Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

_AtomExpr	An internal (SMARTS parser) atomic expression
_BondExpr	An internal (SMARTS parser) bond expression
AliasData	Indicate atoms as aliases for larger functional groups
AtomSpec	An internal (SMARTS parser) atom specification
BondSpec	An internal (SMARTS parser) bond specification
CharPtrLess	Case insensitive string comparison for PluginMapType key
DLHandler	Interface for dynamic libraries
DoubleType	Used for internal random number generation OBRandom (unless the system random generator is used)
FastSearch	Class to search fingerprint index files
FastSearchIndexer	Class to prepare fingerprint index files See FastSearch class for details
FilteringInputStreambuf	Delivers characters from an istream or streambuf from a source while filtering
FptIndex	Structure of fastsearch index files
FptIndexHeader	Header for fastsearch index file
GasteigerState	Helper class for OBGastChrg which stores the Gasteiger states of a given atom
LineEndingExtractor	Replaces CRLF (DOS) and CR (Mac OS 9) line endings by LF (POSIX)
LineSearchType	The type of line search to be used for optimization -- simple or Newton numeric
matrix3x3	Represents a real 3x3 matrix
OBAngle	Used to hold the 3 atoms in an angle and the angle itself
OBAngleData	Used to hold all angles in a molecule as generic data for OBMol
OBAromaticTyper	Assigns aromatic typing to atoms and bonds
OBAtom	Atom class
OBAtomAtomIter	Iterate over all neighboring atoms to an OBAtom
OBAtomBondIter	Iterate over all bonds on an OBAtom
OBAtomClassData	Handle atom classes in reaction SMILES/SMIRKS
OBAtomTyper	Assigns atom types, hybridization, implicit valence and formal charges
OBBase	Base Class
OBBitVec	A speed-optimized vector of bits
OBBond	Bond class
OBBondTyper	Assigns bond types for file formats without bond information
OBBuilder	Class to build 3D structures
OBChainsParser	Perceives peptide or nucleotide chains and residues in an OBMol
OBChemTsfm	SMARTS based structural modification (chemical transformation)
OBChiralData	Used to hold chiral inforamtion about the atom as OBGenericData
OBCommentData	Used to store a comment string (can be multiple lines long)
OBConformerData	Used to hold data on conformers or geometry optimization steps
OBConversion	Class to convert from one format to another
OBDescriptor	Base class for molecular properties, descriptors or features
OBElement	Individual element data type
OBElementTable	Periodic Table of the Elements
OBError	Customizable error handling and logging -- store a message, including the method yielding the error, causes, etc
OBExternalBond	Used to store information on an external bond (e.g., SMILES fragments)
OBExternalBondData	Used to store information on external bonds (e.g., in SMILES fragments)
OBFFCalculation2	Internal class for OBForceField to hold energy and gradient calculations on specific force fields
OBFFCalculation3	Internal class for OBForceField to hold energy and gradient calculations on specific force fields
OBFFCalculation4	Internal class for OBForceField to hold energy and gradient calculations on specific force fields
OBFFConstraint	Internal class for OBForceField to hold constraints
OBFFConstraints	Internal class for OBForceField to handle constraints
OBFFParameter	Internal class for OBForceField to hold forcefield parameters
OBFingerprint	The base class for fingerprints
OBFloatGrid	Handle double precision floating point 3D grids (e.g., charge density around an OBMol)
OBForceField	Base class for molecular mechanics force fields
OBFormat	Base class for file formats
OBGastChrg	Assigns Gasteiger partial charges
OBGenericData	Base class for generic data
OBGlobalDataBase	Base data table class, handles reading data files
OBGrid	A base grid class
OBGridData	Store values for numeric grids such as orbitals or electrostatic potential
OBGroupContrib	Handle group contribution algorithms
OBInternalCoord	Used to transform from z-matrix to cartesian coordinates
OBIsotopeTable	Table of atomic isotope masses
OBLocale	Handle the locale for numeric data parsing
obLogBuf	A minimal streambuf derivative to wrap calls to cerr into calls to OBMessageHandler as needed
OBMatrixData	Used to hold a 3x3 matrix item (e.g., a quadrupole moment)
OBMessageHandler	Handle error messages, warnings, debugging information and the like
OBMol	Molecule Class
OBMolAngleIter	Iterate over all angles in an OBMol
