Revision: 18327
          http://sourceforge.net/p/jmol/code/18327
Author:   hansonr
Date:     2013-06-13 22:54:03 +0000 (Thu, 13 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.13"

bug fix: draw ARROW ATOM/BOND broken
bug fix: draw ARROW with offset disallows set picking draw adjustments

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
    trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
    trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java
    trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java
    trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
    trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
    trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
    trunk/Jmol/src/org/jmol/shapespecial/Draw.java
    trunk/Jmol/src/org/jmol/shapespecial/DrawMesh.java
    trunk/Jmol/src/org/jmol/viewer/Jmol.properties
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Added Paths:
-----------
    trunk/Jmol/src/org/jmol/minimize/MinPosition.java

Added: trunk/Jmol/src/org/jmol/minimize/MinPosition.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/MinPosition.java                           
(rev 0)
+++ trunk/Jmol/src/org/jmol/minimize/MinPosition.java   2013-06-13 22:54:03 UTC 
(rev 18327)
@@ -0,0 +1,8 @@
+package org.jmol.minimize;
+
+public class MinPosition extends MinObject {
+  MinPosition(int[] data, double[] ddata) {
+    this.data = data;
+    this.ddata = ddata;
+  }
+}

Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java       
2013-06-13 22:44:57 UTC (rev 18326)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/Calculations.java       
2013-06-13 22:54:03 UTC (rev 18327)
@@ -30,6 +30,7 @@
 import org.jmol.minimize.MinAngle;
 import org.jmol.minimize.MinAtom;
 import org.jmol.minimize.MinBond;
+import org.jmol.minimize.MinPosition;
 import org.jmol.minimize.MinTorsion;
 import org.jmol.minimize.Util;
 import org.jmol.util.ArrayUtil;
@@ -54,7 +55,8 @@
   final static int CALC_OOP = 4;
   final static int CALC_VDW = 5;
   final static int CALC_ES = 6;
-  final static int CALC_MAX = 7;
+  final static int CALC_POSITION = 7; 
+  final static int CALC_MAX = 8;
 
   ForceField ff;
   JmolList<Object[]>[] calculations = 
ArrayUtil.createArrayOfArrayList(CALC_MAX);
@@ -67,6 +69,7 @@
   MinBond[] minBonds;
   MinAngle[] minAngles;
   MinTorsion[] minTorsions;
+  MinPosition[] minPositions;
   JmolList<Object[]> constraints;
   boolean isPreliminary;
 
@@ -76,13 +79,14 @@
 
   Calculations(ForceField ff, 
       MinAtom[] minAtoms, MinBond[] minBonds,
-      MinAngle[] minAngles, MinTorsion[] minTorsions, 
+      MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] 
minPositions,
       JmolList<Object[]> constraints) {
     this.ff = ff;
     this.minAtoms = minAtoms;
     this.minBonds = minBonds;
     this.minAngles = minAngles;
     this.minTorsions = minTorsions;
+    this.minPositions = minPositions;
     atomCount = minAtoms.length;
     bondCount = minBonds.length;
     angleCount = minAngles.length;
@@ -154,10 +158,10 @@
   private double calc(int iType, boolean gradients) {
     logging = loggingEnabled && !silent;
     this.gradients = gradients;
-    JmolList<Object[]> calc = calculations[iType];
+    JmolList<Object[]> calcs = calculations[iType];
     int nCalc;
     double energy = 0;
-    if (calc == null || (nCalc = calc.size()) == 0)
+    if (calcs == null || (nCalc = calcs.size()) == 0)
       return 0;
     if (logging)
       appendLogData(getDebugHeader(iType));
@@ -194,6 +198,10 @@
     return calc(CALC_OOP, gradients);
   }
 
