Class List

Here are the classes, structs, unions and interfaces with brief descriptions:
_AtomExprAn internal (SMARTS parser) atomic expression
_BondExprAn internal (SMARTS parser) bond expression
AliasDataIndicate atoms as aliases for larger functional groups
AtomSpecAn internal (SMARTS parser) atom specification
BondSpecAn internal (SMARTS parser) bond specification
CharPtrLessCase insensitive string comparison for PluginMapType key
OBSquarePlanarStereo::ConfigStereochemical configuration for square planar stereocenters
OBCisTransStereo::ConfigStereochemical configuration for double-bond cis/trans stereochemistry
OBTetrahedralStereo::ConfigStereochemical configuration for tetrahedral stereocenters
DeleteObjectFunctor for deleting containers of pointers. Scott Meyers, Effective STL, Item 7
DLHandlerInterface for dynamic libraries
DoubleTypeUsed for internal random number generation OBRandom (unless the system random generator is used)
FastSearchClass to search fingerprint index files
FastSearchIndexerClass to prepare fingerprint index files See FastSearch class for details
FilteringInputStreambuf< Extractor >Delivers characters from an istream or streambuf from a source while filtering
FptIndexStructure of fastsearch index files
FptIndexHeaderHeader for fastsearch index file
OBIsomorphismMapper::FunctorFunctor base class to be used in combination with MapGeneric
GasteigerStateHelper class for OBGastChrg which stores the Gasteiger states of a given atom
LineEndingExtractorReplaces CRLF (DOS) and CR (Mac OS 9) line endings by LF (POSIX)
LineSearchTypeThe type of line search to be used for optimization -- simple or Newton numeric
matrix3x3Represents a real 3x3 matrix
max_value< T, size >A C++ template to return the maximum value of a type (e.g., int)
max_value< T, 0 >A C++ template to return the maximum value of a type (e.g., int)
OBAlignPerform a least-squares alignment of two molecules or two vectors of vector3 objects
OBAngleUsed to hold the 3 atoms in an angle and the angle itself
OBAngleDataUsed to hold all angles in a molecule as generic data for OBMol
OBAromaticTyperAssigns aromatic typing to atoms and bonds
OBAtomAtom class
OBAtomAtomIterIterate over all neighboring atoms to an OBAtom
OBAtomBondIterIterate over all bonds on an OBAtom
OBAtomClassDataHandle atom classes in reaction SMILES/SMIRKS
OBAtomTyperAssigns atom types, hybridization, implicit valence and formal charges
OBBaseBase Class
OBBitVecA speed-optimized vector of bits
OBBondBond class
OBBondTyperAssigns bond types for file formats without bond information
OBBuilderClass to build 3D structures
OBChainsParserPerceives peptide or nucleotide chains and residues in an OBMol
OBChargeModelAtomic partial charge models
OBChemTsfmSMARTS based structural modification (chemical transformation)
OBChiralDataUsed to hold chiral inforamtion about the atom as OBGenericData
OBCisTransStereoClass for handling and storing cis/trans stereochemistry
OBColorColor class used by OBDepict
OBCommentDataUsed to store a comment string (can be multiple lines long)
OBConformerDataUsed to hold data on conformers or geometry optimization steps
OBConformerFilterInterface used by OBConformerSearch for filtering conformers
OBConformerFiltersClass for combining OBConformerFilter objects
OBConformerScoreInterface used by OBConformerSearch for scoring conformers
OBConformerSearchConformer searching using genetic algorithm. See Conformer Searching
OBConversionClass to convert from one format to another
OBDepict2D depiction of molecules using OBPainter
OBDescriptorBase class for molecular properties, descriptors or features
OBDOSDataUsed to hold density of states information
OBElectronicTransitionDataUsed to hold information about electronic transitions
OBElementIndividual element data type
OBElementTablePeriodic Table of the Elements
OBEnergyConformerScoreA lowest energy conformer scoring class
