- sequence = new Sequence("PDB_seq",seq,1,seq.length());\r
- System.out.println("PDB Sequence is :\nSequence = " + seq);\r
- System.out.println("No of residues = " +residues.size());\r
- }\r
-\r
- public void setChargeColours() {\r
- for (int i = 0; i < bonds.size(); i++) {\r
- try {\r
- Bond b = (Bond)bonds.elementAt(i);\r
-\r
- if (b.at1.resName.toUpperCase().equals("ASP") || b.at1.resName.toUpperCase().equals("GLU")) {\r
- b.startCol = Color.red;\r
- } else if (b.at1.resName.toUpperCase().equals("LYS") || b.at1.resName.toUpperCase().equals("ARG")) {\r
- b.startCol = Color.blue;\r
- } else if (b.at1.resName.toUpperCase().equals("CYS")) {\r
- b.startCol = Color.yellow;\r
- } else {\r
- int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();\r
- b.startCol = Color.lightGray;\r
- }\r
- if (b.at2.resName.toUpperCase().equals("ASP") || b.at2.resName.toUpperCase().equals("GLU")) {\r
- b.endCol = Color.red;\r
- } else if (b.at2.resName.toUpperCase().equals("LYS") || b.at2.resName.toUpperCase().equals("ARG")) {\r
- b.endCol = Color.blue;\r
- } else if (b.at2.resName.toUpperCase().equals("CYS")) {\r
- b.endCol = Color.yellow;\r
- } else {\r
- int atno = ((Integer)ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();\r
- b.endCol = Color.lightGray;\r
+\r
+ public void setChargeColours() {\r
+ for (int i = 0; i < bonds.size(); i++) {\r
+ try {\r
+ Bond b = (Bond) bonds.elementAt(i);\r
+\r
+ if (b.at1.resName.toUpperCase().equals("ASP") ||\r
+ b.at1.resName.toUpperCase().equals("GLU")) {\r
+ b.startCol = Color.red;\r
+ } else if (b.at1.resName.toUpperCase().equals("LYS") ||\r
+ b.at1.resName.toUpperCase().equals("ARG")) {\r
+ b.startCol = Color.blue;\r
+ } else if (b.at1.resName.toUpperCase().equals("CYS")) {\r
+ b.startCol = Color.yellow;\r
+ } else {\r
+ //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at1.resName.toUpperCase())).intValue();\r
+ b.startCol = Color.lightGray;\r
+ }\r
+\r
+ if (b.at2.resName.toUpperCase().equals("ASP") ||\r
+ b.at2.resName.toUpperCase().equals("GLU")) {\r
+ b.endCol = Color.red;\r
+ } else if (b.at2.resName.toUpperCase().equals("LYS") ||\r
+ b.at2.resName.toUpperCase().equals("ARG")) {\r
+ b.endCol = Color.blue;\r
+ } else if (b.at2.resName.toUpperCase().equals("CYS")) {\r
+ b.endCol = Color.yellow;\r
+ } else {\r
+ //int atno = ((Integer) ResidueProperties.getAA3Hash().get(b.at2.resName.toUpperCase())).intValue();\r
+ b.endCol = Color.lightGray;\r
+ }\r
+ } catch (Exception e) {\r
+ Bond b = (Bond) bonds.elementAt(i);\r
+ b.startCol = Color.gray;\r
+ b.endCol = Color.gray;\r
+ }\r