On 14/09/2011 14:18, Weerapong Phadungsukanan wrote: > Dear all, > > I found that if the white space characters are found before and not after > the root ending tag, babel will not be able to read the CML file properly > (even if they all represent the same molecule). Here is the command I used > to comvert the file > > babel -icml molecule.cml -osmi molecule.smi > > I have attached the test files, only the first one failed the conversion
I have fixed this bug in r4574 in the development code. There is another bug though. The molecule is a radical, but is not being recognized as such. (MarvinView also fails.) Because atoms in CML can have implicit hydrogen it is necessary to give extra assistance for alkoxy radicals (i.e. SMILES *[O]) by giving the O atom a radical="monovalent", spinMultiplicity="2" or hydrogenCount="0" attribute. The spinMultiplicity on the whole molecule is not enough and I suspect would require a lot of programming to make it sufficient in the general case and so would encourage the use of one of the attributes above on radical centers. Chris ------------------------------------------------------------------------------ BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA Learn about the latest advances in developing for the BlackBerry® mobile platform with sessions, labs & more. See new tools and technologies. Register for BlackBerry® DevCon today! http://p.sf.net/sfu/rim-devcon-copy1 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
