X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=9f65fef005fe9128138e3902e81958618d6aa685;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=2c7bd9dbd49205afa07ec946bed02cedea67cd94;hpb=ededfcf0edb588601c4354523b0f399c600a7241;p=jalview.git
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index 2c7bd9d..9f65fef 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,20 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package MCview;
@@ -23,50 +23,74 @@ import java.util.*;
import java.awt.*;
+import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
+import jalview.io.FileParse;
-public class PDBfile
- extends jalview.io.AlignFile
+public class PDBfile extends jalview.io.AlignFile
{
public Vector chains;
+
public String id;
/**
* set to true to add chain alignment annotation as visible annotation.
*/
- boolean VisibleChainAnnotation=false;
- public PDBfile(String inFile, String inType)
- throws IOException
+ boolean VisibleChainAnnotation = false;
+
+ public PDBfile(String inFile, String inType) throws IOException
{
super(inFile, inType);
}
+ public PDBfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
public String print()
{
return null;
}
- public void parse()
- throws IOException
+ public void parse() throws IOException
{
- // TODO set the filename sensibly
- id = (inFile==null) ? "PDBFILE" : inFile.getName();
- try
- {
- chains = new Vector();
+ // TODO set the filename sensibly - try using data source name.
+ id = safeName(getDataName());
- PDBChain tmpchain;
- String line;
- boolean modelFlag = false;
- boolean terFlag = false;
+ chains = new Vector();
+ ArrayList rna=new ArrayList(), prot=new ArrayList();
+ PDBChain tmpchain;
+ String line = null;
+ boolean modelFlag = false;
+ boolean terFlag = false;
+ String lastID = "";
- int index = 0;
- while ( (line = nextLine()) != null)
+ int index = 0;
+ String atomnam = null;
+ try
+ {
+ while ((line = nextLine()) != null)
{
if (line.indexOf("HEADER") == 0)
{
- id = line.substring(62, 67).trim();
- continue;
+ if (line.length() > 62)
+ {
+ String tid;
+ if (line.length() > 67)
+ {
+ tid = line.substring(62, 67).trim();
+ }
+ else
+ {
+ tid = line.substring(62).trim();
+ }
+ if (tid.length() > 0)
+ {
+ id = tid;
+ }
+ continue;
+ }
}
// Were we to do anything with SEQRES - we start it here
if (line.indexOf("SEQRES") == 0)
@@ -88,13 +112,13 @@ public class PDBfile
break;
}
if (line.indexOf("ATOM") == 0
- || (line.indexOf("HETATM") == 0 && !terFlag)
- )
+ || (line.indexOf("HETATM") == 0 && !terFlag))
{
terFlag = false;
- //Jalview is only interested in CA bonds????
- if (!line.substring(12, 15).trim().equals("CA"))
+ // Jalview is only interested in CA bonds????
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
{
continue;
}
@@ -103,6 +127,11 @@ public class PDBfile
tmpchain = findChain(tmpatom.chain);
if (tmpchain != null)
{
+ if (tmpatom.resNumIns.trim().equals(lastID))
+ {
+ // phosphorylated protein - seen both CA and P..
+ continue;
+ }
tmpchain.atoms.addElement(tmpatom);
}
else
@@ -111,6 +140,7 @@ public class PDBfile
chains.addElement(tmpchain);
tmpchain.atoms.addElement(tmpatom);
}
+ lastID = tmpatom.resNumIns.trim();
}
index++;
}
@@ -124,41 +154,196 @@ public class PDBfile
}
for (int i = 0; i < chains.size(); i++)
{
- SequenceI dataset = ( (PDBChain) chains.elementAt(i)).
- sequence;
+ SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence;
dataset.setName(id + "|" + dataset.getName());
PDBEntry entry = new PDBEntry();
entry.setId(id);
+ entry.setProperty(new Hashtable());
+ if (((PDBChain)chains.elementAt(i)).id!=null) {
+ entry.getProperty().put("CHAIN", ((PDBChain)chains.elementAt(i)).id);
+ }
if (inFile != null)
{
entry.setFile(inFile.getAbsolutePath());
}
+ else
+ {
+ // TODO: decide if we should dump the datasource to disk
+ entry.setFile(getDataName());
+ }
dataset.addPDBId(entry);
- SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects maintain reference to dataset
+ SequenceI chainseq = dataset.deriveSequence(); // PDBChain objects
+ // 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)
+
+ if (chainannot != null)
{
- for (int ai=0; ai0)
+ 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();
+
+ };
+ 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");
throw new IOException("Out of memory loading PDB File");
+ } catch (NumberFormatException ex)
+ {
+ if (line != null)
+ {
+ System.err.println("Couldn't read number from line:");
+ System.err.println(line);
+ }
}
}
+ private void processPdbFileWithJmol(ArrayList prot) throws Exception
+ {
+ try {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl!=null)
+ {
+ Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
+ cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
+ replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ } catch (ClassNotFoundException q)
+ {}
+ }
+ private void processPdbFileWithAnnotate3d(ArrayList rna) throws Exception {
+// System.out.println("this is a PDB format and RNA sequence");
+ // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service
+ try {
+ Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
+ if (cl!=null)
+ {
+ // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service
+ Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(new Object[] {});
+ AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)}));
+ replaceMatchingSeqsWith(rna, al, AlignSeq.DNA);
+ }
+ } catch (ClassNotFoundException x)
+ {
+ //ignore classnotfounds - occurs in applet
+ };
+ }
+ private void replaceMatchingSeqsWith(ArrayList ochains, AlignmentI al, String dnaOrProtein)
+ {
+ if (al!=null && al.getHeight()>0)
+ {
+ ArrayList matches=new ArrayList();
+ ArrayList aligns=new ArrayList();
+
+ 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-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 -1 && p < dataName.length())
+ {
+ dataName = dataName.substring(p + 1);
+ }
+ return dataName;
+ }
public void makeResidueList()
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).makeResidueList();
+ ((PDBChain) chains.elementAt(i)).makeResidueList();
}
}
@@ -166,7 +351,7 @@ public class PDBfile
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).makeCaBondList();
+ ((PDBChain) chains.elementAt(i)).makeCaBondList();
}
}
@@ -174,7 +359,7 @@ public class PDBfile
{
for (int i = 0; i < chains.size(); i++)
{
- if ( ( (PDBChain) chains.elementAt(i)).id.equals(id))
+ if (((PDBChain) chains.elementAt(i)).id.equals(id))
{
return (PDBChain) chains.elementAt(i);
}
@@ -187,7 +372,7 @@ public class PDBfile
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).setChargeColours();
+ ((PDBChain) chains.elementAt(i)).setChargeColours();
}
}
@@ -195,7 +380,7 @@ public class PDBfile
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).setChainColours(cs);
+ ((PDBChain) chains.elementAt(i)).setChainColours(cs);
}
}
@@ -203,9 +388,21 @@ public class PDBfile
{
for (int i = 0; i < chains.size(); i++)
{
- ( (PDBChain) chains.elementAt(i)).setChainColours(
- Color.getHSBColor(1.0f / (float) i, .4f, 1.0f)
- );
+ ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+ 1.0f / (float) i, .4f, 1.0f));
}
}
+ public boolean isRNA(SequenceI seqs)
+ {
+ for (int i=0;i