Hi Christian, On Fri, Jun 3, 2011 at 4:18 PM, Christian Spiteri <[email protected]> wrote: > I'm using Mol2Writer to write a molecule to a file, and it's working > fine until I happen to run into this type of atom: > > Atom(860069, S:P, 3D:[(47.423, 10.1752, 27.0577)], AtomType(860069, > N:P.3, FC:0, H:SP3, NC:0, EV:0, Isotope(860069, Element(860069, S:P, > ID:P))))
Can you share (as LGPL preferably so that we can use it for a unit test) the full structure, or point to a PubChem entry? Phosphors are currently somewhat underrepresented in the CDK atom type list. We have a few bug reports about that already, but your example may not be captured by those examples. That would be problem 1. > in which case it throws a NullPointerException. This is being caused > by SybylAtomTypeMatcher (called at Mol2Writer:257), which is not > finding any matches for P.3. I'm not sure if this is a bug, but any > help would be much appreciated. The second problem is that even if this happens, the mol2 writer should probably not fail on that, but just use the generic unknown atom type in writing. That I filed as a bug report (basically just copying your email) as: https://sourceforge.net/tracker/?func=detail&aid=3315503&group_id=20024&atid=120024 I hope someone can look at it soon. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensure content is compliant with Accessibility Checking. http://p.sf.net/sfu/ephox-dev2dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