OBMolAtomBFSIter	Iterate over all atoms in an OBMol in a breadth-first search (BFS)
OBMolAtomDFSIter	Iterate over all atoms in an OBMol in a depth-first search (DFS)
OBMolAtomIter	Iterate over all atoms in an OBMol
OBMolBondIter	Iterate over all bonds in an OBMol
OBMoleculeFormat	An OBFormat convenience subclass for conversion to/from OBMol data
OBMolPairIter	Iterate over all pairs of atoms (>1-4) in an OBMol
OBMolRingIter	Iterate over all rings in an OBMol
OBMolTorsionIter	Iterate over all torsions in an OBMol
OBNasaThermoData	Thermodynamic data in old style NASA polynomial form for OBMol
OBOp	Operations to modify molecules before output
OBPairData	Used to store arbitrary text attribute/value relationships
OBPairTemplate	Used to store arbitrary attribute/value relationsips of any type
OBPhModel	Corrections for pH used by OBMol::CorrectForPH()
OBPlugin	Base class for all types of dynamic classes discovered at runtime
OBPointGroup	Brute-force point group symmetry perception
OBProxGrid	A grid for determining the proximity of a given point to atoms in an OBMol
OBRandom	Random number generator
OBRateData	Holds rate constant data for OBReaction
OBReaction	Used to store chemical reactions (i.e., reactants -> products)
OBResidue	Residue information
OBResidueAtomIter	Iterate over all atoms in an OBResidue
OBResidueData	Table of common biomolecule residues (for PDB or other files)
OBResidueIter	Iterate over all residues in an OBMol
OBRing	Stores information on rings in a molecule from SSSR perception
OBRingData	Used to store the SSSR set (filled in by OBMol::GetSSSR())
OBRingSearch	Internal class to facilitate OBMol::FindSSSR()
OBRingTyper	Assigns ring types
OBRotamerList	Supports a set of rotamer coordinate sets for some number of potentially rotatable bonds
OBRotationData	Used to hold the rotational constants and symmetry numbers
OBRotor	A single rotatable OBBond as part of rotamer searching
OBRotorKeys	A class to generate all possible rotorKeys
OBRotorList	Given an OBMol, set up a list of possibly rotatable torsions,
OBRotorRule	A rule for torsional conformer searching, defined by a SMARTS pattern
OBRotorRules	Database of default hybridization torsional rules and SMARTS-defined OBRotorRule objects
OBRTree	Internal class for OBRing search algorithms to create a search tree of OBAtom objects
OBScoreGrid	A base class for scoring docking interactions between multiple molecules
OBSerialNums	Defines a map between serial numbers (e.g., in a PDB file) and OBAtom objects inside a molecule
OBSetData	Used to store arbitrary attribute/set relationships. Should be used to store a set of OBGenericData based on an attribute
OBSmartsPattern	SMARTS (SMiles ARbitrary Target Specification) substructure searching
OBSqrtTbl	Square Root lookup table - given a distance squared returns distance
OBSSMatch	Internal class: performs fast, exhaustive matching used to find just a single match in match() using recursion and explicit stack handling
OBStopwatch	Stopwatch class used for timing length of execution
OBSymmetryData	Used to hold the point-group and/or space-group symmetry
OBTorsion	Used to hold the torsion data for a single rotatable bond and all four atoms around it
OBTorsionData	Used to hold torsions as generic data for OBMol
OBTypeTable	Atom Type Translation Table
OBUnitCell	Used for storing information about periodic boundary conditions with conversion to/from translation vectors and (a, b, c, alpha, beta, gamma)
OBVectorData	Used to hold a 3D vector item (e.g., a dipole moment)
OBVibrationData	Used to hold the normal modes of a molecule, etc
OBVirtualBond	Used to temporarily store bonds that reference an atom that has not yet been added to a molecule
OpTransform	Applies molecular transforms (OBChemTsfm class) read from a datafile
Pattern	A SMARTS parser internal pattern
patty	Programmable Atom Typer
quad	A 4-element templated, based on the design of the STL pair<>
SpaceGroup	Handle crystallographic space group symmetry
transform3d	Handle 3D transformations, such as space group definitions
triple	A 3-element templated, based on the design of the STL pair<>
vector3	Represents a vector in 3-dimensional real space
XMLBaseFormat	Abstract class containing common functionality for XML formats
XMLConversion	A subclass for conversion of XML formats
XMLMoleculeFormat	Abstract class for XML formats which represent molecules