+  double energyPos(boolean gradients) {
+    return calc(CALC_POSITION, gradients);
+  }
+
   double energyVDW(boolean gradients) {
     return calc(CALC_VDW, gradients);
   }
@@ -402,6 +410,12 @@
     case -1:
       //Override to give reference
       break;
+    case CALC_POSITION:
+      return
+          "\nA T O M   P O S I T I O N\n\n"
+         +"  ATOM  TYPE  POSITION                    FORCE\n"
+         +"              X        Y        Z        CONSTANT   DELTA   
ENERGY\n"
+         +"----------------------------------------------------------------";
     case CALC_DISTANCE:
       return
            "\nB O N D   S T R E T C H I N G (" + bondCount + " bonds)\n\n"
@@ -455,6 +469,13 @@
   protected String getDebugLineC(int iType, Calculation c) {
     float energy = ff.toUserUnits(c.energy);
     switch (iType) {
+    case CALC_POSITION:
+      return TextFormat.sprintf(
+          "%3d  %-5s %8.3f    %8.3f    %8.3f    %8.3f    %8.3f",
+          "sFI", new Object[] { minAtoms[c.ia].sType, 
+          new float[] { (float)c.dData[0], (float)c.dData[1], 
(float)c.dData[2], (float)c.dData[3], 
+              (float)c.delta, energy },
+          new int[] { minAtoms[c.ia].atom.getAtomNumber() }});
     case CALC_DISTANCE:
       return TextFormat.sprintf(
           "%3d %3d  %-5s %-5s  %4.2f%8.3f   %8.3f     %8.3f   %8.3f   %8.3f",

Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java   
2013-06-13 22:44:57 UTC (rev 18326)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsMMFF.java   
2013-06-13 22:54:03 UTC (rev 18327)
@@ -32,7 +32,9 @@
 import org.jmol.minimize.MinAtom;
 import org.jmol.minimize.MinBond;
 import org.jmol.minimize.MinObject;
+import org.jmol.minimize.MinPosition;
 import org.jmol.minimize.MinTorsion;
+import org.jmol.minimize.forcefield.CalculationsUFF.PositionCalc;
 import org.jmol.util.TextFormat;
 
 /**
@@ -56,14 +58,15 @@
   VDWCalc vdwCalc;
   ESCalc esCalc;
   SBCalc sbCalc;
+  PositionCalc posCalc;
   
   ForceFieldMMFF mmff;
   
   CalculationsMMFF(ForceField ff, Map<Integer, Object> ffParams, 
       MinAtom[] minAtoms, MinBond[] minBonds, 
-      MinAngle[] minAngles, MinTorsion[] minTorsions,
+      MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] 
minPositions,
       JmolList<Object[]> constraints) {
-    super(ff, minAtoms, minBonds, minAngles, minTorsions, constraints);
+    super(ff, minAtoms, minBonds, minAngles, minTorsions, minPositions, 
constraints);
     mmff = (ForceFieldMMFF) ff;
     this.ffParams = ffParams;
     bondCalc = new DistanceCalc();
@@ -73,6 +76,7 @@
     oopCalc = new OOPCalc();
     vdwCalc = new VDWCalc();
     esCalc = new ESCalc();
+    posCalc = new PositionCalc();
   }
   
   @Override
@@ -112,6 +116,14 @@
       if (isInvertible(minAtoms[i]))
         oopCalc.setData(calc, i);
 
+    if (minPositions != null) {
+      calc = calculations[CALC_POSITION] = new JmolList<Object[]>();
+      // set up the special atom arrays
+      PositionCalc posCalc = new PositionCalc();
+      for (int i = minPositions.length; --i >= 0;)
+        posCalc.setData(calc, minPositions[i].data, minPositions[i].ddata);
+    }
+
     pairSearch(calculations[CALC_VDW] = new  JmolList<Object[]>(), new 
VDWCalc(),
         calculations[CALC_ES] = new  JmolList<Object[]>(), new ESCalc());
 
