Difference: MoleculeExample (1 vs. 2)

Revision 210 Nov 2004 - PhilipCouch

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META TOPICPARENT name="DataRepresentations"
Molecule entity
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Question: What properties 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?
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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)

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Revision 110 Nov 2004 - PhilipCouch

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META TOPICPARENT name="DataRepresentations"
Molecule entity

Example 1. (CML)


<cml:molecule id="mol1">
<cml:atomArray>
<cml:atom id="a1" elementType="C" xyz3="0.0003482 0.9443707 0.0000000" />
<cml:atom id="a2" elementType="C" xyz3="-1.7820833 1.5720639 0.0000000" />
<cml:atom id="a3" elementType="C" xyz3="0.0003482 -0.9453544 0.0000000" />
<cml:atom id="a4" elementType="C" xyz3="0.8884300 1.5764903 -1.5436310" />
<cml:atom id="a5" elementType="C" xyz3="0.8884300 1.5764903 1.5436310" />
<cml:atom id="a6" elementType="C" xyz3="-1.7820833 -1.5730476 0.0000000" />
<cml:atom id="a7" elementType="C" xyz3="0.8915640 -1.5730476 -1.5436310" />
<cml:atom id="a8" elementType="C" xyz3="0.8915640 -1.5730476 1.5436310" />
</cml:atomArray>
</cml:molecule>

Question: What properties 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)


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

-- PhilipCouch - 10 Nov 2004

 
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