X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=3f9bc9def3b3f22e6ddeb5cc43d7fc62667abc26;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=f97216b2a8879b1132540db8ba65a456af1706ec;hpb=6386a2fdc5000b7fda564cb58a99567c81a2607e;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index f97216b..3f9bc9d 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,155 +1,266 @@ -/* -* 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 jalview.datamodel.*; - -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[] 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 { - 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() { - 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.err.println("Caught" + e); - System.err.println("Record not added to PDB model:" + - lineArray.elementAt(i).toString()); - } - } - } - } - - 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(Sequence 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(); - } - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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 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(); + + 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); + 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)); + } + } +}