[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel AminoPolymer.java,1.5,1.6 Group.java,1.12,1.13

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

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2173/src/org/openscience/jmol/viewer/datamodel

Modified Files:
	AminoPolymer.java Group.java 
Log Message:
added hbond group offset to group


Index: AminoPolymer.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/AminoPolymer.java,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- AminoPolymer.java	18 May 2004 21:35:22 -0000	1.5
+++ AminoPolymer.java	21 May 2004 17:14:36 -0000	1.6
@@ -160,9 +160,19 @@
     return energy;
   }
 
-  void createResidueHydrogenBond(int indexAmino, int indexCarbonyl) {
+  void createResidueHydrogenBond(int indexAminoGroup,
+                                 int indexCarbonylGroup) {
     int order;
-    switch (indexAmino - indexCarbonyl) {
+    int aminoBackboneHbondOffset = indexAminoGroup - indexCarbonylGroup;
+    /*
+    System.out.println("aminoBackboneHbondOffset=" +
+                       aminoBackboneHbondOffset +
+                       " amino:" +
+                       groups[indexAminoGroup].getSeqcodeString() +
+                       " carbonyl:" +
+                       groups[indexCarbonylGroup].getSeqcodeString());
+    */
+    switch (aminoBackboneHbondOffset) {
     case 2:
       order = JmolConstants.BOND_H_PLUS_2;
       break;
@@ -184,10 +194,12 @@
     default:
       order = JmolConstants.BOND_H_REGULAR;
     }
-    //    System.out.println("createResidueHydrogenBond(" + indexAmino +
-    //                       "," + indexCarbonyl);
-    Atom nitrogen = groups[indexAmino].getNitrogenAtom();
-    Atom oxygen = groups[indexCarbonyl].getCarbonylOxygenAtom();
+    //    System.out.println("createResidueHydrogenBond(" + indexAminoGroup +
+    //                       "," + indexCarbonylGroup);
+    Group groupDonor = groups[indexAminoGroup];
+    groupDonor.setAminoBackboneHbondOffset(aminoBackboneHbondOffset);
+    Atom nitrogen = groupDonor.getNitrogenAtom();
+    Atom oxygen = groups[indexCarbonylGroup].getCarbonylOxygenAtom();
     Frame frame = chain.pdbmodel.pdbfile.frame;
     frame.bondAtoms(nitrogen, oxygen, order);
   }

Index: Group.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Group.java,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- Group.java	18 May 2004 13:16:12 -0000	1.12
+++ Group.java	21 May 2004 17:14:36 -0000	1.13
@@ -52,6 +52,8 @@
   int nucleicCount = 0;
 
 
+  short aminoBackboneHbondOffset = 0;
+
 
   public Group(Chain chain,
                   int sequenceNumber, char insertionCode, String group3) {
@@ -450,4 +452,13 @@
     return "[" + getGroup3() + "-" + getSeqcodeString() + "]";
   }
 
+  ////////////////////////////////////////////////////////////////
+
+  void setAminoBackboneHbondOffset(int aminoBackboneHbondOffset) {
+    this.aminoBackboneHbondOffset = (short)aminoBackboneHbondOffset;
+  }
+  
+  int getAminoBackboneHbondOffset() {
+    return aminoBackboneHbondOffset;
+  }
 }