[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer JmolConstants.java,1.80,1.81

[Michael T H. <mic...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16021/src/org/openscience/jmol/viewer

Modified Files:
	JmolConstants.java 
Log Message:
changed atomID registration mechanism to be from a fixed specialAtomID table


Index: JmolConstants.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/JmolConstants.java,v
retrieving revision 1.80
retrieving revision 1.81
diff -u -r1.80 -r1.81
--- JmolConstants.java	26 Mar 2004 18:17:51 -0000	1.80
+++ JmolConstants.java	27 Mar 2004 09:20:36 -0000	1.81
@@ -1822,18 +1822,21 @@
     0xFFffffff, // pewhite
   };
 
-  public final static short ATOMID_MAINCHAIN_MAX = 4;
+  public final static int SPECIALATOMID_MAINCHAIN_MAX = 4;
   // some pdbfiles do not have sidechain atoms labeled properly
   // we call these MAINCHAIN_IMPOSTERS
   // the residue will accept the first atom with the proper name
   // others will get their atomid changed
-  public final static short ATOMID_MAINCHAIN_IMPOSTERS = 4;
+  public final static int SPECIALATOMID_MAINCHAIN_IMPOSTERS = 4;
 
-  public final static String[] predefinedAtomNames4 = {
+  public final static String[] specialAtomNames = {
     "N",  // 0
     "CA",
     "C",
     "O", // 3
+    // note that these entries are really no longer used
+    // remove them when we rearrange the specialAtomName
+    // and redefine the predefined set expressions
     "N", // imposter N
     "C", // imposter CA
     "C", // imposter C
@@ -1862,42 +1865,8 @@
     "H5T",
     "H3T",
     "2HO*", // 30
-    /*
-    " N  ",  // 0
-    " CA ",
-    " C  ",
-    " O  ", // 3
-    " N  ", // imposter N
-    " C  ", // imposter CA
-    " C  ", // imposter C
-    " O  ", // imposter O
-    
-    " P  ",
-    " O1P",
-    " O2P", // 10
-    " O3P",
-    " O5*",
-    " O4*",
-    " O3*",
-    " O2*", // 15
-    " C5*",
-    " C4*",
-    " C3*",
-    " C2*",
-    " C1*", // 20
-    "1H5*",
-    "2H5*",
-    " H4*",
-    " H3*",
-    "1H2*", // 25
-    "2H2*",
-    " H1*",
-    " H5T",
-    " H3T",
-    "2HO*", // 30
-    */
   };
-  
+
   public final static short RESID_AMINO_MAX = 22;
 
   /****************************************************************