mySQL Tables

The fundamental governing principle of JThermodynamics is flexibility by having as little 'hard-coded' chemical information as possible. This is accomplished by the extenisve use of substructures and their association with their thermodynamic contribution. The key to implementing this principle is the use of a database of chemical and structural information. A commonly used database within information technology is the mySQL database. The mySQL database is an industry standard and has multiple platform independent interfaces. Within the JAVA implementation of JThermodynamics the mySQL database is queried and managed. However, due to its ubiquitous nature, mySQL also offers multiple interfaces, regardless of computer platform.

Tables of information

The different sets of database information is arranged in mySQL in tables.

  • AtomCounts: In order to facilitate the detection of the same molecule, every molecule has associated with it the number of atoms of each type (atom counts).

  • BondLength: The 'standard' bond lengths of atom pairs.

  • CMLStructures: The molecular structures used within JThermodynamics stored in CML form.

  • DatabaseMolecule: The structure of molecules in CML form.

  • DisassociationEnergy: The hydrogen disassociation value of a radical

  • GroupElement: The Benson atom structure information

  • GroupStandardEnthalpy: The enthalpy associated with the Benson atom

  • GroupStandardEntropy: The entropy association with the Benson atom

  • HeatCapacityElement: The set of temperature dependent heat capacity values

  • MetaAtomInfo: Definition of a meta-atom

  • Molecule

  • NameListSet

  • ReferenceTag

  • SourceTag

  • StructureAtom

  • StructureBond:

  • StructureType: Gives the connection between the CML structure and the type of structure it represents.

  • SymmetryDefinition: Relates a structure to the type of symmetry and the resulting symmetry factor.

  • SymmetryPairAssignments: Atom pairings between the CML structure and the symmetry

  • Vectors:

  • VibrationalStructures: Pairs the CMLStructure with the vibrational frequency and symmetry.