Molecule entity

Example 1. (CML)


<molecule xmlns="http://www.xml-cml.org/schema/cml2/comp" id="mol1">
<atomArray>
<atom id="a1" elementType="C" xyz3="0.0003482 0.9443707 0.0000000" />
<atom id="a2" elementType="C" xyz3="-1.7820833 1.5720639 0.0000000" />
<atom id="a3" elementType="C" xyz3="0.0003482 -0.9453544 0.0000000" />
<atom id="a4" elementType="C" xyz3="0.8884300 1.5764903 -1.5436310" />
<atom id="a5" elementType="C" xyz3="0.8884300 1.5764903 1.5436310" />
<atom id="a6" elementType="C" xyz3="-1.7820833 -1.5730476 0.0000000" />
<atom id="a7" elementType="C" xyz3="0.8915640 -1.5730476 -1.5436310" />
<atom id="a8" elementType="C" xyz3="0.8915640 -1.5730476 1.5436310" />
</atomArray>
</molecule>

Question: What data should be included as part of the molecule entity? For example, should the molecular name, charge and spin multiplicity be included (example 2), or should they be associated by links?

Example 2. (CML)


<molecule xmlns="http://www.xml-cml.org/schema/cml2/comp" id="mol1">
<name convention="SMILES">CC</cml:name>
<scalar dictRef="eccp:charge">1</cml:scalar>
<scalar dictRef="eccp:spinMultiplicity">1</cml:scalar>
<atomArray>
<atom id="a1" elementType="C" xyz3="0.0003482 0.9443707 0.0000000" />
<atom id="a2" elementType="C" xyz3="-1.7820833 1.5720639 0.0000000" />
<atom id="a3" elementType="C" xyz3="0.0003482 -0.9453544 0.0000000" />
<atom id="a4" elementType="C" xyz3="0.8884300 1.5764903 -1.5436310" />
<atom id="a5" elementType="C" xyz3="0.8884300 1.5764903 1.5436310" />
<atom id="a6" elementType="C" xyz3="-1.7820833 -1.5730476 0.0000000" />
<atom id="a7" elementType="C" xyz3="0.8915640 -1.5730476 -1.5436310" />
<atom id="a8" elementType="C" xyz3="0.8915640 -1.5730476 1.5436310" />
<atomArray>
</molecule>

-- PhilipCouch - 10 Nov 2004

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Topic revision: r2 - 10 Nov 2004 - PhilipCouch
 
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