Classes Overview

Chemical Storage and Manipulation:

• OBBase - General base class of OBAtom, OBMol, OBResidue, etc. for storing generic, arbitrary custom data
  • OBMol - Central molecule class, properties, ...
  • OBAtom - Central atom class, properties, coordinates, ...
  • OBBond - Bond connection between two OBAtom, properties, bond orders, ...
  • OBResidue - Biomolecule residues (amino acids, nucleic acids)
  • OBReaction - Used to store chemical reactions (i.e., reactants -> products)
  • OBGrid - A base grid class (e.g., 3D functions like electrostatic potential, evaluated on a grid)
  • OBText - An object containing just text
• OBRing - Ring cycle perception, Smallest Set of Smallest Rings (SSSR), Largest Set of Smallest Rings (LSSR)

Import / Export:

• OBConversion - Conversion between file formats. Interface for import or export
• OBFormat - Parent class for file format types for any sort of data

Chemical Utilities:

• OBFingerprint - Generating molecular fingerprints for databases and similarity searches
• OBForceField - Molecular mechanics force fields for energy evaluation, conformational searching, coordinate generation, etc.
• OBChemTsfm - SMARTS based structural modification (chemical transformation)

Substructure Searching:

• OBSmartsPattern - Parsing SMARTS chemical search patterns and matching against OBMol objects
• OBQuery
• OBQueryAtom
• OBQueryBond
• OBIsomorphismMapper

Utility Classes:

• OBBitVec - Efficient bit vector (e.g., for marking visit to atoms)
• OBMessageHandler - Error and warning handling, filtering, and logging
• OBRandom - Random number generator
• OBStopwatch - Stopwatch class used for timing length of execution
• OBSqrtTbl - Square Root lookup table - given a distance squared returns distance

Coordinate Manipulation:

• OBBuilder - 3D structure generation
• OBAlign - Kabsch alignment
• OBInternalCoord - Internal coordinates
• OBConformerSearch - Conformer searching using genetic algorithm
• OBRotorList - Class for detecting rotatable bonds
• OBRotamerList - Supports a set of rotamer coordinate sets for some number of potentially rotatable bonds

Stereochemistry:

• OBStereo
• OBStereoBase
  • OBTetraNonPlanarStereo
    • OBTetrahedralStereo
  • OBTetraPlanarStereo
    • OBCisTransStereo
    • OBSquarePlanarStereo
• OBStereoFacade

Arbitrary Data:

• OBGenericData - General base class for arbitrary data types
  • OBPairData - Arbitrary text key/value data
  • OBPairTemplate - Arbitrary T key/value data
  • OBUnitCell - Storage and manipulation of crystal structure / reciprocal unit cells
  • AliasData, OBAngleData, OBCommentData, OBConformerData, OBDOSData, OBElectronicTransitionData, OBExternalBondData, OBGridData, OBMatrixData, OBNasaThermoData, OBOrbitalEnergyData, OBPairData, OBRateData, OBRingData, OBRotamerList, OBRotationData, OBSerialNums, OBSetData, OBStereoBase, OBSymmetryData, OBTorsionData, OBUnitCell, OBVectorData, OBVibrationData, OBVirtualBond

Plugins:

• OBPlugin
  • OBChargeModel - assign partial (and formal) charges to a molecule
  • OBDescriptor - molecular properties, descriptors or features for filtering or searching
  • OBFingerprint - condensed representations of molecules as a set of bits
  • OBForceField - implementation of molecular mechanics force field methods
  • OBFormat - file formats for chemical data
  • OBOp - operation for modifying a molecule or file (e.g., adding hydrogens)

Math Utilities:

• matrix3x3 - Square 3x3 matrices for 3D transformations and rotations
• vector3 - 3D vector class for translations and planes