3 import jalview.gui.*;
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9 public class PDBfile extends jalview.io.FileParse {
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11 public Vector chains = new Vector();
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13 Vector lineArray = new Vector();
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15 public PDBfile(String inFile, String inType) throws IOException {
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17 super(inFile,inType);
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20 this.lineArray = new Vector();
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21 BufferedReader dataIn;
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23 if (inType.equals("File"))
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24 dataIn = new BufferedReader(new FileReader( inFile ));
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28 URL url = new URL(inFile);
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30 dataIn = new BufferedReader(new InputStreamReader(url.openStream()));
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33 while ((line = dataIn.readLine()) != null) {
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34 lineArray.addElement(line);
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36 noLines = lineArray.size();
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43 public void parse() {
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45 System.out.println("Parsing");
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47 for (int i = 0; i < lineArray.size(); i++) {
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48 StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
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49 if (str.hasMoreTokens()) {
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50 String inStr = str.nextToken();
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52 if (inStr.indexOf("ATOM") != -1) {
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54 myAtom tmpatom = new myAtom(str);
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55 if (findChain(tmpatom.chain) != null) {
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56 System.out.println("Adding to chain " + tmpatom.chain);
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57 findChain(tmpatom.chain).atoms.addElement(tmpatom);
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59 System.out.println("Making chain " + tmpatom.chain);
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60 PDBChain tmpchain = new PDBChain(tmpatom.chain);
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61 chains.addElement(tmpchain);
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62 tmpchain.atoms.addElement(tmpatom);
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64 } catch(NumberFormatException e) {
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65 System.out.println("Caught" + e);
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66 System.out.println("Atom not added");
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73 // for (int i=0; i < chains.size() ; i++) {
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74 // String pog = ((PDBChain)chains.elementAt(i)).print();
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75 // System.out.println(pog);
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79 public void makeResidueList() {
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80 for (int i=0; i < chains.size() ; i++) {
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81 ((PDBChain)chains.elementAt(i)).makeResidueList();
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84 public void makeCaBondList() {
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85 for (int i=0; i < chains.size() ; i++) {
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86 ((PDBChain)chains.elementAt(i)).makeCaBondList();
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90 public PDBChain findChain(String id) {
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91 for (int i=0; i < chains.size(); i++) {
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92 // System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
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93 if (((PDBChain)chains.elementAt(i)).id.equals(id)) {
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94 return (PDBChain)chains.elementAt(i);
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101 public void setChargeColours() {
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102 for (int i=0; i < chains.size(); i++) {
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103 ((PDBChain)chains.elementAt(i)).setChargeColours();
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107 public void setHydrophobicityColours() {
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108 for (int i=0; i < chains.size(); i++) {
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109 ((PDBChain)chains.elementAt(i)).setHydrophobicityColours();
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113 public void colourBySequence(DrawableSequence seq) {
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115 // int max = seq.maxchain;
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116 // if (seq.maxchain != -1) {
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117 // ((PDBChain)chains.elementAt(max)).colourBySequence(seq);
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121 public void setChainColours() {
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122 for (int i=0; i < chains.size(); i++) {
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123 ((PDBChain)chains.elementAt(i)).setChainColours();
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126 public static void main(String[] args) {
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128 PDBfile pdb = new PDBfile("enkp1.pdb","File");
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129 } catch(IOException e) {
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130 System.out.println(e);
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