-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 29 April 2004 01:48, Miguel wrote: > Jmol v10 HEAD can now read *some* cml files on the Java 1.4 platform. > > This is an initial/simple implementation ... in fact it is quite a hack. > But the code is very small and is a start for me. > > I created a samples/cml subdirectory and moved *.cml into there. There are > a total of 6 files ... I am unable to read 2 of them. > > I can read neither methanol1.cml nor SN1_reaction.cml. They both die with > a null pointer exception somewhere down in the sax parser implementation. > Interestingly, both of these problem files are using the 'atomArray' > construct ... maybe that is a clue. > > Q: Egon, The last time I had difficulties you were able to very quickly > identify the problem. Can you try to load methanol1.cml and see what is > going on?
No problem. BTW, I would suggest that we make this new CMLReader CML2 only... and drop CML1 support. So I will review the examples too, and make them CML2 formated. (Though strictly speaking CML2 is CML1 compatible, so CML1 is automatically CML2 ... ). > Several of these files contain a "charge" value which is a float. > > <atom id="a1"> > <string builtin="elementType">C</string> > <coordinate3 builtin="xyz3">-2.2599 -8.0814 -4.2081</coordinate3> > <float title="charge">0.818317</float> > </atom> > > If I understood Peter's message from a few weeks ago, this is not valid > CML. Should be ok; it was valid CML1, and see comment above. Anyway, as said, I will transform them into common CML2. > Q: Peter, can you confirm that this is incorrect? > > Finally, I would appreciate it if Henry or Peter could send me a message > with a few attached CML files that are valid/compliant with current > standards. You can use OpenBabel or CDK and grep some MDL molfiles, and transform those in CML2. 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) iD8DBQFAkLQcd9R8I9Yza6YRAkTAAJ43ydrnmLGpeZCdB0+0mp1tTqLbLwCeOS4L bEOY62egcPUegkekDAuyh+o= =VTJV -----END PGP SIGNATURE----- ------------------------------------------------------- This SF.Net email is sponsored by: Oracle 10g Get certified on the hottest thing ever to hit the market... Oracle 10g. Take an Oracle 10g class now, and we'll give you the exam FREE. http://ads.osdn.com/?ad_id149&alloc_id�66&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
