import java.awt.*;
+
+import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
import jalview.io.FileParse;
+import jalview.ws.jws1.Annotate3D;
public class PDBfile extends jalview.io.AlignFile
{
*/
boolean VisibleChainAnnotation = false;
- public PDBfile(String inFile, String inType) throws IOException
+ public PDBfile(String inFile, String inType) throws Exception
{
super(inFile, inType);
}
- public PDBfile(FileParse source) throws IOException
+ public PDBfile(FileParse source) throws Exception
{
super(source);
}
return null;
}
- public void parse() throws IOException
+ public void parse() throws Exception
{
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
chains = new Vector();
-
+ ArrayList<SequenceI> rna=new ArrayList<SequenceI>(), prot=new ArrayList<SequenceI>();
PDBChain tmpchain;
String line = null;
boolean modelFlag = false;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
+ entry.setProperty(new Hashtable());
+ entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
// maintain reference to
// dataset
seqs.addElement(chainseq);
+ if(isRNA(chainseq)==true)
+ {
+ rna.add(chainseq);
+ } else {
+ prot.add(chainseq);
+ }
+
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
+
if (chainannot != null)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
+
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
+ if (rna.size()>0)
+ try {
+ processPdbFileWithAnnotate3d(rna);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
+ if (prot.size()>0)
+ try {
+ processPdbFileWithJmol(prot);
+ } catch (Exception x)
+ {
+ System.err.println("Exceptions when dealing with RNA in pdb file");
+ x.printStackTrace();
+
+ };
} catch (OutOfMemoryError er)
{
System.out.println("OUT OF MEMORY LOADING PDB FILE");
}
}
}
-
+ private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
+ {
+// System.out.println("this is a PDB format and RNA sequence");
+ Annotate3D an3d = new Annotate3D();
+ AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
+ replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna) throws Exception {
+// System.out.println("this is a PDB format and RNA sequence");
+ Annotate3D an3d = new Annotate3D();
+ AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type));
+ replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ }
+ private void replaceMatchingSeqsWith(ArrayList<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
+ {
+ if (al!=null && al.getHeight()>0)
+ {
+ ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
+ ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
+
+ for (SequenceI sq:ochains)
+ {
+ SequenceI bestm=null;
+ AlignSeq bestaseq=null;
+ int bestscore=0;
+ for (SequenceI msq:al.getSequences())
+ {
+ AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
+ if (bestm==null || aseq.getMaxScore()>bestscore)
+ {
+ bestscore=aseq.getMaxScore();
+ bestaseq= aseq;
+ bestm=msq;
+ }
+ }
+ System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
+ matches.add(bestm);
+ aligns.add(bestaseq);
+ al.deleteSequence(bestm);
+ }
+ for (int p=0,pSize=seqs.size();p<pSize;p++)
+ {
+ SequenceI sq,sp=seqs.get(p);
+ int q;
+ if ((q=ochains.indexOf(sp))>-1)
+ {
+ seqs.set(p, sq=matches.get(q));
+ sq.setName(sp.getName());
+ sq.setDescription(sp.getDescription());
+ sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
+ int inspos=-1;
+ for (int ap=0;ap<annotations.size();)
+ {
+ if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
+ if (inspos==-1)
+ {
+ inspos=ap;
+ }
+ annotations.remove(ap);
+ } else {
+ ap++;
+ }
+ }
+ annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
+ }
+ }
+ }
+ }
/**
* make a friendly ID string.
*
1.0f / (float) i, .4f, 1.0f));
}
}
+ public boolean isRNA(SequenceI seqs)
+ {
+ for (int i=0;i<seqs.getLength();i++){
+ if((seqs.getCharAt(i)!='A') &&(seqs.getCharAt(i)!='C')&&(seqs.getCharAt(i)!='G')&&(seqs.getCharAt(i)!='U'))
+ {
+ return false;
+ }
+ }
+
+ return true;
+
+
+ }
}