [GSIM] of bitsets
 CCDPL::ForceField::UFFAtomTypePropertyTableData structure for the storage and lookup of various properties associated with numeric UFF atom types
 CCDPL::Math::UnitLowerTag selecting the unit-lower-triangular view (zero above the diagonal, one on the diagonal) for Math::TriangularAdapter
 CCDPL::Math::UnitUpperTag selecting the unit-upper-triangular view (zero below the diagonal, one on the diagonal) for Math::TriangularAdapter
 CCDPL::Math::UpperTag selecting the upper-triangular view (entries strictly below the diagonal read as zero) for Math::TriangularAdapter
 CCDPL::Math::VectorArrayAlignmentCalculator< VA, V, T >Convenience wrapper around Math::KabschAlgorithm that operates directly on Math::VectorArray inputs
 CCDPL::Math::VectorArrayAlignmentCalculator< Math::Vector3DArray >
 CCDPL::Math::VectorBinary1Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::VectorBinary1 instantiation <E1, E2, F>
 CCDPL::Math::VectorBinary2Traits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::VectorBinary2 instantiation <E1, E2, F>
 ►CCDPL::Math::VectorBinaryFunctor< V1, V2 >Base class for binary functors that take two vectors and return a vector (Math::VectorCrossProduct)
 ►CCDPL::Math::VectorBooleanBinaryFunctor< V1, V2 >Base class for binary functors that take two vectors and return a boolean (Math::VectorEquality and similar)
 CCDPL::Math::VectorElementAccessor< E >Access functor used by Math::VectorIteratorTraits to read mutable vector elements via Util::IndexedElementIterator
 CCDPL::Math::VectorElementAccessor< const E >Specialization of Math::VectorElementAccessor for const vector references (read-only iteration)
 CCDPL::Math::VectorIteratorTraits< E >Traits selecting the element accessor and Util::IndexedElementIterator specialization for mutable iteration over E
 CCDPL::Math::VectorIteratorTraits< const E >Specialization of Math::VectorIteratorTraits for read-only iteration over E
 CCDPL::Math::VectorMatrixBinaryTraits< E1, E2, F >Traits selecting the expression-template node and its result type for the Math::VectorMatrixBinary instantiation <E1, E2, F>
 ►CCDPL::Math::VectorMatrixUnaryFunctor< V >Base class for unary functors that produce a matrix element from a vector expression and (i, j) cell indices (Math::DiagonalMatrixFromVector, Math::CrossProductMatrixFromVector)
 CCDPL::Math::VectorMatrixUnaryTraits< E, F >Traits selecting the expression-template node and its result type for the Math::VectorMatrixUnary instantiation <E, F>
 ►CCDPL::Math::VectorScalarBinaryFunctor< V1, V2 >Base class for binary functors that take two vectors and return a scalar (Math::VectorInnerProduct, Math::VectorAngleCosine)
 ►CCDPL::Math::VectorScalarIndexUnaryFunctor< V >Base class for unary functors that take a vector and return a vector-element index (Math::VectorNormInfinityIndex)
 ►CCDPL::Math::VectorScalarRealUnaryFunctor< V >Base class for unary functors that take a vector and return a real-valued scalar (Math::VectorNorm1, Math::VectorNorm2, Math::VectorNormInfinity)
 ►CCDPL::Math::VectorScalarUnaryFunctor< V >Base class for unary functors that take a vector and return a scalar (Math::VectorElementSum)
 ►CCDPL::Math::VectorTemporaryTraits< V >Selects a concrete temporary vector type compatible with the vector expression V
 CCDPL::Math::VectorTemporaryTraits< const QuaternionVectorAdapter< Q > >Math::VectorTemporaryTraits specialization selecting Math::CVector as the temporary type for a const Math::QuaternionVectorAdapter view
 ►CCDPL::Math::VectorTemporaryTraits< M >
 CCDPL::Math::VectorTemporaryTraits< QuaternionVectorAdapter< Q > >Math::VectorTemporaryTraits specialization selecting Math::CVector as the temporary type for a Math::QuaternionVectorAdapter view
 CCDPL::Math::VectorUnaryTraits< E, F >Traits selecting the expression-template node and its result type for the Math::VectorUnary instantiation <E, F>
 CCDPL::Util::DGCoordinatesGenerator< 3, T >::VolumeConstraintA constraint that pins the signed tetrahedral volume spanned by four points to the interval [lb, ub]
 CCDPL::Pharm::XBondingInteractionConstraintConstraint functor that tests whether a halogen-bond donor/acceptor feature pair satisfies the geometric criteria for a halogen bond (halogen-acceptor distance plus the two characteristic angles)
 CCDPL::MolProp::XLogPCalculatorCalculation of the octanol/water partition coefficient ( \( \log P \)) of molecular graphs using the atom-additive method of Wang, Gao and Lai
 Cbool
 CCMatrix< double, 4, 4 >
 CMatrix< double >
 CVector< double >
 ►CVectorArray< Vector2D >
 ►CVectorArray< Vector3D >
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