+ 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.equalsIgnoreCase("ASP") ||\r
+ b.at1.resName.equalsIgnoreCase("GLU")) {\r
+ b.startCol = Color.red;\r
+ } else if (b.at1.resName.equalsIgnoreCase("LYS") ||\r
+ b.at1.resName.equalsIgnoreCase("ARG")) {\r
+ b.startCol = Color.blue;\r
+ } else if (b.at1.resName.equalsIgnoreCase("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.equalsIgnoreCase("ASP") ||\r
+ b.at2.resName.equalsIgnoreCase("GLU")) {\r
+ b.endCol = Color.red;\r
+ } else if (b.at2.resName.equalsIgnoreCase("LYS") ||\r
+ b.at2.resName.equalsIgnoreCase("ARG")) {\r
+ b.endCol = Color.blue;\r
+ } else if (b.at2.resName.equalsIgnoreCase("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