OBErrorCustomizable error handling and logging -- store a message, including the method yielding the error, causes, etc
OBExternalBondUsed to store information on an external bond (e.g., SMILES fragments)
OBExternalBondDataUsed to store information on external bonds (e.g., in SMILES fragments)
OBFFCalculation2Internal class for OBForceField to hold energy and gradient calculations on specific force fields
OBFFCalculation3Internal class for OBForceField to hold energy and gradient calculations on specific force fields
OBFFCalculation4Internal class for OBForceField to hold energy and gradient calculations on specific force fields
OBFFConstraintInternal class for OBForceField to hold constraints
OBFFConstraintsInternal class for OBForceField to handle constraints
OBFFParameterInternal class for OBForceField to hold forcefield parameters
OBFingerprintThe base class for fingerprints
OBFloatGridHandle double precision floating point 3D grids (e.g., charge density around an OBMol)
OBFontMetricsFont metrics class used by OBDepict
OBForceFieldBase class for molecular mechanics force fields
OBFormatBase class for file formats
OBGastChrgAssigns Gasteiger partial charges
OBGenericDataBase class for generic data
OBGlobalDataBaseBase data table class, handles reading data files
OBGraphSymHandle and perceive graph symmtery for canonical numbering
OBGridA base grid class
OBGridDataStore values for numeric grids such as orbitals or electrostatic potential
OBGroupContribHandle group contribution algorithms
OBInternalCoordUsed to transform from z-matrix to cartesian coordinates
OBIsomorphismMapperAbstract class defining interface for isomorphism (i.e. substructure) searches
OBIsotopeTableTable of atomic isotope masses
OBLocaleHandle the locale for numeric data parsing
obLogBufA minimal streambuf derivative to wrap calls to cerr into calls to OBMessageHandler as needed
OBMatrixDataUsed to hold a 3x3 matrix item (e.g., a quadrupole moment)
OBMessageHandlerHandle error messages, warnings, debugging information and the like
OBMinimizingEnergyConformerScoreA lowest energy conformer scoring class (after minimization)
OBMolMolecule Class
OBMolAngleIterIterate over all angles in an OBMol
OBMolAtomBFSIterIterate over all atoms in an OBMol in a breadth-first search (BFS)
OBMolAtomDFSIterIterate over all atoms in an OBMol in a depth-first search (DFS)
OBMolAtomIterIterate over all atoms in an OBMol
OBMolBondBFSIterIterate over all bonds in an OBMol in a breadth-first search (BFS)
OBMolBondIterIterate over all bonds in an OBMol
OBMoleculeFormatAn OBFormat convenience subclass for conversion to/from OBMol data
OBMolPairIterIterate over all pairs of atoms (>1-4) in an OBMol
OBMolRingIterIterate over all rings in an OBMol
OBMolTorsionIterIterate over all torsions in an OBMol
OBNasaThermoDataThermodynamic data in old style NASA polynomial form for OBMol
OBOpOperations to modify molecules before output
OBOrbitalUsed to store energy, occupation, and orbital symmetry of a particular orbital
OBOrbitalDataUsed to hold information about orbital energies
OBPainterAbstract painter base class used by OBDepict
OBPairDataUsed to store arbitrary text attribute/value relationships
OBPairTemplate< ValueT >Used to store arbitrary attribute/value relationsips of any type
OBPhModelCorrections for pH used by OBMol::CorrectForPH()
OBPluginBase class for all types of dynamic classes discovered at runtime
OBPointGroupBrute-force point group symmetry perception
OBProxGridA grid for determining the proximity of a given point to atoms in an OBMol
OBQueryA substructure query
OBQueryAtomAtom in an OBQuery
OBQueryBondBond in an OBQuery
OBRandomRandom number generator
OBRateDataHolds rate constant data for OBReaction
OBReactionUsed to store chemical reactions (i.e., reactants -> products)
OBResidueResidue information
OBResidueAtomIterIterate over all atoms in an OBResidue
OBResidueDataTable of common biomolecule residues (for PDB or other files)
OBResidueIterIterate over all residues in an OBMol
