X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBfile.java;h=c55a5192276be25dc36873f75697785f43edc392;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=6fdd9787028e0f3d55742872e0f3f81b6753f0d0;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 6fdd978..c55a519 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 2.6) + * Copyright (C) 2010 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; @@ -24,27 +23,39 @@ import java.util.*; import java.awt.*; import jalview.datamodel.*; +import jalview.io.FileParse; -public class PDBfile - extends jalview.io.AlignFile +public class PDBfile extends jalview.io.AlignFile { public Vector chains; + public String id; - public PDBfile(String inFile, String inType) - throws IOException + /** + * 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 + public void parse() throws IOException { + // TODO set the filename sensibly - try using data source name. + id = safeName(getDataName()); + try { chains = new Vector(); @@ -53,14 +64,31 @@ public class PDBfile String line; boolean modelFlag = false; boolean terFlag = false; + String lastID = ""; int index = 0; - while ( (line = nextLine()) != null) + String atomnam = null; + while ((line = nextLine()) != null) { if (line.indexOf("HEADER") == 0) { - id = line.substring(62, 67).trim(); - continue; + 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) @@ -82,13 +110,13 @@ public class PDBfile break; } if (line.indexOf("ATOM") == 0 - || (line.indexOf("HETATM") == 0 && !terFlag) - ) + || (line.indexOf("HETATM") == 0 && !terFlag)) { terFlag = false; - //Jalview is only interested in CA bonds???? - if (!line.substring(12, 15).trim().equals("CA")) + // Jalview is only interested in CA bonds???? + atomnam = line.substring(12, 15).trim(); + if (!atomnam.equals("CA") && !atomnam.equals("P")) { continue; } @@ -97,6 +125,11 @@ public class PDBfile 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 @@ -105,6 +138,7 @@ public class PDBfile chains.addElement(tmpchain); tmpchain.atoms.addElement(tmpatom); } + lastID = tmpatom.resNumIns.trim(); } index++; } @@ -118,8 +152,7 @@ public class PDBfile } for (int i = 0; i < chains.size(); i++) { - SequenceI dataset = ( (PDBChain) chains.elementAt(i)). - sequence; + SequenceI dataset = ((PDBChain) chains.elementAt(i)).sequence; dataset.setName(id + "|" + dataset.getName()); PDBEntry entry = new PDBEntry(); entry.setId(id); @@ -127,22 +160,54 @@ public class PDBfile { entry.setFile(inFile.getAbsolutePath()); } + else + { + // TODO: decide if we should dump the datasource to disk + entry.setFile(getDataName()); + } dataset.addPDBId(entry); - getSeqs().addElement(dataset.deriveSequence()); // PDBChain objects maintain reference to dataset + 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) + } catch (OutOfMemoryError er) { System.out.println("OUT OF MEMORY LOADING PDB FILE"); throw new IOException("Out of memory loading PDB File"); } } + /** + * 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(); + ((PDBChain) chains.elementAt(i)).makeResidueList(); } } @@ -150,7 +215,7 @@ public class PDBfile { for (int i = 0; i < chains.size(); i++) { - ( (PDBChain) chains.elementAt(i)).makeCaBondList(); + ((PDBChain) chains.elementAt(i)).makeCaBondList(); } } @@ -158,7 +223,7 @@ public class PDBfile { for (int i = 0; i < chains.size(); i++) { - if ( ( (PDBChain) chains.elementAt(i)).id.equals(id)) + if (((PDBChain) chains.elementAt(i)).id.equals(id)) { return (PDBChain) chains.elementAt(i); } @@ -171,7 +236,7 @@ public class PDBfile { for (int i = 0; i < chains.size(); i++) { - ( (PDBChain) chains.elementAt(i)).setChargeColours(); + ((PDBChain) chains.elementAt(i)).setChargeColours(); } } @@ -179,7 +244,7 @@ public class PDBfile { for (int i = 0; i < chains.size(); i++) { - ( (PDBChain) chains.elementAt(i)).setChainColours(cs); + ((PDBChain) chains.elementAt(i)).setChainColours(cs); } } @@ -187,9 +252,8 @@ public class PDBfile { 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(Color.getHSBColor( + 1.0f / (float) i, .4f, 1.0f)); } } }