/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* 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 .
*/
package MCview;
import java.io.*;
import java.util.*;
import java.awt.*;
import javax.xml.parsers.ParserConfigurationException;
import org.xml.sax.SAXException;
import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
import jalview.datamodel.*;
import jalview.io.FileParse;
import jalview.io.RnamlFile;
import jalview.ws.jws1.Annotate3D;
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, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(inFile, inType);
}
public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
{
super(source);
}
public String print()
{
return null;
}
public void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
{
// TODO set the filename sensibly - try using data source name.
id = safeName(getDataName());
chains = new Vector();
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);
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)
{
String path =inFile.getPath();
System.out.println("this is a PDB format and RNA sequence");
Annotate3D an3d = new Annotate3D(path);
System.out.println(id);
//BufferedWriter r = an3d.getReader();
// BufferedReader in = new BufferedReader(new FileReader("temp.rnaml"));
//String str;
// while ((str = in.readLine()) != null) {
// System.out.println(str);
// System.out.println("toto");
// }
//String type = "File";
//RnamlFile rnaml =new RnamlFile("temp.rnaml",type);
System.out.println("Create rnamfile object");
//rnaml.parse("temp");
//this.annotations =rnaml.getAnnot();
}
AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
if (chainannot != null)
{
for (int ai = 0; ai < chainannot.length; ai++)
{
chainannot[ai].visible = VisibleChainAnnotation;
annotations.addElement(chainannot[ai]);
}
}
}
} 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);
}
}
}
/**
* 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