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
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
FilteringInputStreambufDelivers characters from an istream or streambuf from a source while filtering
FptIndexStructure of fastsearch index files
FptIndexHeaderHeader for fastsearch index file
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
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
OBChemTsfmSMARTS based structural modification (chemical transformation)
OBChiralDataUsed to hold chiral inforamtion about the atom as OBGenericData
OBCommentDataUsed to store a comment string (can be multiple lines long)
OBConformerDataUsed to hold data on conformers or geometry optimization steps
OBConversionClass to convert from one format to another
OBDescriptorBase class for molecular properties, descriptors or features
OBElementIndividual element data type
OBElementTablePeriodic Table of the Elements
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)
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
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
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
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
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
OBPairDataUsed to store arbitrary text attribute/value relationships
OBPairTemplateUsed 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
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
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
OBSmartsPatternSMARTS (SMiles ARbitrary Target Specification) substructure searching
OBSqrtTblSquare Root lookup table - given a distance squared returns distance
OBSSMatchInternal class: performs fast, exhaustive matching used to find just a single match in match() using recursion and explicit stack handling
OBStopwatchStopwatch class used for timing length of execution
OBSymmetryDataUsed to hold the point-group and/or space-group symmetry
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 transforms (OBChemTsfm class) read from a datafile
PatternA SMARTS parser internal pattern
pattyProgrammable Atom Typer
quadA 4-element templated, based on the design of the STL pair<>
SpaceGroupHandle crystallographic space group symmetry
transform3dHandle 3D transformations, such as space group definitions
tripleA 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