Re: [Open Babel] CML bugs

[Peter Murray-R. <pm...@ca...>]

At 10:02 20/09/2003 +0100, Chris Morley wrote:

>2) With the new version of cml.cpp I seem to get an error message with this
>(and every CML2 file I have tried):
>
><molecule xmlns="http://www.xml-cml.org" id="m1">
>   <atomArray>
>     <atom id="a1" elementType="C" />
>     <atom id="a2" elementType="C" />
>     <atom id="a3" elementType="C" />
>     <atom id="a4" elementType="C" />
>   </atomArray>
>   <bondArray>
>     <bond atomRefs2="a1 a2" order="2"/>
>     <bond atomRefs2="a2 a3" order="1"/>
>     <bond atomRefs2="a3 a4" order="D"/>
>   </bondArray>
></molecule>
>
>The error message is:
>afterStartAtomArray 0
>atomRef arrays must be given for bonds
>
>but the output files (in cml2 mol or smi) seems ok

I hope I have mended the error. It occurred with CML1+array files. (I can't 
see anything wrong with the above). I have run the roundtrip and it should 
work anyway. Pleas let me know if it's OK.

NB. the attributes are confusing, though logical.

atomRef refers to a single atom (or in <fooArray> to an array of atoms when 
only one atomRef is required per array element)
CML1 with bondArray/bond uses two <string builtin="atomRef"/> elements

atomRef1 only occurs in CML2+bondArray and refers to the first atom in the 
bonds
atomRef2 only occurs in CML2+bondArray and refers to the second atom in the 
bonds

atomRefs is a variable length array of references to atoms
atomRefs2 is a 2-element array of references to atoms (e.g in CML2+bond or 
length)
atomRefs3 is a 3-element array of references to atoms (e.g in angle)
atomRefs4 is a 4-element array of references to atoms (e.g in torsion)

It is easy to get these wrong. The examples in test/cmltest should now be 
definitive

P.