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#1140 Mol2Writer throwing NullPointerException

cdk-1.4.x
closed
nobody
None
9
2012-11-03
2011-06-12
Egon Willighagen
No

From the user mailing list:

"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))))

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."

Discussion

  • Rajarshi Guha

    Rajarshi Guha - 2011-06-19

    Can't reproduce the NPE. Added a test case and the suggested test data file.

    (However, the fact that the P is not typed still remains)

     

  • SourceForge Robot

    SourceForge Robot - 2011-07-03

    This Tracker item was closed automatically by the system. It was
    previously set to a Pending status, and the original submitter
    did not respond within 14 days (the time period specified by
    the administrator of this Tracker).