@@ -179,6 +191,8 @@
       return vdwCalc.compute(dataIn);
     case CALC_ES:
       return esCalc.compute(dataIn);
+    case CALC_POSITION:
+      return posCalc.compute(dataIn);
     }
     return 0.0;
   }
@@ -384,6 +398,21 @@
     }
   }
   
+  class PositionCalc extends Calculation {
+
+    @Override
+    double compute(Object[] dataIn) {
+      // TODO
+      return 0;
+    }
+
+    public void setData(JmolList<Object[]> calc, int[] data, double[] ddata) {
+      // TODO
+      
+    }
+    
+  }
+  
   class OOPCalc extends Calculation {
 
     final static double FOOPD = 0.043844 * RAD_TO_DEG;

Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java    
2013-06-13 22:44:57 UTC (rev 18326)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/CalculationsUFF.java    
2013-06-13 22:54:03 UTC (rev 18327)
@@ -31,6 +31,7 @@
 import org.jmol.minimize.MinAngle;
 import org.jmol.minimize.MinAtom;
 import org.jmol.minimize.MinBond;
+import org.jmol.minimize.MinPosition;
 import org.jmol.minimize.MinTorsion;
 import org.jmol.minimize.Util;
 
@@ -71,19 +72,21 @@
   TorsionCalc torsionCalc;
   OOPCalc oopCalc;
   VDWCalc vdwCalc;
+  PositionCalc posCalc;
   //ESCalc esCalc;
     
   CalculationsUFF(ForceField ff, Map<Object, FFParam> ffParams, 
       MinAtom[] minAtoms, MinBond[] minBonds, 
-      MinAngle[] minAngles, MinTorsion[] minTorsions, 
+      MinAngle[] minAngles, MinTorsion[] minTorsions, MinPosition[] 
minPositions,
       JmolList<Object[]> constraints) {
-    super(ff, minAtoms, minBonds, minAngles, minTorsions, constraints);    
+    super(ff, minAtoms, minBonds, minAngles, minTorsions, minPositions, 
constraints);    
     this.ffParams = ffParams;
     bondCalc = new DistanceCalc();
     angleCalc = new AngleCalc();
     torsionCalc = new TorsionCalc();
     oopCalc = new OOPCalc();
     vdwCalc = new VDWCalc();
+    posCalc = new PositionCalc();
     //esCalc = new ESCalc();
   }
   
@@ -98,28 +101,28 @@
     JmolList<Object[]> calc;
 
     DistanceCalc distanceCalc = new DistanceCalc();
-    calc = calculations[CALC_DISTANCE] = new  JmolList<Object[]>();
+    calc = calculations[CALC_DISTANCE] = new JmolList<Object[]>();
     for (int i = 0; i < bondCount; i++) {
       MinBond bond = minBonds[i];
       double bondOrder = bond.order;
       if (bond.isAromatic)
         bondOrder = 1.5;
       if (bond.isAmide)
-        bondOrder = 1.41;  
+        bondOrder = 1.41;
       distanceCalc.setData(calc, bond.data[0], bond.data[1], bondOrder);
     }
 
-    calc = calculations[CALC_ANGLE] = new  JmolList<Object[]>();
+    calc = calculations[CALC_ANGLE] = new JmolList<Object[]>();
     AngleCalc angleCalc = new AngleCalc();
     for (int i = minAngles.length; --i >= 0;)
       angleCalc.setData(calc, minAngles[i].data);
 
-    calc = calculations[CALC_TORSION] = new  JmolList<Object[]>();
+    calc = calculations[CALC_TORSION] = new JmolList<Object[]>();
     TorsionCalc torsionCalc = new TorsionCalc();
     for (int i = minTorsions.length; --i >= 0;)
       torsionCalc.setData(calc, minTorsions[i].data);
 
-    calc = calculations[CALC_OOP] = new  JmolList<Object[]>();
+    calc = calculations[CALC_OOP] = new JmolList<Object[]>();
     // set up the special atom arrays
     OOPCalc oopCalc = new OOPCalc();
     int elemNo;
@@ -129,11 +132,20 @@
         oopCalc.setData(calc, i, elemNo);
     }
 
