[Jmol-commits] SF.net SVN: jmol: [7136] trunk/Jmol/src/org/jmol/viewer/Isosurface.java

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

Revision: 7136
          http://svn.sourceforge.net/jmol/?rev=7136&view=rev
Author:   hansonr
Date:     2007-03-15 10:26:10 -0700 (Thu, 15 Mar 2007)

Log Message:
-----------
temporary checkin

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/Isosurface.java

Modified: trunk/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Isosurface.java	2007-03-15 17:23:09 UTC (rev 7135)
+++ trunk/Jmol/src/org/jmol/viewer/Isosurface.java	2007-03-15 17:26:10 UTC (rev 7136)
@@ -120,6 +120,8 @@
     myType = "isosurface";
   }
 
+  boolean solventTest = true;
+  
   boolean logMessages = false;
   boolean logCompression = false;
   boolean logCube = false;
@@ -298,6 +300,7 @@
         + " = " + value);
 
     if ("init" == propertyName) {
+      solventTest = true;
       script = (String) value;
       initializeIsosurface();
       if (!(iHaveBitSets = getScriptBitSets()))
@@ -4697,6 +4700,17 @@
       if (pt.z + rA > xyzMax.z)
         xyzMax.z = pt.z + rA;
     }
+    if (!Float.isNaN(scale)) {
+      Vector3f v = new Vector3f(xyzMax);
+      v.sub(xyzMin);
+      v.scale(0.5f);
+      xyzMin.add(v);
+      v.scale(scale);
+      xyzMax.set(xyzMin);
+      xyzMax.add(v);
+      xyzMin.sub(v);
+    }
+
     Logger.info("surface range " + xyzMin + " to " + xyzMax);
     jvxlFileHeader = new StringBuffer();
     jvxlFileHeader.append("solvent-"
@@ -4824,8 +4838,9 @@
           for (int k = pt0.z; k < pt1.z; k++) {
             float v = ptXyzTemp.distance(ptA) - rA;
             if (v < voxelData[i][j][k]) {
-              voxelData[i][j][k] = (isNearby || isWithin && ptXyzTemp.distance(point) > distance ? Float.NaN : v);
-                if (isProperty && iAtom < solvMax         
+              voxelData[i][j][k] = (isNearby || isWithin
+                  && ptXyzTemp.distance(point) > distance ? Float.NaN : v);
+              if (isProperty && iAtom < solvMax
                   && (iPt = solvent_atomNo[iAtom]) >= 0 && iPt < propMax) {
                 property[i][j][k] = theProperty[iPt];
                 //System.out.println("theprop "+ iPt + " ijk " + i + " " + j + " " + k + " = " + theProperty[iPt]);
@@ -4841,7 +4856,7 @@
       }
     }
     if ((dataType == SURFACE_SOLVENT || dataType == SURFACE_MOLECULAR)
-        && solventRadius > 0) {
+        && solventRadius > 0 && !solventTest) {
       Point3i ptA0 = new Point3i();
       Point3i ptB0 = new Point3i();
       Point3i ptA1 = new Point3i();
@@ -4889,11 +4904,12 @@
                     float v = solventRadius - dVS;
                     if (v < voxelData[i][j][k]) {
                       voxelData[i][j][k] = v;
-                      if (isProperty && iAtom < solvMax         
-                          && (iPt = solvent_atomNo[iAtom]) >= 0 && iPt < propMax) {
+                      if (isProperty && iAtom < solvMax
+                          && (iPt = solvent_atomNo[iAtom]) >= 0
+                          && iPt < propMax) {
                         property[i][j][k] = theProperty[iPt];
                         //System.out.println("theprop "+ iPt + " ijk " + i + " " + j + " " + k + " = " + theProperty[iPt]);
-                        }
+                      }
                     }
                   }
                   ptXyzTemp.add(volumetricVectors[2]);
@@ -4907,6 +4923,39 @@
           }
         }
     }
+
+    for (int iAtom = 0; iAtom < solvent_nAtoms; iAtom++) {
+      ptA = solvent_ptAtom[iAtom];
+      rA = solvent_atomRadius[iAtom];
+      if (rA > maxRadius)
+        maxRadius = rA;
+      if (isWithin && ptA.distance(point) > distance + rA + 0.5)
+        continue;
+      setGridLimitsForAtom(ptA, rA, pt0, pt1);
+      voxelPtToXYZ(pt0.x, pt0.y, pt0.z, ptXyzTemp);
+      if (solventTest)
+        for (int i = pt0.x; i < pt1.x; i++) {
+          ptY0.set(ptXyzTemp);
+          for (int j = pt0.y; j < pt1.y; j++) {
+            ptZ0.set(ptXyzTemp);
+            for (int k = pt0.z; k < pt1.z; k++) {
+              if (voxelData[i][j][k] > 0) {
+                //System.out.println("set echo myech"+i+""+j+""+k+" " + StateManager.escape(ptXyzTemp)+";echo " + TextFormat.formatDecimal(voxelData[i][j][k],1));
+                System.out.println("draw " + StateManager.escape(ptXyzTemp));
+                //float v = -(ptXyzTemp.distance(ptA) - rA - 0.4f);
+              //if (v < voxelData[i][j][k])
+                //voxelData[i][j][k] = v;
+            }
+            ptXyzTemp.add(volumetricVectors[2]);
+          }
+          ptXyzTemp.set(ptZ0);
+          ptXyzTemp.add(volumetricVectors[1]);
+        }
+        ptXyzTemp.set(ptY0);
+        ptXyzTemp.add(volumetricVectors[0]);
+      }
+    }
+    
     if (dataType == SURFACE_PROPERTY)
       voxelData = property;
     if (thePlane == null) {
@@ -4924,13 +4973,15 @@
             if (voxelData[x][y][z] < maxValue) {
               // Float.NaN will also match ">=" this way  
             } else {
-              voxelData[x][y][z] = maxValue;
+              voxelData[x][y][z] = (solventTest ? -maxValue : maxValue);
             }
     }
     Logger.debug("solvent surface time:" + (System.currentTimeMillis() - time));
   }
 
   void setGridLimitsForAtom(Point3f ptA, float rA, Point3i pt0, Point3i pt1) {
+    if (solventTest)
+      rA = rA + 1.4f;
     xyzToVoxelPt(ptA.x - rA, ptA.y - rA, ptA.z - rA, pt0);
     pt0.x -= 1;
     pt0.y -= 1;


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