Dear Bob,
We are employing JMol API to parse some structure files in Jalview. For the
sake of flexibility and a bunch of other reasons, I'm generating sequences by
iterating through the atom collection from Jmol's API and then making residues
from significant atoms (i.e. CA or P atoms/hetatoms).
Now the problem is that sometimes extra unwanted residues are added to the
sequences. I've tracked down the problem to including CA HETATMs which falls
after the ‘TER' statement in a PDB file for a given chain to the list of
significant atoms. The snippet below shows the bit of code that converts
significant atoms from Jmol’s data model to Jalview’s data model.
private List<Atom> convertSignificantAtoms(ModelSet ms)
{
List<Atom> significantAtoms = new ArrayList<Atom>();
for (org.jmol.modelset.Atom atom : ms.at)
{
if (atom.getAtomName().equalsIgnoreCase("CA")
|| atom.getAtomName().equalsIgnoreCase("P"))
{
Atom curAtom = new Atom(atom.x, atom.y, atom.z);
curAtom.atomIndex = atom.getIndex();
curAtom.chain = atom.getChainIDStr();
curAtom.insCode = atom.group.getInsertionCode();
curAtom.name = atom.getAtomName();
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
significantAtoms.add(curAtom);
}
}
return significantAtoms;
}
Is there an existing method in Jmol to determine if an atom is before TER
record of its chain? if such method exists say atom.isBeforeChainTER(). Then
modifying the snippet above as below would ignore insignificant CA and P
HETATMs and would solve the problem.
private List<Atom> convertSignificantAtoms(ModelSet ms)
{
List<Atom> significantAtoms = new ArrayList<Atom>();
for (org.jmol.modelset.Atom atom : ms.at)
{
if (atom.getAtomName().equalsIgnoreCase("CA")
|| atom.getAtomName().equalsIgnoreCase("P"))
{
if (atom.isHetero() && !atom.isBeforeChainTer())
{
continue;
}
Atom curAtom = new Atom(atom.x, atom.y, atom.z);
curAtom.atomIndex = atom.getIndex();
curAtom.chain = atom.getChainIDStr();
curAtom.insCode = atom.group.getInsertionCode();
curAtom.name = atom.getAtomName();
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumber = atom.getResno();
curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
.getIndex()] : Float.valueOf(atom.getOccupancy100());
curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
significantAtoms.add(curAtom);
}
}
return significantAtoms;
}
I don’t know if this is the best way to go about this. I’m looking forward to
your prompt reply as usual and would welcome alternative solutions.
Thanks and regards,
Charles
Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
School of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org<http://www.jalview.org/>
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/>
The University of Dundee is a registered Scottish Charity, No: SC015096
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