| _AtomExpr | An internal (SMARTS parser) atomic expression |
| _BondExpr | An internal (SMARTS parser) bond expression |
| AtomSpec | An internal (SMARTS parser) atom specification |
| BondSpec | An internal (SMARTS parser) bond specification |
| CharPtrLess | Case insensitive string comparison for FormatsMap 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) |
| 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 |
| OBAtomTyper | Assigns atom types, hybridization, implicit valence and formal charges |
| OBBase | Base Class |
| OBBitVec | Fast and efficient bitstring class |
| OBBond | Bond class |
| OBBondTyper | Assigns bond types for file formats without bond information |
| 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 |
| 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) |
| OBFFCalculation | Internal class for OBForceField to hold energy and gradient calculations on specific force fields |
| OBFFParameter | Internal class for OBForceField to hold forcefield parameters |
| OBFingerprint | The base class for fingerprints |
| OBFloatGrid | Handle 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 |
| OBGroupContrib | Handle group contribution algorithms |
| OBInternalCoord | Used to transform from z-matrix to cartesian coordinates |
| OBIsotopeTable | Table of atomic isotope masses |
| obLogBuf | A minimal streambuf derivative to wrap calls to cerr into calls to OBMessageHandler as needed |
| OBLogP | Calculate the LogP (octanol/water partition coefficient) |
| 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 |
| OBMR | Calculate the MR (molar refractivity) |
| OBNasaThermoData | Thermodynamic data in old style NASA polynomial form for OBMol |
| 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() |
| OBProxGrid | A grid for determining the proximity of a given point to atoms in an OBMol |
| OBPSA | Calculate the TPSA (topological polar surface area) |
| 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() |
| OBRotamerList | Supports a set of rotamer coordinate sets for some number of potentially rotatable bonds |
| OBRotor | A single rotatable OBBond as part of rotamer searching |
| 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) |
| 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 |
| Pattern | A SMARTS parser internal pattern |
| patty | Programmable Atom Typer |
| PluginIter | Template class used to simplify dynamic classes discovered at runtime |
| quad | A 4-element templated, based on the design of the STL pair<> |
| 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 |
This file is part of the documentation for Open Babel, version 2.1.0.
1.5.2.