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#1142 another phosphor not properly recognized

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Egon Willighagen
cdk-atomtype (42)
5
2012-10-08
2011-06-19
Egon Willighagen
No

"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."

See PDB entry: 1a0i

Discussion

  • Rajarshi Guha

    Rajarshi Guha - 2011-06-19

    Can you provide an example file containing this atom type. Or example code

     

  • Egon Willighagen

    Egon Willighagen - 2011-06-19

    The example data is the PDB file (see mailing list). The quote was copied from an email on (I think) the -user ML.