OBRingStores information on rings in a molecule from SSSR perception
OBRingDataUsed to store the SSSR set (filled in by OBMol::GetSSSR())
OBRingSearchInternal class to facilitate OBMol::FindSSSR()
OBRingTyperAssigns ring types
OBRMSDConformerScoreA RMSD conformer scoring class
OBRotamerListSupports a set of rotamer coordinate sets for some number of potentially rotatable bonds
OBRotationDataUsed to hold the rotational constants and symmetry numbers
OBRotorA single rotatable OBBond as part of rotamer searching
OBRotorKeysA class to generate all possible rotorKeys
OBRotorListGiven an OBMol, set up a list of possibly rotatable torsions,
OBRotorRuleA rule for torsional conformer searching, defined by a SMARTS pattern
OBRotorRulesDatabase of default hybridization torsional rules and SMARTS-defined OBRotorRule objects
OBRTreeInternal class for OBRing search algorithms to create a search tree of OBAtom objects
OBScoreGridA base class for scoring docking interactions between multiple molecules
OBSerialNumsDefines a map between serial numbers (e.g., in a PDB file) and OBAtom objects inside a molecule
OBSetDataUsed to store arbitrary attribute/set relationships. Should be used to store a set of OBGenericData based on an attribute
OBSmartsMatcherInternal class: performs matching; a wrapper around previous C matching code to make it thread safe
OBSmartsPatternSMARTS (SMiles ARbitrary Target Specification) substructure searching
OBSpectrophoreClass to compute Spectrophores™
OBSqrtTblSquare Root lookup table - given a distance squared returns distance
OBSquarePlanarStereoClass for handling and storing square planar stereochemistry
OBSSMatchInternal class: performs fast, exhaustive matching used to find just a single match in match() using recursion and explicit stack handling
OBStereoPlaceholder for enums & Ref/Refs related functions
OBStereoBaseBase class for all stereochemistry classes
OBStereoFacadeFacade to simplify retrieval of OBStereoBase derived objects
OBStereoUnitStruct representing a single stereogenic unit
OBStericConformerFilterA steric conformer filter class
OBStopwatchStopwatch class used for timing length of execution
OBSymmetryDataUsed to hold the point-group and/or space-group symmetry
OBTetrahedralStereoClass for handling and storing tetrahedral atom stereochemistry
OBTetraNonPlanarStereoBase class for handling and storing non-planar stereochemistry with 4 reference atom ids
OBTetraPlanarStereoBase class for handling and storing planar stereochemistry with 4 reference atoms
OBTextAn object containing just text
OBTorsionUsed to hold the torsion data for a single rotatable bond and all four atoms around it
OBTorsionDataUsed to hold torsions as generic data for OBMol
OBTypeTableAtom Type Translation Table
OBUnitCellUsed for storing information about periodic boundary conditions with conversion to/from translation vectors and (a, b, c, alpha, beta, gamma)
OBVectorDataUsed to hold a 3D vector item (e.g., a dipole moment)
OBVibrationDataUsed to hold the normal modes of a molecule, etc
OBVirtualBondUsed to temporarily store bonds that reference an atom that has not yet been added to a molecule
OpTransformApplies molecular reactions/transforms (OBChemTsfm class) read from a datafile
ParseStateA SMARTS parser internal state
PatternA SMARTS parser internal pattern
pattyProgrammable Atom Typer
quad< T1, T2, T3, T4 >A 4-element templated, based on the design of the STL pair<>
SpaceGroupHandle crystallographic space group symmetry
transform3dHandle 3D transformations, such as space group definitions
triple< T1, T2, T3 >A 3-element templated, based on the design of the STL pair<>
vector3Represents a vector in 3-dimensional real space
XMLBaseFormatAbstract class containing common functionality for XML formats
XMLConversionA subclass for conversion of XML formats
XMLMoleculeFormatAbstract class for XML formats which represent molecules
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines