- 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
- // System.out.println("Making chain " + tmpatom.chain);\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
+ Atom tmpatom = new Atom(line);\r
+ tmpchain = findChain(tmpatom.chain);\r
+ if (tmpchain != null)\r
+ {\r
+ tmpchain.atoms.addElement(tmpatom);\r
+ }\r
+ else\r
+ {\r
+ tmpchain = new PDBChain(tmpatom.chain);\r
+ chains.addElement(tmpchain);\r
+ tmpchain.atoms.addElement(tmpatom);\r