import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
-import jalview.datamodel.DBRefSource;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
import jalview.util.MessageManager;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Vector;
@Override
public void parse() throws IOException
{
- String dataName = getDataName();
- if (dataName.endsWith(".cif"))
- {
- setDbRefType(DBRefSource.MMCIF);
- }
- else
- {
- setDbRefType(DBRefSource.PDB);
- }
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
if (getId() == null)
{
- setId(inFile.getName());
+ setId(safeName(getDataName()));
}
for (PDBChain chain : getChains())
{
prot.add(chainseq);
}
- if (StructureViewSettings.isPredictSecondaryStructure())
+ if (StructureImportSettings.isProcessSecondaryStructure())
{
createAnnotation(chainseq, chain, ms.at);
}
private List<Atom> convertSignificantAtoms(ModelSet ms)
{
List<Atom> significantAtoms = new ArrayList<Atom>();
+ HashMap<String, org.jmol.modelset.Atom> chainTerMap = new HashMap<String, org.jmol.modelset.Atom>();
+ org.jmol.modelset.Atom prevAtom = null;
for (org.jmol.modelset.Atom atom : ms.at)
{
if (atom.getAtomName().equalsIgnoreCase("CA")
|| atom.getAtomName().equalsIgnoreCase("P"))
{
+ if (!atomValidated(atom, prevAtom, chainTerMap))
+ {
+ 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.insCode = atom.group.getInsertionCode() == '\000' ? ' '
+ : atom.group.getInsertionCode();
curAtom.name = atom.getAtomName();
curAtom.number = atom.getAtomNumber();
curAtom.resName = atom.getGroup3(true);
curAtom.resNumIns = "" + curAtom.resNumber + curAtom.insCode;
curAtom.tfactor = atom.getBfactor100() / 100f;
curAtom.type = 0;
- significantAtoms.add(curAtom);
+ // significantAtoms.add(curAtom);
+ // ignore atoms from subsequent models
+ if (!significantAtoms.contains(curAtom))
+ {
+ significantAtoms.add(curAtom);
+ }
+ prevAtom = atom;
}
}
return significantAtoms;
}
+ private boolean atomValidated(org.jmol.modelset.Atom curAtom,
+ org.jmol.modelset.Atom prevAtom,
+ HashMap<String, org.jmol.modelset.Atom> chainTerMap)
+ {
+ // System.out.println("Atom: " + curAtom.getAtomNumber()
+ // + " Last atom index " + curAtom.group.lastAtomIndex);
+ if (chainTerMap == null || prevAtom == null)
+ {
+ return true;
+ }
+ String curAtomChId = curAtom.getChainIDStr();
+ String prevAtomChId = prevAtom.getChainIDStr();
+ // new chain encoutered
+ if (!prevAtomChId.equals(curAtomChId))
+ {
+ // On chain switch add previous chain termination to xTerMap if not exists
+ if (!chainTerMap.containsKey(prevAtomChId))
+ {
+ chainTerMap.put(prevAtomChId, prevAtom);
+ }
+ // if current atom belongs to an already terminated chain and the resNum
+ // diff < 5 then mark as valid and update termination Atom
+ if (chainTerMap.containsKey(curAtomChId))
+ {
+ if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ {
+ chainTerMap.put(curAtomChId, curAtom);
+ return true;
+ }
+ return false;
+ }
+ }
+ // atom with previously terminated chain encountered
+ else if (chainTerMap.containsKey(curAtomChId))
+ {
+ if ((curAtom.getResno() - chainTerMap.get(curAtomChId).getResno()) < 5)
+ {
+ chainTerMap.put(curAtomChId, curAtom);
+ return true;
+ }
+ return false;
+ }
+ // HETATM with resNum jump > 2
+ return !(curAtom.isHetero() && ((curAtom.getResno() - prevAtom
+ .getResno()) > 2));
+ }
+
private void createAnnotation(SequenceI sequence, PDBChain chain,
org.jmol.modelset.Atom[] jmolAtoms)
{