I was delighted to see that both Jmol and JChempaint manage nested molecules in CML. As an example:
<molecule id="ambf4" title="ammonium tetrafluoroborate">
<molecule id="nh4">
<atomArray>
<atom id="n" elementType="N" hydrogenCount="4" formalCharge="1"/>
</atomArray>
</molecule>
<molecule id="bf4">
<atomArray>
<atom id="a1" elementType="B" formalCharge="-1"/>
<atom id="a2" elementType="F"/>
<atom id="a3" elementType="F"/>
<atom id="a4" elementType="F"/>
<atom id="a5" elementType="F"/>
</atomArray>
<bondArray>
<bond id="b1" atomRefs2="a1 a2"/>
<bond id="b2" atomRefs2="a1 a3"/>
<bond id="b3" atomRefs2="a1 a4"/>
<bond id="b4" atomRefs2="a1 a5"/>
</bondArray>
</molecule>
</molecule>I have omitted coordinates...
In Jmol the display correctly renders all the atoms in the correct relative positions
In JChempaint it creates two separate "frames" with 2D coordinates local to each.
Firstly, many thanks - exactly what is wanted and I hadn't realised it had been done
The only problem is the layout of the separate molecules in JChempaint - only one is ever visible at once. Could the user have controls to select (say) 4 molecules per row and make the rows closer together? Perhaps the preferences can be set in the .jchempaint directory?
I have developed a set of software (not completely tested) which reads a file, splits it into molecules, and creates a final CML output files with new layout and nested molecules.
I think this general area of multiple molecules (either nested, or in a list, or different conformations, etc.) is going to be an important aspect of these programs
P.
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