>> > Q: Can someone take the existing files and save them in CML format >> with >> > the same coordinates? >> > samples/caffeine.xyz >> > samples/aspirina.mol >> > samples/1crn.pdb > > These can also be converted to CML with OpenBabel.
Well, I have never compiled openbabel either ... another *barrier to entry*. > (http://openbabel.sf.net) This contains a complete set of examples of > conversion to and from the various dialects of CML. The dialects are: > > CML-1 deprecated for new applications but supported > CML-1-array deprecated for new applications but supported > > CML-2 probably the commonest now > CML-2-array > > There are two syntaxes for CML2. The first is more explicit and easier to > parse while the second is more compact. I have people who will not use CML > unless it is in array form and people who are the exact opposite. > Fortunately modern XML tools make this fairly easy to support. OK >> > Q: Where can I find other .cml files? > > See http://www.xml-cml.org I looked here about 10 days ago. As I recall I only saw fragments and small samples. Will look again. > and > > http://wwmm.ch.cam.ac.uk/moin/ChemicalMarkupLanguage. These pages will > have > the complete and emerging specs OK >> > Q: Can someone give me 25 word definitions of 'charge' vs. 'formal >> charge'? >> >>The formal charge is a charge indication given by humans, but molecules >>spread >>this charge over the atoms, leading to 'partial charges'. "Charge" can be >>both, but if having a decimal expect it to be a partial charge. > > "formalCharge" is an attribute of atom in CML and has precisely defined > semantics. "charge" is not part of CML and would have to have a non CML > namespace. So a file with a charge attribute is invalid. Good. Jmol cannot deal with fractional charge values anyway. >> > I am looking at cmlCore.pdf >> > When I look up the element 'atom' I see interesting attributes like >> > 'formalCharge' and 'occupancy'. But I do not see these defined in >> > cmlCore.pdf as elements. > > Where did you get cmlCore.pdf from? www.xml-cml.org >> > Q: Is there a tool that I should use to browse/read cmlCore.xsd? > > XML-spy has a demo version which you can use for a limited period. Have a > look on the http://www.w3.org pages fro XML schema. But we should have a > proper version of the PDF mounted OK Uhhh ... this is probably not news to you ... but I am finding the learning curve and the tools/infrastructure support for CML rather steep. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
