The CMLStructure table is the mySQL table storing the structures and substructures used by JThermodynamics.
CMLStructures have the following fields:
ElementName: The keyword corresponding to the structure. This keyword is used in other SQL tables to reference the structure. This could be a molecule name, such as ch3/co/ch3, a benson structure, such as c-(h)/3-(c) or a substructure, such as GeneralCarbonAtom.
CMLStructure: This is the CML form of the structure, which is an XML ASCII representation of a 2-D (bonds and connectivity) structure.
Source: This is a keyword specifying the source of the structure. A common ''source'' is '''Standard''' which means that the structure is part of the standard database. The source can be used to differential, for example, new data from a new source or for testing purposes. It is convenient to use because then the data associated with a given source can be referenced (or even erased) in a block.
These structures are put into this table in conjunction with other table entries. The correspondence with this table and other tables is through the entry ElementName. This name not only appears in this table, but also the corresponding information table.
For example, the table entry for a radical on the primary has the ElementName as PrimaryCarbonRadical and the Source as Standard. The CML structure looks like:
<?xml version="1.0" encoding="ISO-8859-1"?>
<molecule id="PrimaryCarbonRadical" xmlns="http://www.xml-cml.org/schema">
<atomArray>
<atom id="a0" elementType="C" formalCharge="0" spinMultiplicity="2"/>
<atom id="a1" elementType="H" formalCharge="0"/>
<atom id="a2" elementType="H" formalCharge="0"/>
<atom id="a3" elementType="C" formalCharge="0"/>
</atomArray>
<bondArray>
<bond id="b1" atomRefs2="a1 a0" order="S"/>
<bond id="b2" atomRefs2="a2 a0" order="S"/>
<bond id="b3" atomRefs2="a3 a0" order="S"/>
</bondArray>
</molecule>
This structure is used to identify a primary carbon radical. The radical carbon, with the spinMultiplicity="2", is connected to two other hydrogens and one other carbon. The non-radical carbon is not shown with any bonds, so it matches any carbon in this position.