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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