- try {\r
- Atom tmpatom = new Atom(line);\r
-\r
- //Jalview is only interested in CA bonds????\r
- if(!tmpatom.name.equals("CA"))\r
- continue;\r
-\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
- }\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
+ //Jalview is only interested in CA bonds????\r
+ if (!line.substring(12, 15).trim().equals("CA"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ Atom tmpatom = new Atom(line);\r
+\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
+ }\r
+\r
+ }\r