Class List

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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
CairoPainter |
CharPtrLess | Case insensitive string comparison for PluginMapType key
OBCisTransStereo::Config | Stereochemical configuration for double-bond cis/trans stereochemistry
OBSquarePlanarStereo::Config | Stereochemical configuration for square planar stereocenters
OBTetrahedralStereo::Config | Stereochemical configuration for tetrahedral stereocenters
DeleteObject | Functor for deleting containers of pointers. Scott Meyers, Effective STL, Item 7
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< Extractor > | Delivers characters from an istream or streambuf from a source while filtering
FptIndex | Structure of fastsearch index files
FptIndexHeader | Header for fastsearch index file
OBIsomorphismMapper::Functor | Functor base class to be used in combination with MapGeneric
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
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)
OBAlign | Perform a least-squares alignment of two molecules or two vectors of vector3 objects
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
OBChargeModel | Atomic partial charge models
OBChemTsfm | SMARTS based structural modification (chemical transformation)
OBChiralData | Used to hold chiral inforamtion about the atom as OBGenericData
OBCisTransStereo | Class for handling and storing cis/trans stereochemistry
OBColor | Color class used by OBDepict
OBCommentData | Used to store a comment string (can be multiple lines long)
OBConformerData | Used to hold data on conformers or geometry optimization steps
OBConformerFilter | Interface used by OBConformerSearch for filtering conformers
OBConformerFilters | Class for combining OBConformerFilter objects
OBConformerScore | Interface used by OBConformerSearch for scoring conformers
OBConformerSearch | Conformer searching using genetic algorithm. See Conformer Searching
OBConversion | Class to convert from one format to another
OBDepict | 2D depiction of molecules using OBPainter
OBDescriptor | Base class for molecular properties, descriptors or features
OBDOSData | Used to hold density of states information
OBElectronicTransitionData | Used to hold information about electronic transitions
OBElement | Individual element data type
OBElementTable | Periodic Table of the Elements
OBEnergyConformerScore | A lowest energy conformer scoring class
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)
OBFontMetrics | Font metrics class used by OBDepict
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
OBGraphSym | Handle and perceive graph symmtery for canonical numbering
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
OBIsomorphismMapper | Abstract class defining interface for isomorphism (i.e. substructure) searches
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
OBMolBondBFSIter | Iterate over all bonds in an OBMol in a breadth-first search (BFS)
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
OBOrbital | Used to store energy, occupation, and orbital symmetry of a particular orbital
OBOrbitalData | Used to hold information about orbital energies
OBPainter | Abstract painter base class used by OBDepict
OBPairData | Used to store arbitrary text attribute/value relationships
OBPairTemplate< ValueT > | 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
OBQuery | A substructure query
OBQueryAtom | Atom in an OBQuery
OBQueryBond | Bond in an OBQuery
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
OBRMSDConformerScore | A RMSD conformer scoring class
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
OBSmartsMatcher | Internal class: performs matching; a wrapper around previous C matching code to make it thread safe
OBSmartsPattern | SMARTS (SMiles ARbitrary Target Specification) substructure searching
OBSpectrophore | Class to compute Spectrophores™
OBSqrtTbl | Square Root lookup table - given a distance squared returns distance
OBSquarePlanarStereo | Class for handling and storing square planar stereochemistry
OBSSMatch | Internal class: performs fast, exhaustive matching used to find just a single match in match() using recursion and explicit stack handling
OBStereo | Placeholder for enums & Ref/Refs related functions
OBStereoBase | Base class for all stereochemistry classes
OBStereoFacade | Facade to simplify retrieval of OBStereoBase derived objects
OBStereoUnit | Struct representing a single stereogenic unit
OBStericConformerFilter | A steric conformer filter class
OBStopwatch | Stopwatch class used for timing length of execution
OBSymmetryData | Used to hold the point-group and/or space-group symmetry
OBTetrahedralStereo | Class for handling and storing tetrahedral atom stereochemistry
OBTetraNonPlanarStereo | Base class for handling and storing non-planar stereochemistry with 4 reference atom ids
OBTetraPlanarStereo | Base class for handling and storing planar stereochemistry with 4 reference atoms
OBText | An object containing just text
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 reactions/transforms (OBChemTsfm class) read from a datafile
ParseState | A SMARTS parser internal state
Pattern | A SMARTS parser internal pattern
patty | Programmable Atom Typer
quad< T1, T2, T3, T4 > | 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< T1, T2, T3 > | 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

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