[Jmol-commits] SF.net SVN: jmol: [5455] branches/v10_9/Jmol/src/org/jmol/viewer/ AminoPolymer.java

[<ha...@us...>]

Revision: 5455
          http://svn.sourceforge.net/jmol/?rev=5455&view=rev
Author:   hansonr
Date:     2006-08-30 16:20:15 -0700 (Wed, 30 Aug 2006)

Log Message:
-----------
10.9.50    11.0 beta  hydrogen bonding update

modifying hydrogen bond routine to more appropriately represent hydrogen bonds.

Modified Paths:
--------------
    branches/v10_9/Jmol/src/org/jmol/viewer/AminoPolymer.java

Modified: branches/v10_9/Jmol/src/org/jmol/viewer/AminoPolymer.java
===================================================================
--- branches/v10_9/Jmol/src/org/jmol/viewer/AminoPolymer.java	2006-08-30 21:12:12 UTC (rev 5454)
+++ branches/v10_9/Jmol/src/org/jmol/viewer/AminoPolymer.java	2006-08-30 23:20:15 UTC (rev 5455)
@@ -47,15 +47,16 @@
 
   boolean hbondsAlreadyCalculated;
 
-  final static boolean debugHbonds = false;
+  boolean debugHbonds;
 
   void calcHydrogenBonds(BitSet bsA, BitSet bsB) {
+    debugHbonds = Logger.isActiveLevel(Logger.LEVEL_DEBUG);
     initializeHbondDataStructures();
     //Frame frame = model.mmset.frame;
     //hbondMax2 = frame.hbondMax * frame.hbondMax;
     calcProteinMainchainHydrogenBonds(bsA, bsB);
     
-    if (debugHbonds) {
+    if (false && debugHbonds) {
       Logger.debug("calcHydrogenBonds");
       for (int i = 0; i < monomerCount; ++i) {
         Logger.debug("  min1Indexes=" + min1Indexes[i] +
@@ -115,13 +116,11 @@
   }
 
 
-//  private float hbondMax2;
-
   private final static float maxHbondAlphaDistance = 9;
   private final static float maxHbondAlphaDistance2 =
     maxHbondAlphaDistance * maxHbondAlphaDistance;
   private final static float minimumHbondDistance2 = 0.5f; // note: RasMol is 1/2 this. RMH
-  private final static double QConst = -332 * 0.42 * 0.2 * 1000;
+  private final static double QConst = -332 * 0.42 * 0.2 * 1000;  
 
   void bondAminoHydrogen(int indexDonor, Point3f hydrogenPoint,
                          BitSet bsA, BitSet bsB) {
@@ -140,9 +139,7 @@
       float dist2 = sourceAlphaPoint.distanceSquared(targetAlphaPoint);
       if (dist2 > maxHbondAlphaDistance2)
         continue;
-      int energy = calcHbondEnergy(sourceNitrogenPoint, hydrogenPoint, target);
-      if (debugHbonds)
-        Logger.debug("HbondEnergy=" + energy + " dist2="+dist2+" max^2="+maxHbondAlphaDistance2);
+      int energy = calcHbondEnergy(source.getNitrogenAtom(), sourceNitrogenPoint, hydrogenPoint, target);
       if (energy < energyMin1) {
         energyMin2 = energyMin1;
         indexMin2 = indexMin1;
@@ -166,61 +163,60 @@
     }
   }
 
-  int calcHbondEnergy(Point3f nitrogenPoint, Point3f hydrogenPoint,
-                      AminoMonomer target) {
+  int hPtr = 0;
+  int calcHbondEnergy(Atom nitrogen, Point3f nitrogenPoint,
+                      Point3f hydrogenPoint, AminoMonomer target) {
     Point3f targetOxygenPoint = target.getCarbonylOxygenAtomPoint();
 
+    /*
+     * the following were changed from "return -9900" to "return 0"
+     * Bob Hanson 8/30/06
+     */
     float distON2 = targetOxygenPoint.distanceSquared(nitrogenPoint);
     if (distON2 < minimumHbondDistance2)
-      return -9900;
+      return 0;
 
-    //why would this not have been in here? RMH 03/8/06
-    //   if (distON2 > hbondMax2)
-    //      return 0;
-    //nevermind! :)
-    
-    if (debugHbonds)
-      Logger.debug("calchbondenergy: "+hydrogenPoint.x+","+hydrogenPoint.y+","+hydrogenPoint.z);
-
     float distOH2 = targetOxygenPoint.distanceSquared(hydrogenPoint);
     if (distOH2 < minimumHbondDistance2)
-      return -9900;
+      return 0;
 
     Point3f targetCarbonPoint = target.getCarbonylCarbonAtomPoint();
     float distCH2 = targetCarbonPoint.distanceSquared(hydrogenPoint);
     if (distCH2 < minimumHbondDistance2)
-      return -9900;
+      return 0;
 
     float distCN2 = targetCarbonPoint.distanceSquared(nitrogenPoint);
     if (distCN2 < minimumHbondDistance2)
-      return -9900;
-
+      return 0;
+    
+    /*
+     * I'm adding these two because they just makes sense -- Bob Hanson
+     */
+    
     double distOH = Math.sqrt(distOH2);
     double distCH = Math.sqrt(distCH2);
     double distCN = Math.sqrt(distCN2);
     double distON = Math.sqrt(distON2);
 
-    int energy =
-      (int)((QConst/distOH - QConst/distCH + QConst/distCN - QConst/distON));
+    int energy = (int) ((QConst / distOH - QConst / distCH + QConst / distCN - QConst
+        / distON));
 
+    boolean isHbond = (distCN2 > distCH2 && distOH <= 3.0f && energy <= -500);
     if (debugHbonds)
-      Logger.debug(" distOH=" + distOH +
-                         " distCH=" + distCH +
-                         " distCN=" + distCN +
-                         " distON=" + distON +
-                         " energy=" + energy);
-    if (energy < -9900)
-      return -9900;
-    if (energy > -500)
-      return 0;
-    return energy;
+      Logger.debug("draw calcHydrogen"+(++hPtr)+ " ("+nitrogen.getInfo()+") {" + hydrogenPoint.x + " "
+          + hydrogenPoint.y + " " + hydrogenPoint.z + "} #" + isHbond + " "
+          + nitrogen.getInfo() + " " + target.getLeadAtom().getInfo()
+          + " distOH=" + distOH + " distCH=" + distCH + " distCN=" + distCN
+          + " distON=" + distON + " energy=" + energy);
+
+    return (!isHbond ? 0 : energy < -9900 ? -9900 : energy);
   }
 
   void createResidueHydrogenBond(int indexAminoGroup, int indexCarbonylGroup,
                                  BitSet bsA, BitSet bsB) {
     short order;
     int aminoBackboneHbondOffset = indexAminoGroup - indexCarbonylGroup;
-    if (debugHbonds) 
+    if (false && debugHbonds) 
       Logger.debug("aminoBackboneHbondOffset=" +
                          aminoBackboneHbondOffset +
                          " amino:" +
@@ -249,9 +245,6 @@
     default:
       order = JmolConstants.BOND_H_REGULAR;
     }
-    if (debugHbonds)
-      Logger.debug("createResidueHydrogenBond(" + indexAminoGroup +
-                         "," + indexCarbonylGroup);
     AminoMonomer donor = (AminoMonomer)monomers[indexAminoGroup];
     Atom nitrogen = donor.getNitrogenAtom();
     AminoMonomer recipient = (AminoMonomer)monomers[indexCarbonylGroup];


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