Charles Musgui wrote:
> Hello,
>
> I would like to know how I can interact with a protein model loaded
> within JMol. To be more precise, here is what I'd like to do, directly
> using the JMol API:
> 1. get the protein model, then get the Chain IDs contained in the
> model (I suppose here I handle a protein 3D structure)
> 2. get a particular Chain using its ID,
> 3. given the chain, get its protein sequence
>
> I've tried to understand the JMol API and I've found the package
> "org.jmol.modelsetbio", but I've failed to figure out how to retrieve
> a "BioModel" out of the JMolViewer.
>
Not all objects are public. Realize that in general multiple models may
be loaded, so even if you aren't doing that, getting the chain ids
themselves is a bit tricky. Still, a lot of the objects are public. The
primary public interface is via Viewer. you can refer to it as a
JmolViewer or Viewer. If via JmolViewer, then you are restricted to the
JmolViewer interface, which gives you several useful methods. If you
refer to it as Viewer, then you have many more public methods, BUT
realize that future Jmol development may modify the signatures of these
non-JmolViewer methods at a developer's whim. So...
JmolViewer methods:
abstract public int getModelCount();
abstract public int getDisplayModelIndex();
abstract public int getAtomCount();
abstract public int getBondCount();
abstract public int getGroupCount(); //for all models; DOES include
water "chain"
abstract public int getChainCount();
abstract public int getPolymerCount();
abstract public int getAtomCountInModel(int modelIndex);
abstract public int getBondCountInModel(int modelIndex);
abstract public int getGroupCountInModel(int modelIndex);
abstract public int getChainCountInModel(int modelIindex); //does NOT
include the water "chain"
abstract public int getPolymerCountInModel(int modelIndex);
So there you can get the number of chains in one or more models.
Viewer methods:
public ModelSet getModelSet() {
return modelSet;
}
public Hashtable getAllChainInfo(Object atomExpression) {
return modelSet.getAllChainInfo(getAtomBitSet(atomExpression));
}
This last should be all you need. It delivers information from methods
in modelset.ModelCollection:
public Hashtable getAllChainInfo(BitSet bs) {
Hashtable finalInfo = new Hashtable();
Vector modelVector = new Vector();
for (int i = 0; i < modelCount; ++i) {
Hashtable modelInfo = new Hashtable();
Vector info = getChainInfo(i, bs);
if (info.size() > 0) {
modelInfo.put("modelIndex",new Integer(i));
modelInfo.put("chains",info);
modelVector.addElement(modelInfo);
}
}
finalInfo.put("models",modelVector);
return finalInfo;
}
private Vector getChainInfo(int modelIndex, BitSet bs) {
Model model = models[modelIndex];
int nChains = model.getChainCount(true);
Vector infoChains = new Vector();
for(int i = 0; i < nChains; i++) {
Chain chain = model.getChain(i);
Vector infoChain = new Vector();
int nGroups = chain.getGroupCount();
Hashtable arrayName = new Hashtable();
for (int igroup = 0; igroup < nGroups; igroup++) {
Group group = chain.getGroup(igroup);
if (! bs.get(group.firstAtomIndex))
continue;
Hashtable infoGroup = new Hashtable();
infoGroup.put("groupIndex", new Integer(igroup));
infoGroup.put("groupID", new Short(group.getGroupID()));
infoGroup.put("seqCode", group.getSeqcodeString());
infoGroup.put("_apt1", new Integer(group.firstAtomIndex));
infoGroup.put("_apt2", new Integer(group.lastAtomIndex));
infoGroup.put("atomInfo1", getAtomInfo(group.firstAtomIndex));
infoGroup.put("atomInfo2", getAtomInfo(group.lastAtomIndex));
infoGroup.put("visibilityFlags", new
Integer(group.shapeVisibilityFlags));
infoChain.addElement(infoGroup);
}
if (! infoChain.isEmpty()) {
arrayName.put("residues",infoChain);
infoChains.addElement(arrayName);
}
}
return infoChains;
}
That covers just about anything you would want to get in relation to chains.
> Thanks for your help,
> Charles
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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