X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=26d44b1a976a34866baa6ab4b9286a073b3cbb71;hb=e5b366e9af81b30196c3c31727fd6b0091502527;hp=ce98a0698a8e4c0fd7e9fad745f4c68a7001050c;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index ce98a06..26d44b1 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,137 +1,170 @@ -package MCview; - -import jalview.gui.*; -import java.io.*; -import java.net.*; -import java.util.*; - - -public class PDBfile extends jalview.io.FileParse { - - public Vector chains = new Vector(); - - Vector lineArray = new Vector(); - - 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 - { - 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(); - -} - - - public void parse() { - - System.out.println("Parsing"); - - for (int i = 0; i < lineArray.size(); i++) { - StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString()); - if (str.hasMoreTokens()) { - String inStr = str.nextToken(); - - if (inStr.indexOf("ATOM") != -1) { - try { - myAtom tmpatom = new myAtom(str); - if (findChain(tmpatom.chain) != null) { - System.out.println("Adding to chain " + tmpatom.chain); - findChain(tmpatom.chain).atoms.addElement(tmpatom); - } else { - System.out.println("Making chain " + tmpatom.chain); - PDBChain tmpchain = new PDBChain(tmpatom.chain); - chains.addElement(tmpchain); - tmpchain.atoms.addElement(tmpatom); - } - } catch(NumberFormatException e) { - System.out.println("Caught" + e); - System.out.println("Atom not added"); - } - } - } - } - makeResidueList(); - makeCaBondList(); - // for (int i=0; i < chains.size() ; i++) { - // String pog = ((PDBChain)chains.elementAt(i)).print(); - // System.out.println(pog); - // } - } - - 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++) { - // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id); - 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 colourBySequence(DrawableSequence seq) { -//SMJS TODO -// int max = seq.maxchain; -// if (seq.maxchain != -1) { -// ((PDBChain)chains.elementAt(max)).colourBySequence(seq); -// } - } - - public void setChainColours() { - for (int i=0; i < chains.size(); i++) { - ((PDBChain)chains.elementAt(i)).setChainColours(); - } - } - public static void main(String[] args) { - try { - PDBfile pdb = new PDBfile("enkp1.pdb","File"); - } catch(IOException e) { - System.out.println(e); - System.exit(0); - } - } -} - - - +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2006 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 jalview.datamodel.*; + +import java.io.*; + +import java.util.*; +import java.awt.Color; + + +public class PDBfile extends jalview.io.AlignFile { + public Vector chains; + public String id; + + public PDBfile(String inFile, String inType) throws IOException + { + super(inFile, inType); + } + + public String print() + { + return null; + } + + public void parse() throws IOException + { + try{ + chains = new Vector(); + + PDBChain tmpchain; + String line; + boolean modelFlag = false; + boolean terFlag = false; + + int index = 0; + while ( (line = nextLine()) != null) + { + if (line.indexOf("HEADER") == 0) + { + id = line.substring(62, 67).trim(); + 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???? + 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(id,tmpatom.chain); + chains.addElement(tmpchain); + tmpchain.atoms.addElement(tmpatom); + } + } + 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()); + dataset.addPDBId(entry); + getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset + } + }catch(OutOfMemoryError er) + { + System.out.println("OUT OF MEMORY LOADING PDB FILE"); + throw new IOException("Out of memory loading PDB File"); + } + } + + 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) + ); + } + } +}