- while ((line = dataIn.readLine()) != null) {\r
- lineArray.addElement(line);\r
- }\r
- noLines = lineArray.size();\r
+ public void parse() {\r
+ for (int i = 0; i < lineArray.size(); i++) {\r
+ StringTokenizer str = new StringTokenizer(lineArray.elementAt(i)\r
+ .toString());\r
+\r
+ if (str.hasMoreTokens()) {\r
+ String inStr = str.nextToken();\r
+\r
+ if (inStr.indexOf("ATOM") != -1) {\r
+ try {\r
+ myAtom tmpatom = new myAtom(str);\r
+\r
+ if (findChain(tmpatom.chain) != null) {\r
+ // System.out.println("Adding to chain " + tmpatom.chain);\r
+ findChain(tmpatom.chain).atoms.addElement(tmpatom);\r
+ } else {\r
+ PDBChain tmpchain = new PDBChain(tmpatom.chain);\r
+ chains.addElement(tmpchain);\r
+ tmpchain.atoms.addElement(tmpatom);\r
+ }\r
+ } catch (NumberFormatException e) {\r
+ System.err.println("Caught" + e);\r
+ System.err.println("Record not added to PDB model:" +\r
+ lineArray.elementAt(i).toString());\r
+ }\r
+ }\r
+ }\r
+ }\r