+    if (minPositions != null) {
+      calc = calculations[CALC_POSITION] = new JmolList<Object[]>();
+      // set up the special atom arrays
+      PositionCalc posCalc = new PositionCalc();
+      for (int i = minPositions.length; --i >= 0;)
+        posCalc.setData(calc, minPositions[i].data, minPositions[i].ddata);
+    }
+
     // Note that while the UFF paper mentions an electrostatic term,
     // it does not actually use it. Both Towhee and the UFF FAQ
     // discourage the use of electrostatics with UFF.
 
-    pairSearch(calculations[CALC_VDW] = new  JmolList<Object[]>(), new 
VDWCalc(), null, null);
+    pairSearch(calculations[CALC_VDW] = new JmolList<Object[]>(),
+        new VDWCalc(), null, null);
     return true;
   }
 
@@ -181,6 +193,8 @@
       return oopCalc.compute(dataIn);
     case CALC_VDW:
       return vdwCalc.compute(dataIn);
+    case CALC_POSITION:
+      return posCalc.compute(dataIn);
     //case CALC_ES:
       //return esCalc.compute(dataIn);
     }
@@ -490,6 +504,21 @@
   final static double KCAL22 = 22.0 * KCAL_TO_KJ;
   final static double KCAL44 = 44.0 * KCAL_TO_KJ;
   
+  class PositionCalc extends Calculation {
+
+    @Override
+    double compute(Object[] dataIn) {
+      // TODO
+      return 0;
+    }
+
+    public void setData(JmolList<Object[]> calc, int[] data, double[] ddata) {
+      // TODO
+      
+    }
+    
+  }
+  
   class OOPCalc extends Calculation {
 
     void setData(JmolList<Object[]> calc, int ib, int elemNo) {

Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java 2013-06-13 
22:44:57 UTC (rev 18326)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceField.java 2013-06-13 
22:54:03 UTC (rev 18327)
@@ -35,6 +35,7 @@
 import org.jmol.minimize.MinAngle;
 import org.jmol.minimize.MinAtom;
 import org.jmol.minimize.MinBond;
+import org.jmol.minimize.MinPosition;
 import org.jmol.minimize.MinTorsion;
 import org.jmol.minimize.Minimizer;
 import org.jmol.minimize.Util;
@@ -89,6 +90,7 @@
   MinBond[] minBonds;
   MinAngle[] minAngles;
   MinTorsion[] minTorsions;
+  MinPosition[] minPositions;
   BS bsFixed;
   
   Minimizer minimizer;
@@ -324,6 +326,10 @@
     return calc.energyOOP(gradients); 
   }
 
+  double energyPosition(boolean gradients) {
+    return calc.energyPos(gradients); 
+  }
+
   double energyVDW(boolean gradients) {
     return calc.energyVDW(gradients);
   }

Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java     
2013-06-13 22:44:57 UTC (rev 18326)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldMMFF.java     
2013-06-13 22:54:03 UTC (rev 18327)
@@ -249,7 +249,7 @@
     setModelFields();
     fixTypes();
     calc = new CalculationsMMFF(this, ffParams, minAtoms, minBonds, 
-        minAngles, minTorsions, minimizer.constraints);
+        minAngles, minTorsions, minPositions, minimizer.constraints);
     calc.setLoggingEnabled(true);
     return calc.setupCalculations();
   }

Modified: trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java      
2013-06-13 22:44:57 UTC (rev 18326)
+++ trunk/Jmol/src/org/jmol/minimize/forcefield/ForceFieldUFF.java      
2013-06-13 22:54:03 UTC (rev 18327)
@@ -64,7 +64,7 @@
       return false;
     setAtomTypes(bsElements, elemnoMax);
     calc = new CalculationsUFF(this, ffParams, minAtoms, minBonds, 
-        minAngles, minTorsions, minimizer.constraints);
+        minAngles, minTorsions, minPositions, minimizer.constraints);
     return calc.setupCalculations();
   }
   

