Vibration Association

Example 1. (CML)


<!-- Molecule entity -->

<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>

<!-- Matrix entity -->

<eccpns:associate role="eccp:vibration">
<cml:matrix columns="3" dictRef="eccp:vibration_matrix" id="vib1">
-0.1710295      0.0000275      0.0358451
 0.0029979      0.3303069     -0.0915037
 0.1705754      0.0000402     -0.0358940
 0.2907602     -0.2253423      0.1641621
 0.3693960     -0.1054255     -0.2110303
-0.0029076      0.3292294      0.0919408
-0.2879387     -0.2249261     -0.1638394
-0.3669007     -0.1046491      0.2108522
</cml:matrix>
<cml:scalar dictRef="eccp:frequency" units="cm^{-1}">
983.3
</cml:scalar>
</eccpns:associate>

<!-- Link forming the vibration asociation -->

<link xmlns="http://grids.ac.uk/eccp/ns" xlink:role="http://grids.ac.uk/eccp/association/vibration">
<locator xlink:href="#xpointer(//cml:molecule[@id='mol1'])"/>
<locator xlink:href="#xpointer(//eccpns:associate[@role='eccp:vibration'][1])"/>
</link>

-- PhilipCouch - 10 Nov 2004

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Topic revision: r2 - 10 Nov 2004 - PhilipCouch
 
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