import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.io.FileParse;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureImportSettings;
+import jalview.util.Format;
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;
{
Viewer viewer = null;
- public JmolParser(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- String inFile, String type) throws IOException
+ public JmolParser(String inFile, String type) throws IOException
{
super(inFile, type);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
- }
-
- public JmolParser(boolean addAlignmentAnnotations,
- boolean predictSecondaryStructure, boolean externalSecStr,
- FileParse fp) throws IOException
- {
- super(fp);
- this.visibleChainAnnotation = addAlignmentAnnotations;
- this.predictSecondaryStructure = predictSecondaryStructure;
- this.externalSecondaryStructure = externalSecStr;
}
public JmolParser(FileParse fp) throws IOException
super(fp);
}
- public JmolParser(String inFile, String type) throws IOException
- {
- super(inFile, type);
- }
-
public JmolParser()
{
}
@Override
public void parse() throws IOException
{
-
setChains(new Vector<PDBChain>());
Viewer jmolModel = getJmolData();
jmolModel.openReader(getDataName(), getDataName(), getReader());
*/
if (jmolModel.ms.mc > 0)
{
+ // ideally we do this
+ // try
+ // {
+ // setStructureFileType(jmolModel.evalString("show _fileType"));
+ // } catch (Exception q)
+ // {
+ // }
+ // ;
+ // instead, we distinguish .cif from non-.cif by filename
+ setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
+ .toString() : "PDB");
+
transformJmolModelToJalview(jmolModel.ms);
}
}
{
try
{
+ /*
+ * params -o (output to sysout) -i (no info logging, less verbose)
+ * -n (nodisplay) -x (exit when finished)
+ * see http://wiki.jmol.org/index.php/Jmol_Application
+ */
viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
- null, "-x -o -n", this);
+ null, "-x -o -n -i", this);
// ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
viewer.setBooleanProperty("defaultStructureDSSP", true);
} catch (ClassCastException x)
}
lastID = tmpatom.resNumIns.trim();
}
+ xferSettings();
+
makeResidueList();
makeCaBondList();
if (getId() == null)
{
- setId(inFile.getName());
+ setId(safeName(getDataName()));
}
for (PDBChain chain : getChains())
{
SequenceI chainseq = postProcessChain(chain);
- createAnnotation(chainseq, chain, ms.at);
if (isRNA(chainseq))
{
rna.add(chainseq);
{
prot.add(chainseq);
}
+
+ if (StructureImportSettings.isProcessSecondaryStructure())
+ {
+ createAnnotation(chainseq, chain, ms.at);
+ }
}
} catch (OutOfMemoryError er)
{
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.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.group.;
+ String fmt = new Format("%4i").form(curAtom.resNumber);
+ curAtom.resNumIns = (fmt + 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())
+ {
+ return false;
+ }
+ 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())
+ {
+ return false;
+ }
+ 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)
{
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')
{
- asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
- secstrcode[p], Float.NaN);
- ssFound = true;
+ try
+ {
+ asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
+ secstrcode[p], Float.NaN);
+ ssFound = true;
+ } catch (Exception e)
+ {
+ // e.printStackTrace();
+ }
}
}
this.predictSecondaryStructure = predictSecondaryStructure;
}
+ public boolean isVisibleChainAnnotation()
+ {
+ return visibleChainAnnotation;
+ }
+
+ public void setVisibleChainAnnotation(boolean visibleChainAnnotation)
+ {
+ this.visibleChainAnnotation = visibleChainAnnotation;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff