X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=dede37e6c7ba96fc4da3c8e89c57a09bce84de97;hb=c5677e9860106a821a3e6e0429b20ede7b9a732a;hp=f4a213f0137f9740d380717f6d4b1cdec110f572;hpb=b68dc1d95eeed4ab36914797f7d97c72ad54c11d;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index f4a213f..dede37e 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,178 +1,314 @@ /* -* 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 jalview.datamodel.*; +import jalview.io.FileParse; +import jalview.io.RnamlFile; +import jalview.ws.jws1.Annotate3D; -import java.io.*; +public class PDBfile extends jalview.io.AlignFile +{ + public Vector chains; -import java.util.*; -import java.awt.Color; + public String id; + /** + * set to true to add chain alignment annotation as visible annotation. + */ + boolean VisibleChainAnnotation = false; -public class PDBfile extends jalview.io.AlignFile { - public Vector chains; - public String id; + public PDBfile(String inFile, String inType) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException + { + super(inFile, inType); + } - public PDBfile(String inFile, String inType) throws IOException - { - super(inFile, inType); - } + public PDBfile(FileParse source) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException + { + super(source); + } - public String print() - { - return null; - } + public String print() + { + return null; + } - public void parse() throws IOException - { - try{ - chains = new Vector(); + 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; - boolean modelFlag = false; - boolean terFlag = false; + PDBChain tmpchain; + String line=null; + boolean modelFlag = false; + boolean terFlag = false; + String lastID = ""; - int index = 0; - while ( (line = nextLine()) != null) + int index = 0; + String atomnam = null; + try + { + while ((line = nextLine()) != null) + { + if (line.indexOf("HEADER") == 0) { - if (line.indexOf("HEADER") == 0) + if (line.length() > 62) { - 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")) + String tid; + if (line.length() > 67) { - continue; + tid = line.substring(62, 67).trim(); } - - Atom tmpatom = new Atom(line); - tmpchain = findChain(tmpatom.chain); - if (tmpchain != null) + else { - tmpchain.atoms.addElement(tmpatom); + tid = line.substring(62).trim(); } - else + if (tid.length() > 0) { - tmpchain = new PDBChain(tmpatom.chain); - chains.addElement(tmpchain); - tmpchain.atoms.addElement(tmpatom); + id = tid; } + continue; } - index++; + } + // Were we to do anything with SEQRES - we start it here + if (line.indexOf("SEQRES") == 0) + { + } + + if (line.indexOf("MODEL") == 0) + { + modelFlag = true; } - makeResidueList(); - makeCaBondList(); + if (line.indexOf("TER") == 0) + { + terFlag = true; + } - if (id == null) + if (modelFlag && line.indexOf("ENDMDL") == 0) { - id = inFile.getName(); + break; } - for (int i = 0; i < chains.size(); i++) + if (line.indexOf("ATOM") == 0 + || (line.indexOf("HETATM") == 0 && !terFlag)) { - SequenceI seq = ( (PDBChain) chains.elementAt(i)). - sequence; - seq.setName(id + "|" + seq.getName()); - Sequence dataset = new Sequence(seq. - getName(), - seq.getSequence().toString(), - seq.getStart(), seq.getEnd()); - dataset.setSequenceFeatures(seq.getSequenceFeatures()); - PDBEntry entry = new PDBEntry(); - entry.setId(id); - if (inFile != null) - entry.setFile(inFile.getAbsolutePath()); - - seq.setDatasetSequence(dataset); - dataset.addPDBId(entry); - - getSeqs().addElement(seq); + 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(); } - }catch(OutOfMemoryError er) + index++; + } + + makeResidueList(); + makeCaBondList(); + + if (id == null) { - System.out.println("OUT OF MEMORY LOADING PDB FILE"); - throw new IOException("Out of memory loading PDB File"); + 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) + { + System.out.println("this is a PDB format and RNA sequence"); + Annotate3D an3d = new Annotate3D(id); + 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"); - public void makeResidueList() { - for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeResidueList(); + } + 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); + } + } + } - public void makeCaBondList() { - for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).makeCaBondList(); - } + /** + * 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 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); - } - } + public void makeResidueList() + { + for (int i = 0; i < chains.size(); i++) + { + ((PDBChain) chains.elementAt(i)).makeResidueList(); + } + } - return null; + public void makeCaBondList() + { + for (int i = 0; i < chains.size(); i++) + { + ((PDBChain) chains.elementAt(i)).makeCaBondList(); } + } - public void setChargeColours() { - for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChargeColours(); - } + 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); + } } - public void setColours(jalview.schemes.ColourSchemeI cs) { - for (int i = 0; i < chains.size(); i++) { - ((PDBChain) chains.elementAt(i)).setChainColours(cs); - } + return null; + } + + public void setChargeColours() + { + for (int i = 0; i < chains.size(); i++) + { + ((PDBChain) chains.elementAt(i)).setChargeColours(); } + } - public void setChainColours() + public void setColours(jalview.schemes.ColourSchemeI cs) + { + for (int i = 0; i < chains.size(); i++) { - for (int i = 0; i < chains.size(); i++) - { - ((PDBChain) chains.elementAt(i)).setChainColours( - Color.getHSBColor(1.0f / (float)i, .4f, 1.0f) - ); - } + ((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