/*
* 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 < 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++;
}
}
if (sq.getAnnotation() != null)
{
annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
}
}
}
}
}
/**
* make a friendly ID string.
*
* @param dataName
* @return truncated dataName to after last '/'
*/
private String safeName(String dataName)
{
int p = 0;
while ((p = dataName.indexOf("/")) > -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 < seqs.getLength(); i++)
{
if ((seqs.getCharAt(i) != 'A') && (seqs.getCharAt(i) != 'C')
&& (seqs.getCharAt(i) != 'G') && (seqs.getCharAt(i) != 'U'))
{
return false;
}
}
return true;
}
}