Hi Daniel,
On Thursday 04 January 2007 11:03, Daniel Gottstein wrote:
> I'm a Bioinformatics student from Frankfurt and currently working on a
> project in which I need to add Hydrogens to a PDBfile. The problem I'm
> experiencing is that the HydrogenAdder() Class object seems to be adding
> too many Hydrogens to the Molecule I've extracted from the pdbfile.
> Assuming I've extracted the first model from the 1fjs.pdb file.
>
> InputStream pdbfile =
> this.getClass().getClassLoader().getResourceAsStream("1FJS.pdb");
<snip>
The code is generally OK, except for one thing...
> This is my output
>
> before h2add:
> 2475
> after h2add:
> 5927
PDB files normally do not have bonds defined, and basically consist of a cloud
of atoms. The HydrogenAdder, however, assumes things to be bonded. For
example, an unbonded oxygen will get 2 hydrogen (to form water), which will
likely be the carbonyl-oxygen of the backbone with zero hydrogens!
> I compared these results with the pymol h_add() method and received the
> following...:
>
> PyMOL>print cmd.count_atoms()
> 2475
> PyMOL>cmd.h_add()
> PyMOL>print cmd.count_atoms()
> 5062
>
> ... meaning my java code must be adding about 900 additional Hydrogens
> (assuming the correctness of the pymol results).
>
> Is there a mistake in my java code? Or have I forgotten something?
You should run the RebondTool [1] prior to adding hydrogens. This tool
requires vanderwaals radii to be assigned to the atoms, so the full use looks
like this:
RebondTool rebonder = new RebondTool(2.0, 0.5, 0.5);
Molecule methane = new Molecule();
methane.addAtom(new Atom("C", new Point3d(0.0, 0.0, 0.0)));
methane.addAtom(new Atom("H", new Point3d(0.6, 0.6, 0.6)));
methane.addAtom(new Atom("H", new Point3d(-0.6, -0.6, 0.6)));
methane.addAtom(new Atom("H", new Point3d(0.6, -0.6, -0.6)));
methane.addAtom(new Atom("H", new Point3d(-0.6, 0.6, -0.6)));
try {
// configure atoms
AtomTypeFactory factory =
AtomTypeFactory.getInstance(
"org/openscience/cdk/config/data/jmol_atomtypes.txt",
methane.getBuilder()
);
for (int i=0; i<methane.getAtomCount(); i++) {
factory.configure(methane.getAtom(i));
}
// rebond
rebonder.rebond(methane);
} catch (Exception exception) {
fail()
}
(taken from cdk.test.graph.rebond.RebondToolTest).
> I'd be thankful for every hint I can get.
Please let me know, how many hydrogens are added *after* the use of the
RebondTool.
Egon
1.http://cdk.sourceforge.net/api/org/openscience/cdk/graph/rebond/RebondTool.html
--
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Cologne University Bioinformatics Center (CUBIC)
Blog: http://chem-bla-ics.blogspot.com/
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