public PDBChain findChain(String id) {
for (int i = 0; i < chains.size(); i++) {
// System.out.println("ID = " + id + " " +((PDBChain)chains.elementAt(i)).id);
if (((PDBChain) chains.elementAt(i)).id.equals(id)) {
return (PDBChain) chains.elementAt(i);
}
}
return null;
}
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);
// }
}
public void setChainColours() {
for (int i = 0; i < chains.size(); i++) {
((PDBChain) chains.elementAt(i)).setChainColours();
}
}
public void makeCaBondList() {
for (int i = 0; i < chains.size(); i++) {
((PDBChain) chains.elementAt(i)).makeCaBondList();
}
}