Modified: trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java     2013-06-13 
22:44:57 UTC (rev 18326)
+++ trunk/Jmol/src/org/jmol/renderspecial/DrawRenderer.java     2013-06-13 
22:54:03 UTC (rev 18327)
@@ -300,9 +300,9 @@
     for (int i = 0; i < 4; i++)
       viewer.transformPtScr(vertices[i], screens[i]);
 
-    float f = 1; // bendiness
+    float f = 4 * getArrowScale(); // bendiness
     float endoffset = 0.2f;
-    float offsetside = 10 * width;
+    float offsetside = (width == 0 ? 0.1f : width);
     
     pt0.set(screens[0].x, screens[0].y, screens[0].z);
     pt1.set(screens[1].x, screens[1].y, screens[1].z);
@@ -380,11 +380,7 @@
                                boolean isBarb) {
     if (dmesh.noHead)
       return;
-    float fScale = dmesh.drawArrowScale;
-    if (fScale == 0)
-      fScale = viewer.getFloat(T.defaultdrawarrowscale) * (dmesh.connections 
== null ? 1f : 0.5f);
-    if (fScale <= 0)
-      fScale = 0.5f;
+    float fScale = getArrowScale();
     if (isTransformed)
       fScale *= 40;
     if (factor2 > 0)
@@ -431,6 +427,15 @@
       g3d.fillCylinderScreen3I(GData.ENDCAPS_OPENEND, diameter, pt0i, pt1i, 
null, null, mad / 2000f);
   }
 
+  private float getArrowScale() {
+    float fScale = dmesh.scale;
+    if (fScale == 0)
+      fScale = viewer.getFloat(T.defaultdrawarrowscale) * (dmesh.connections 
== null ? 1f : 0.5f);
+    if (fScale <= 0)
+      fScale = 0.5f;
+    return fScale;
+  }
+
   private final BS bsHandles = new BS();
   
   private void renderHandles() {

Modified: trunk/Jmol/src/org/jmol/shapespecial/Draw.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/Draw.java      2013-06-13 22:44:57 UTC 
(rev 18326)
+++ trunk/Jmol/src/org/jmol/shapespecial/Draw.java      2013-06-13 22:54:03 UTC 
(rev 18327)
@@ -1032,11 +1032,11 @@
      * have to watch out for double-listed vertices
      * 
      */
-    if (newScale == 0 || dmesh.vertexCount == 0 || dmesh.scale == newScale)
+    if (newScale == 0 || dmesh.vertexCount == 0 && dmesh.connections == null 
|| dmesh.scale == newScale)
       return;
     float f = newScale / dmesh.scale;
     dmesh.scale = newScale;
-    if (dmesh.haveXyPoints || dmesh.drawType == EnumDrawType.ARC || 
dmesh.drawType == EnumDrawType.CIRCLE || dmesh.drawType == 
EnumDrawType.CIRCULARPLANE)
+    if (dmesh.isRenderScalable())
       return; // done in renderer
     V3 diff = new V3();
     int iptlast = -1;
@@ -1223,7 +1223,7 @@
     }
     P3 pt = new P3();
     int ptVertex = vertexes[iVertex];
-    P3 coord = P3.newP(mesh.vertices[ptVertex]);
+    P3 coord = P3.newP(mesh.altVertices == null ? mesh.vertices[ptVertex] : 
(P3) mesh.altVertices[ptVertex]);
     P3 newcoord = new P3();
     V3 move = new V3();
     viewer.transformPt3f(coord, pt);
@@ -1260,8 +1260,7 @@
    * @param bsVisible
    * @return true if found
    */
-  private boolean findPickedObject(int x, int y, boolean isPicking,
-                                   BS bsVisible) {
+  private boolean findPickedObject(int x, int y, boolean isPicking, BS 
bsVisible) {
     int dmin2 = MAX_OBJECT_CLICK_DISTANCE_SQUARED;
     if (gdata.isAntialiased()) {
       x <<= 1;
@@ -1286,7 +1285,9 @@
           for (int iVertex = (m.isTriangleSet ? 3
               : m.polygonIndexes[iModel].length); --iVertex >= 0;) {
             try {
-              P3 pt = m.vertices[m.polygonIndexes[iModel][iVertex]];
+              int iv = m.polygonIndexes[iModel][iVertex];
+              P3 pt = (m.altVertices == null ? m.vertices[iv]
+                  : (P3) m.altVertices[iv]);
               int d2 = coordinateInRange(x, y, pt, dmin2, ptXY);
               if (d2 >= 0) {
                 pickedMesh = m;
@@ -1344,7 +1345,7 @@
     else if (dmesh.isBarb)
       str.append(" barb");
     if (dmesh.scale != 1
-        && (dmesh.haveXyPoints || dmesh.drawType == EnumDrawType.CIRCLE || 
dmesh.drawType == EnumDrawType.ARC))
+        && (dmesh.haveXyPoints || dmesh.connections != null || dmesh.drawType 
== EnumDrawType.CIRCLE || dmesh.drawType == EnumDrawType.ARC))
       str.append(" scale ").appendF(dmesh.scale);
     if (dmesh.width != 0)
       str.append(" diameter ").appendF(

