Geoffrey Hutchison wrote:
 > Isn't there a way you could have multiple coordinate sets inside
 > <molecule></molecule> pairs?

You could store the various coordinates and energies as properties of a 
molecule... something along the lines of:

<molecule id="m1" xmlns="http://www.xml-cml.org/schema";
   xmlns:bo="http://www.blueobelisk.org/cml-dict";
   xmlns:xsd="http://www.w3.org/2001/XMLSchema";
   xmlns:avo="http://avogadro.openmolecules.net";>

   <atomArray> ... </atomArray>
   <bondArray> ... </bondArray>

   <propertyList convention="bo:conformers">

     <metadataList>
       <metadata name="software" content="avogadro">
       <metadata name="software-version" content="1.2.3">
     </metadataList>
     <parameterList>
       <parameter dictRef="avo:temperature"> ... </parameter>
     </parameterList>

     <propertyList id="conf1" convention="bo:conformer">
       <property dictRef="bo:coordinates">
         <matrix rows="14" cols="3" type="xsd:double"> ... </matrix>
       </property>
       <property dictRef="bo:energy">
         <scalar type="xsd:double" energy="bo:eV"> ... </scalar>
       </property>
     </propertyList>

     <propertyList id="conf2" convention="bo:conformer">
       ...
     </propertyList>

   </propertyList>

</molecule>


Sam


--
Unilever Centre for Molecular Science Informatics
Cambridge University Chemical Laboratories             Tel: 01223 763073
Lensfield Road                                    email: [email protected]
Cambridge CB2 1EW




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