2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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26 import java.awt.Color;
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29 public class PDBfile extends jalview.io.FileParse {
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30 public Vector chains = new Vector();
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31 Vector lineArray = new Vector();
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34 public PDBfile(String[] lines) {
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35 for (int i = 0; i < lines.length; i++)
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36 lineArray.addElement(lines[i]);
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38 noLines = lineArray.size();
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42 public PDBfile(String inFile, String inType) throws IOException {
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43 super(inFile, inType);
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46 this.lineArray = new Vector();
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48 BufferedReader dataIn;
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50 if (inType.equals("File")) {
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51 dataIn = new BufferedReader(new FileReader(inFile));
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53 else if(inType.equals("Paste"))
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55 dataIn = new BufferedReader(new StringReader(inFile));
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58 URL url = new URL(inFile);
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60 dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
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63 while ((line = dataIn.readLine()) != null) {
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64 lineArray.addElement(line);
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67 noLines = lineArray.size();
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76 boolean modelFlag = false;
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77 for (int i = 0; i < lineArray.size(); i++)
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80 line = lineArray.elementAt(i).toString();
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82 if (line.indexOf("HEADER") == 0)
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84 id = line.substring(62, 67).trim();
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88 if(line.indexOf("MODEL")==0)
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91 if(modelFlag && line.indexOf("ENDMDL")==0)
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94 if (line.indexOf("ATOM")==0 || line.indexOf("HETATM")==0 )
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97 Atom tmpatom = new Atom(line);
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99 //Jalview is only interested in CA bonds????
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100 if(!tmpatom.name.equals("CA"))
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103 tmpchain = findChain(tmpatom.chain);
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104 if ( tmpchain != null)
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106 tmpchain.atoms.addElement(tmpatom);
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110 tmpchain = new PDBChain(tmpatom.chain);
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111 chains.addElement(tmpchain);
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112 tmpchain.atoms.addElement(tmpatom);
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114 } catch (NumberFormatException e) {
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115 System.err.println("Caught" + e);
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116 System.err.println("Record not added to PDB model:" +
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117 lineArray.elementAt(i).toString());
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126 public void makeResidueList() {
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127 for (int i = 0; i < chains.size(); i++) {
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128 ((PDBChain) chains.elementAt(i)).makeResidueList();
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132 public void makeCaBondList() {
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133 for (int i = 0; i < chains.size(); i++) {
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134 ((PDBChain) chains.elementAt(i)).makeCaBondList();
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138 public PDBChain findChain(String id) {
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139 for (int i = 0; i < chains.size(); i++) {
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140 if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
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141 return (PDBChain) chains.elementAt(i);
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148 public void setChargeColours() {
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149 for (int i = 0; i < chains.size(); i++) {
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150 ((PDBChain) chains.elementAt(i)).setChargeColours();
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154 public void setHydrophobicityColours() {
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155 for (int i = 0; i < chains.size(); i++) {
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156 ((PDBChain) chains.elementAt(i)).setHydrophobicityColours();
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160 public void setChainColours()
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162 for (int i = 0; i < chains.size(); i++)
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164 ((PDBChain) chains.elementAt(i)).setChainColours(
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165 Color.getHSBColor(1.0f / (float)i, .4f, 1.0f)
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