Egon -- that was a bug in BondCollection -- returning atomIndex, not
modelIndex. Fixed in SVN. Or use
int modelIndex =
set.getBondAt(bondIndex).getAtom1().getModelIndex();
On Fri, Oct 30, 2009 at 9:58 AM, Egon Willighagen <
[email protected]> wrote:
> Bob,
>
> I am using 11.8.7 in Jmol and writing CML serialization... my current
> code looks like (JmolMolecule actually just wraps a CMLMolecule):
>
> List<IJmolMolecule> mols = new ArrayList<IJmolMolecule>();
> ModelSet set = jmolPanel.getViewer().getModelSet();
> System.out.println("model count: " + set.getModelCount());
> Map<Integer,CMLMolecule> models = new
> HashMap<Integer,CMLMolecule>();
> for (int atomIndex=0; atomIndex<set.getAtomCount(); atomIndex++) {
> int modelIndex = set.getAtomModelIndex(atomIndex);
> System.out.println("modelindex: " + modelIndex);
> CMLMolecule model = models.get(modelIndex);
> if (model == null) {
> model = new CMLMolecule();
> models.put(modelIndex, model);
> }
> CMLAtom atom = new CMLAtom(set.getAtomName(atomIndex));
> atom.setElementType(set.getAtomLabel(atomIndex));
> Point3f coord = set.getAtomPoint3f(atomIndex);
> atom.setX3(coord.x);
> atom.setY3(coord.y);
> atom.setZ3(coord.z);
> model.addAtom(atom);
> System.out.println("Atom: " + atom.toXML());
> }
> for (int bondIndex=0; bondIndex<set.getBondCount(); bondIndex++) {
> int modelIndex = set.getBondModelIndex(bondIndex);
> System.out.println("modelindex: " + modelIndex);
> CMLMolecule model = models.get(modelIndex);
> if (model == null) {
> model = new CMLMolecule();
> models.put(modelIndex, model);
> }
> System.out.println("model: " + model.toXML());
> System.out.println("bond: " + bondIndex);
> System.out.println(" atom1: " +
> set.getBondAtom1(bondIndex).getAtomName());
> System.out.println(" atom2: " +
> set.getBondAtom2(bondIndex).getAtomName());
> CMLBond bond = new CMLBond(
>
> model.getAtomById(set.getBondAtom1(bondIndex).getAtomName()),
> model.getAtomById(set.getBondAtom2(bondIndex).getAtomName())
> );
> short order = set.getBondOrder(bondIndex);
> if (order == 1) bond.setOrder("s");
> if (order == 2) bond.setOrder("d");
> if (order == 3) bond.setOrder("t");
> model.addBond(bond);
> }
> for (CMLMolecule model : models.values())
> mols.add(new JmolMolecule(model));
> return mols;
>
> Now, this fails because the set.getBondModelIndex(bondIndex) is
> inconsistent...
>
> For the second atom, it actually returns model index = 2 while the
> model count is just 1:
>
> The above code gives to STDOUT:
>
> model count: 1
> modelindex: 0
> Atom: <atom id="C1" x3="-3.0290000438690186" y3="3.165299892425537"
> z3="-2.7702999114990234" />
> modelindex: 0
> Atom: <atom id="C2" x3="-2.1698999404907227" y3="2.392199993133545"
> z3="-3.8304998874664307" />
> modelindex: 0
> Atom: <atom id="C3" x3="-2.5147998332977295" y3="2.2920000553131104"
> z3="-1.2253999710083008" />
> modelindex: 0
> Atom: <atom id="C4" x3="-0.711199939250946" y3="2.7802999019622803"
> z3="-3.5488998889923096" />
> modelindex: 0
> Atom: <atom id="C5" x3="-0.7472000122070312" y3="2.002000093460083"
> z3="-1.2106000185012817" />
> modelindex: 0
> Atom: <atom id="C6" x3="-0.14259999990463257" y3="2.2487998008728027"
> z3="-2.3314998149871826" />
> modelindex: 0
> model: <molecule
> xmlns="http://www.xml-cml.org/schema";><atomArray><atom id="C1"
> x3="-3.0290000438690186" y3="3.165299892425537"
> z3="-2.7702999114990234" /><atom id="C2" x3="-2.1698999404907227"
> y3="2.392199993133545" z3="-3.8304998874664307" /><atom id="C3"
> x3="-2.5147998332977295" y3="2.2920000553131104"
> z3="-1.2253999710083008" /><atom id="C4" x3="-0.711199939250946"
> y3="2.7802999019622803" z3="-3.5488998889923096" /><atom id="C5"
> x3="-0.7472000122070312" y3="2.002000093460083"
> z3="-1.2106000185012817" /><atom id="C6" x3="-0.14259999990463257"
> y3="2.2487998008728027" z3="-2.3314998149871826"
> /></atomArray></molecule>
> bond: 0
> atom1: C1
> atom2: C2
> modelindex: 2
> model: <molecule xmlns="http://www.xml-cml.org/schema"; />
> bond: 1
> atom1: C3
> atom2: C1
>
> As you can see, the last modelIndex = 2, and does not allow me to look
> up the CMLMolecule matching that model number, resulting in the atoms
> C3 and C1 for the second atom not to be found, and consequently giving
> this CML error (because the CMLMolecule for the second 'model' does
> not contain any molecules, let alone C3 and C1):
>
> Caused by: java.lang.RuntimeException: Atoms in bond muct not be null
> at org.xmlcml.cml.element.CMLBond.<init>(CMLBond.java:190)
> at
> net.bioclipse.jmol.editors.JmolEditor.getJmolMolecules(JmolEditor.java:647)
> at
> net.bioclipse.jmol.business.JmolManager.getMolecules(JmolManager.java:142)
>
> I have no clue why the ModelSet return 2 for the second bond... the
> input is this MDL molfile:
>
>
> CDK 10/30/09,16:3
>
> 6 6 0 0 0 0 0 0 0 0999 V2000
> -3.0290 3.1653 -2.7703 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.1699 2.3922 -3.8305 C 0 0 0 0 0 0 0 0 0 0 0 0
> -2.5148 2.2920 -1.2254 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7112 2.7803 -3.5489 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.7472 2.0020 -1.2106 C 0 0 0 0 0 0 0 0 0 0 0 0
> -0.1426 2.2488 -2.3315 C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0 0 0 0
> 3 1 1 0 0 0 0
> 2 4 1 0 0 0 0
> 5 3 1 0 0 0 0
> 4 6 1 0 0 0 0
> 6 5 2 0 0 0 0
> M END
>
> Is this a bug in ModelSet.getBondModelIndex() or am I doing something
> wrong?
>
> Egon
>
> --
> Post-doc @ Uppsala University
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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ahead of the curve. Join us from November 9 - 12, 2009. Register now!
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