-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Tuesday 23 November 2004 16:26, Miguel wrote: > Some file types do not have bond information. Jmol runs an 'autobond' > algorithm based upon covalent bonding distances with some slop. The > algorithm is derived from OpenBabel. > > I recently 'enhanced' this algorithm by placing some upper limits on the > number of bonds that would form. For example, carbon bonds to 4 things and > Xenon bonds to 0 things. > > In large part, I did this because someone created a pathological case of a > mesh of closely-spaced atoms, where each atom was bonded to hundreds of > other atoms. I also did it because of feedback that I got from the > OpenBabel team ... who know much more about bonding than I do. > > The autobonding (and these limits) *only* apply to files that do not > specify bond information. > > I am now hearing feedback that my so-called 'enhancement' is a problem.
It's an atom typing problem... which involves things like formal charge, hybridization, element type, bond orders, etc... not trivial. If it is giving problems, I would say drop it... in your words: Jmol is a display program only. People should not make pathological cases and then expect programs to understand weird things... Egon - -- [EMAIL PROTECTED] - --------------------------------------- CDK: http://cdk.sf.net/ JChemPaint: http://jchempaint.sf.net/ Jmol: http://www.jmol.org/ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFBo1g1d9R8I9Yza6YRAus0AKCEKNylHM/XPrkNELVh6BJSZzh4EwCeJCbA gPf9EfbNuYXgcMDZSBTjh4Y= =GEsa -----END PGP SIGNATURE----- ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://productguide.itmanagersjournal.com/ _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
