X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=9f65fef005fe9128138e3902e81958618d6aa685;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=d7b7c9778115281b9c58e853149c780d1fb867e2;hpb=8893c2ac9824d4c566ae69c73d34889c5316b058;p=jalview.git
diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index d7b7c97..9f65fef 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -1,179 +1,408 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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
-*/
-package MCview;
-
-import java.io.*;
-
-import java.net.*;
-
-import java.util.*;
-import java.awt.Color;
-
-
-public class PDBfile extends jalview.io.FileParse {
- public Vector chains = new Vector();
- Vector lineArray = new Vector();
- String id;
-
- public PDBfile(String[] lines) {
- for (int i = 0; i < lines.length; i++)
- lineArray.addElement(lines[i]);
-
- noLines = lineArray.size();
- parse();
- }
-
- public PDBfile(String inFile, String inType) throws IOException {
- super(inFile, inType);
-
- String line;
- this.lineArray = new Vector();
-
- BufferedReader dataIn;
-
- if (inType.equals("File")) {
- dataIn = new BufferedReader(new FileReader(inFile));
- }
- else if(inType.equals("Paste"))
- {
- dataIn = new BufferedReader(new StringReader(inFile));
- }
- else {
- URL url = new URL(inFile);
- this.fileSize = 0;
- dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
- }
-
- while ((line = dataIn.readLine()) != null) {
- lineArray.addElement(line);
- }
-
- noLines = lineArray.size();
-
- parse();
- lineArray = null;
- }
-
- public void parse()
- {
- PDBChain tmpchain;
- String line;
- boolean modelFlag = false;
- boolean terFlag = false;
-
-
- for (int i = 0; i < lineArray.size(); i++)
- {
-
- line = lineArray.elementAt(i).toString();
-
-
- if (line.indexOf("HEADER") == 0)
- {
- id = line.substring(62, 67).trim();
- continue;
- }
-
- if(line.indexOf("MODEL")==0)
- modelFlag = true;
-
- if(line.indexOf("TER")==0)
- terFlag = true;
-
- if(modelFlag && line.indexOf("ENDMDL")==0)
- break;
-
- if ( line.indexOf("ATOM")==0
- || (line.indexOf("HETATM")==0 && !terFlag)
- )
- {
- terFlag = false;
-
-
- //Jalview is only interested in CA bonds????
- if (!line.substring(12, 15).trim().equals("CA"))
- {
- continue;
- }
-
- Atom tmpatom = new Atom(line);
-
- tmpchain = findChain(tmpatom.chain);
- if (tmpchain != null)
- {
- tmpchain.atoms.addElement(tmpatom);
- }
- else
- {
- tmpchain = new PDBChain(tmpatom.chain);
- chains.addElement(tmpchain);
- tmpchain.atoms.addElement(tmpatom);
- }
-
- }
- }
-
- makeResidueList();
- makeCaBondList();
- }
-
- public void makeResidueList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeResidueList();
- }
- }
-
- public void makeCaBondList() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).makeCaBondList();
- }
- }
-
- public PDBChain findChain(String id) {
- for (int i = 0; i < chains.size(); i++) {
- if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
- return (PDBChain) chains.elementAt(i);
- }
- }
-
- return null;
- }
-
- public void setChargeColours() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setChargeColours();
- }
- }
-
- public void setHydrophobicityColours() {
- for (int i = 0; i < chains.size(); i++) {
- ((PDBChain) chains.elementAt(i)).setHydrophobicityColours();
- }
- }
-
- public void setChainColours()
- {
- for (int i = 0; i < chains.size(); i++)
- {
- ((PDBChain) chains.elementAt(i)).setChainColours(
- Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
- );
- }
- }
-}
+/*
+ * 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;
+
+import java.io.*;
+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 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
+ {
+ super(inFile, inType);
+ }
+
+ public PDBfile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ public String print()
+ {
+ return null;
+ }
+
+ public void parse() throws IOException
+ {
+ // TODO set the filename sensibly - try using data source name.
+ id = safeName(getDataName());
+
+ 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;
+ String atomnam = null;
+ try
+ {
+ while ((line = nextLine()) != null)
+ {
+ if (line.indexOf("HEADER") == 0)
+ {
+ 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)
+ {
+ }
+
+ if (line.indexOf("MODEL") == 0)
+ {
+ modelFlag = true;
+ }
+
+ if (line.indexOf("TER") == 0)
+ {
+ terFlag = true;
+ }
+
+ if (modelFlag && line.indexOf("ENDMDL") == 0)
+ {
+ break;
+ }
+ if (line.indexOf("ATOM") == 0
+ || (line.indexOf("HETATM") == 0 && !terFlag))
+ {
+ terFlag = false;
+
+ // Jalview is only interested in CA bonds????
+ atomnam = line.substring(12, 15).trim();
+ if (!atomnam.equals("CA") && !atomnam.equals("P"))
+ {
+ continue;
+ }
+
+ Atom tmpatom = new Atom(line);
+ 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
+ {
+ tmpchain = new PDBChain(id, tmpatom.chain);
+ chains.addElement(tmpchain);
+ tmpchain.atoms.addElement(tmpatom);
+ }
+ lastID = tmpatom.resNumIns.trim();
+ }
+ index++;
+ }
+
+ makeResidueList();
+ makeCaBondList();
+
+ if (id == null)
+ {
+ id = inFile.getName();
+ }
+ for (int i = 0; i < chains.size(); i++)
+ {
+ 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
+ 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();
+
+ };
+ 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();
+ }
+ }
+
+ public void makeCaBondList()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).makeCaBondList();
+ }
+ }
+
+ public PDBChain findChain(String id)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ if (((PDBChain) chains.elementAt(i)).id.equals(id))
+ {
+ return (PDBChain) chains.elementAt(i);
+ }
+ }
+
+ return null;
+ }
+
+ public void setChargeColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChargeColours();
+ }
+ }
+
+ public void setColours(jalview.schemes.ColourSchemeI cs)
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChainColours(cs);
+ }
+ }
+
+ public void setChainColours()
+ {
+ for (int i = 0; i < chains.size(); i++)
+ {
+ ((PDBChain) chains.elementAt(i)).setChainColours(Color.getHSBColor(
+ 1.0f / (float) i, .4f, 1.0f));
+ }
+ }
+ public boolean isRNA(SequenceI seqs)
+ {
+ for (int i=0;i