public void parse() { System.out.println("Parsing"); 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.out.println("Caught" + e); System.out.println("Atom not added"); } } } } makeResidueList(); makeCaBondList(); // for (int i=0; i < chains.size() ; i++) { // String pog = ((PDBChain)chains.elementAt(i)).print(); // System.out.println(pog); // } }