Modified: trunk/Jmol/src/org/jmol/shapespecial/DrawMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapespecial/DrawMesh.java  2013-06-13 22:44:57 UTC 
(rev 18326)
+++ trunk/Jmol/src/org/jmol/shapespecial/DrawMesh.java  2013-06-13 22:54:03 UTC 
(rev 18327)
@@ -118,4 +118,17 @@
     //no! title = (String[]) ArrayUtil.deleteElements(title, modelIndex, 1);
   }
 
+  public boolean isRenderScalable() {
+    switch (drawType) {
+    case ARROW:
+      return (connections != null);
+    case ARC:
+    case CIRCLE: 
+    case CIRCULARPLANE:
+      return true;
+    default:
+      return haveXyPoints;
+    }
+  }
+
 }

Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties      2013-06-13 22:44:57 UTC 
(rev 18326)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties      2013-06-13 22:54:03 UTC 
(rev 18327)
@@ -9,8 +9,10 @@
 #  The quotes above look odd for a parameter file, but they are 
 #  important for the JavaScript version of Jmol.
 
-___JmolVersion="13.1.17_dev_2013.06.12"
+___JmolVersion="13.1.17_dev_2013.06.13"
 
+bug fix: draw ARROW ATOM/BOND broken
+bug fix: draw ARROW with offset disallows set picking draw adjustments
 bug fix: concurrrent loading of two cif files by two different applets fails 
 bug fix: draw LINEDATA not operative (undocumented, for state; from draw xxx 
INTERSECT yyy)
   -- needs revision to create DATA option; can be huge and very long to 
process state file

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java  2013-06-13 22:44:57 UTC (rev 
18326)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java  2013-06-13 22:54:03 UTC (rev 
18327)
@@ -9732,6 +9732,7 @@
   }
 
   public void cachePut(String key, Object data) {
+    // PyMOL reader and isosurface only
     fileManager.cachePut(key, data);
   }
 
@@ -9766,10 +9767,12 @@
    */
   @Override
   public void cacheFile(String fileName, byte[] bytes) {
+    // PyMOL reader only
     fileManager.cachePut(fileName, bytes);
   }
 
   public int cacheFileByName(String fileName, boolean isAdd) {
+    // cache command in script
     return fileManager.cacheFileByNameAdd(fileName, isAdd);
   }
 

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