[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel GroupBuilder.java,1.6,1.7 NucleicMonomer.java,1.14,1.15

[Miguel <mig...@us...>]

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv13488/src/org/openscience/jmol/viewer/datamodel

Modified Files:
	GroupBuilder.java NucleicMonomer.java 
Log Message:
Nucleic: removed O4* from required atoms + now allow O5* as terminus


Index: GroupBuilder.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/GroupBuilder.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- GroupBuilder.java	3 Jun 2004 14:00:44 -0000	1.6
+++ GroupBuilder.java	3 Jun 2004 16:48:29 -0000	1.7
@@ -105,21 +105,18 @@
   Group distinguishAndAllocateGroup() {

     Atom[] atoms = frameBuilder.atoms;

     Group group = null;

-    int bits = distinguishingBits;

-    if ((bits & JmolConstants.ATOMID_PROTEIN_MASK) ==

+    if ((distinguishingBits & JmolConstants.ATOMID_PROTEIN_MASK) ==

         JmolConstants.ATOMID_PROTEIN_MASK) {

       group = AminoMonomer.validateAndAllocate(chain, group3, seqcode,

                                                firstAtomIndex, lastAtomIndex,

                                                specialAtomIndexes);

-    } else if ((bits & JmolConstants.ATOMID_ALPHA_ONLY_MASK) ==

+    } else if ((distinguishingBits & JmolConstants.ATOMID_ALPHA_ONLY_MASK) ==

                JmolConstants.ATOMID_ALPHA_ONLY_MASK) {

       group = AlphaMonomer.validateAndAllocate(chain, group3, seqcode,

                                                firstAtomIndex, lastAtomIndex,

                                                specialAtomIndexes);

-    } else if (((bits & JmolConstants.ATOMID_NUCLEIC_MASK) ==

-                JmolConstants.ATOMID_NUCLEIC_MASK) ||

-               ((bits & JmolConstants.ATOMID_NUCLEIC_H5T_MASK) ==

-                JmolConstants.ATOMID_NUCLEIC_H5T_MASK)) {

+    } else if (((distinguishingBits & JmolConstants.ATOMID_NUCLEIC_MASK) ==

+                JmolConstants.ATOMID_NUCLEIC_MASK)) {

       group = NucleicMonomer.validateAndAllocate(chain, group3, seqcode,

                                                  firstAtomIndex, lastAtomIndex,

                                                  specialAtomIndexes);


Index: NucleicMonomer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/NucleicMonomer.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- NucleicMonomer.java	3 Jun 2004 14:00:44 -0000	1.14
+++ NucleicMonomer.java	3 Jun 2004 16:48:29 -0000	1.15
@@ -58,6 +58,8 @@
     -JmolConstants.ATOMID_S4,  // 19 S4   tU
 
     -JmolConstants.ATOMID_H5T_TERMINUS, // 20 H5T terminus
+    -JmolConstants.ATOMID_O5T_TERMINUS, // 21 O5T terminus
+    JmolConstants.ATOMID_O5_PRIME       // 22 O5' terminus
   };
 
   static Monomer
@@ -69,7 +71,7 @@
                                     specialAtomIndexes,
                                     interestingNucleicAtomIDs);
 
-    if (offsets == null || (offsets[0] == -1 && offsets[20] == -1))
+    if (offsets == null)
       return null;
     NucleicMonomer nucleicMonomer =
       new NucleicMonomer(chain, group3, seqcode,
@@ -84,8 +86,14 @@
                  byte[] offsets) {
     super(chain, group3, seqcode,
           firstAtomIndex, lastAtomIndex, offsets);
-    if (offsets[0] == -1)
-      offsets[0] = offsets[20];
+    if (offsets[0] == -1) {
+      byte leadOffset = offsets[20];
+      if (leadOffset == -1)
+        leadOffset = offsets[21];
+      if (leadOffset == -1)
+        leadOffset = offsets[22];
+      offsets[0] = leadOffset;
+    }
     this.hasRnaO2Prime = offsets[2] != -1;
     this.isPyrimidine = offsets[9] != -1;
     this.isPurine =