[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel Group.java,1.10,1.11 NucleotidePolymer.java,1.6,1.7

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

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11575/src/org/openscience/jmol/viewer/datamodel

Modified Files:
	Group.java NucleotidePolymer.java 
Log Message:
more debugging of nucleotide chain hbonds


Index: Group.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Group.java,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- Group.java	18 May 2004 07:54:07 -0000	1.10
+++ Group.java	18 May 2004 09:22:22 -0000	1.11
@@ -362,9 +362,6 @@
       nucleotideIndices[atomid -
                         JmolConstants.ATOMID_NUCLEOTIDE_MIN] =
         atomIndex;
-      if (atomid == JmolConstants.ATOMID_N1) {
-        System.out.println("register " + this + " N1=" + atomIndex);
-      }
     }
     ++nucleicCount;
   }
@@ -394,6 +391,21 @@
             nucleicCount > 5);
   }
 
+  Atom getNucleotideAtomID(int atomid) {
+    if (atomid < JmolConstants.ATOMID_NUCLEOTIDE_MIN ||
+        atomid >= JmolConstants.ATOMID_NUCLEOTIDE_MAX) {
+      System.out.println("getNucleotideAtomID out of bounds");
+      return null;
+    }
+    int index = atomid - JmolConstants.ATOMID_NUCLEOTIDE_MIN;
+    Atom atom = getAtomIndex(nucleotideIndices[index]);
+    if (atom == null)
+      System.out.println("getNucleotideAtomID(" + atomid + ") -> null ?" +
+                         " nucleotideIndices[" + index + "]=" +
+                         nucleotideIndices[index]);
+    return atom;
+  }
+
   Atom getAtomIndex(int atomIndex) {
     return (atomIndex < 0
             ? null
@@ -402,17 +414,14 @@
 
   Atom getPurineN1() {
     Atom n1 = ((groupID >= 23 && groupID <= 28)
-               ? getAtomIndex(JmolConstants.ATOMID_N1 -
-                              JmolConstants.ATOMID_NUCLEOTIDE_MIN)
+               ? getNucleotideAtomID(JmolConstants.ATOMID_N1)
                : null);
-    System.out.println("getPurineN1(" + this + ") -> " + n1);
     return n1;
   }
 
   Atom getPyrimidineN3() {
     return ((groupID >= 29 && groupID <= 34)
-            ? getAtomIndex(JmolConstants.ATOMID_N3 -
-                           JmolConstants.ATOMID_NUCLEOTIDE_MIN)
+            ? getNucleotideAtomID(JmolConstants.ATOMID_N3)
             : null);
   }
             
@@ -424,10 +433,16 @@
             groupID >= 54 && groupID <= 56);
   }
 
-  Atom getAtomID(int specialAtomID) {
-    if (specialAtomID >= JmolConstants.ATOMID_NUCLEOTIDE_MIN &&
-        specialAtomID < JmolConstants.ATOMID_NUCLEOTIDE_MAX)
-      return getAtomIndex(specialAtomID - JmolConstants.ATOMID_NUCLEOTIDE_MIN);
-    return null;
+  void dumpNucleotideIndices() {
+    System.out.println("dumpNucleotideIndices(" + this + "," + groupID + ")");
+    if (nucleotideIndices == null) {
+      System.out.println("  nucleotideIndices=null");
+    } else {
+      System.out.println("  ");
+      for (int i = 0; i < nucleotideIndices.length; ++i)
+        System.out.print(nucleotideIndices[i] + " ");
+      System.out.println("\n");
+    }
   }
+
 }

Index: NucleotidePolymer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/NucleotidePolymer.java,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- NucleotidePolymer.java	18 May 2004 07:54:07 -0000	1.6
+++ NucleotidePolymer.java	18 May 2004 09:22:22 -0000	1.7
@@ -108,9 +108,10 @@
   void lookForHbonds(NucleotidePolymer other) {
     for (int i = count; --i >= 0; ) {
       Group myNucleotide = groups[i];
+      myNucleotide.dumpNucleotideIndices();
       Atom myN1 = myNucleotide.getPurineN1();
       if (myN1 != null) {
-        System.out.println("lookForHbonds myN1=" + myN1.atomIndex + " " + myN1);
+        //        System.out.println("lookForHbonds myN1=" + myN1.atomIndex + " " + myN1);
         Atom bestN3 = null;
         float minDist2 = 5*5;
         Group otherNucleotide = null;
@@ -127,20 +128,23 @@
         }
         if (bestN3 != null) {
           if (myNucleotide.isGuanine()) {
-            Atom myN2 = myNucleotide.getAtomID(JmolConstants.ATOMID_N2);
+            Atom myN2 =
+              myNucleotide.getNucleotideAtomID(JmolConstants.ATOMID_N2);
             Atom otherO2 =
-              otherNucleotide.getAtomID(JmolConstants.ATOMID_O2);
+              otherNucleotide.getNucleotideAtomID(JmolConstants.ATOMID_O2);
             if (myN2 != null && otherO2 != null)
               createHydrogenBond(myN2, otherO2);
-            Atom myO6 = myNucleotide.getAtomID(JmolConstants.ATOMID_O6);
+            Atom myO6 =
+              myNucleotide.getNucleotideAtomID(JmolConstants.ATOMID_O6);
             Atom otherN4 =
-              otherNucleotide.getAtomID(JmolConstants.ATOMID_N4);
+              otherNucleotide.getNucleotideAtomID(JmolConstants.ATOMID_N4);
             if (myO6 != null && otherN4 != null)
               createHydrogenBond(myN2, otherO2);
           } else {
-            Atom myN6 = myNucleotide.getAtomID(JmolConstants.ATOMID_N6);
+            Atom myN6 =
+              myNucleotide.getNucleotideAtomID(JmolConstants.ATOMID_N6);
             Atom otherO4 =
-              otherNucleotide.getAtomID(JmolConstants.ATOMID_O4);
+              otherNucleotide.getNucleotideAtomID(JmolConstants.ATOMID_O4);
             if (myN6 != null && otherO4 != null)
               createHydrogenBond(myN6, otherO4);
           }