I don't think we need to worry about the naming conventions of corner cases
just yet. Taking something basic, ethane in cml
<molecule>
<atomArray>
<atom id="a1" elementType="C" x3="0.229656" y3="0.720147" z3="-0.015085"/>
<atom id="a2" elementType="C" x3="-0.229656" y3="-0.720147" z3="0.015085"/>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
</bondArray></molecule>
and my translation to json
{
"atoms": {
"a1": { "element type": "C", "x3": 0.229656, "y3": 0.720147,
"z3": -0.015085 },
"a2": { "element type": "C", "x3": -0.229656, "y3": -0.720147,
"z3": 0.015085 }
}
"bonds": [
{"atom refs": ["a1", "a2"], "order": 1}
]}
it could use some cleaning up, but that's the idea.
On Fri, Jun 7, 2013 at 12:50 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:
> On 06/07/2013 12:25 PM, Patrick Fuller wrote:
>
> > Geoff - Outside of some fairly minor issues, xml translates easily to
> json.
> > Could the chemical xml specification just be translated to json?
>
> If you gloss over things like #[P]CDATA, (elt+), (#CDATA|(foo,bar,baz)),
> it's trivial. Except for attributes: if you have bad xml, like <atom
> idx="1" id="C"/> instead of <atom><idx>1</idx><id>C</id></atom>, then it
> isn't.
>
> --
> Dimitri Maziuk
> Programmer/sysadmin
> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>
>
>
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