-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 01 April 2004 01:05, Miguel wrote: > I am trying to learn about CML > > There are only a few examples of .cml files in the Jmol samples directory. > > Q: Can someone look at these files and tell me whether or not they are > good examples for me to be working with? > 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
Will do at the end of today... > Q: Where can I find other .cml files? cdk/data/cml* *And* cdk/src/org/openscience/cdk/test/io/cml/cmlTestFramework.xml The latter validates if opened with jEdit which has the XML plugin installed. > samples/estron.cml and samples/glycine-crystal.cml have 'charge' values > that are decimal values. When I look at > http://www.xml-cml.org/dtdschema/cmlCore/EXAMPLES/concatenated.xml I see > 'formalCharge' references which are integers. > > 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. > Q: Why are there no references to 'charge' in concatenated.xml? Don't know. > 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. Elements are different than attributes... like in HTML <atom occupancy="0.5"/> Element atom has attribute occupancy. > Q: Is this just a documentation problem? > > I can search cmlCore.xsd and fine these attributes. > > Q: Is there a tool that I should use to browse/read cmlCore.xsd? The cmlCore schema is very big, but you could use jEdit with the XML plugin installed and the plugin which has the Structure Browser plugin window... The latter will give you a very nice browsing tree... Egon - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAa7C+d9R8I9Yza6YRAhwiAJ9luThxHFVz8s/13NWoBojjlvDaywCgvW6q 8okWMh6A1dK4H+2Yn42mJTM= =nB+s -----END PGP SIGNATURE----- ------------------------------------------------------- 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_id70&alloc_id638&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
