[Cdk-devel] valid cml file?

[Miguel <mi...@jm...>]

I have several questions about this CML file:

---begin---
<?xml version="1.0" encoding="UTF-8"?>
<molecule id="m1" xmlns="http://www.xml-cml.org/schema/cml2/core">

<atomArray>
        <atom elementType="C" id="a1" x2="330.35382" y2="217.0"/>
        <atom elementType="C" id="a2" x2="299.1769" y2="235.0"/>
        <atom elementType="C" id="a3" x2="268.0" y2="217.0"/>
        <atom elementType="C" id="a4" x2="268.0" y2="181.0"/>
        <atom elementType="C" id="a5" x2="299.1769" y2="163.0"/>
        <atom elementType="C" id="a6" x2="330.35382" y2="181.0"/>
</atomArray>

<bondArray id="b6">
        <bond atomRefs2="a2 a1"><scalar dataType="xsd:float"
title="order">1.5</scalar></bond>
        <bond atomRefs2="a3 a2"><scalar dataType="xsd:float"
title="order">1.5</scalar></bond>
        <bond atomRefs2="a4 a3"><scalar dataType="xsd:float"
title="order">1.5</scalar></bond>
        <bond atomRefs2="a5 a4"><scalar dataType="xsd:float"
title="order">1.5</scalar></bond>
        <bond atomRefs2="a6 a5"><scalar dataType="xsd:float"
title="order">1.5</scalar></bond>
        <bond atomRefs2="a6 a1"><scalar dataType="xsd:float"
title="order">1.5</scalar></bond>
</bondArray>

</molecule>

---end---

Ola generated it using CDK:

> Thanks for your answers. Here is my simple benzene 2D file,
> it was constructed with CDK in the following way:
>
>	SmilesParser sp = new SmilesParser();
>	Molecule m = sp.parseSmiles("c1ccccc1");
>
>	StructureDiagramGenerator sdg = new StructureDiagramGenerator();
>	sdg.setMolecule(m);
>	sdg.generateCoordinates();
>	Molecule m2 = sdg.getMolecule();
>
>	FileWriter output = new FileWriter("molecule.cml");
>	CMLWriter cmlwriter = new CMLWriter(output);
>	cmlwriter.write(molecule);
>	cmlwriter.close();

I have included the file inline:

Problem/Question:

I realize that these are 2D coordinates, but I expected the coordinates to
be in angstroms ... perhaps shortened or stretched to fit in a flat world.

Either these units are not angstroms or something is wrong ... the carbons
are 36.0 units apart.

Q: What units are used for 2D coordinates?


Regarding the bonds:

Q: Are these bonds defined in acceptable CML2 format? With the order
defined as a part of a scalar tag rather than as an attribute of the bond
tag?

Q: I assume that order==1.5 means aromatic ... please confirm.


Miguel