[Jmol-commits] SF.net SVN: jmol: [6555] trunk/Jmol/src/org/jmol/viewer

[<hansonr@us...>]

Revision: 6555
          http://svn.sourceforge.net/jmol/?rev=6555&view=rev
Author:   hansonr
Date:     2006-12-30 20:26:32 -0800 (Sat, 30 Dec 2006)

Log Message:
-----------
implements 

-select atomX/atomY/atomZ [<,>,=,<=,>=,!=] x.xx
-set navigationPeriodic
-set zShade
-expanded load "filename" {i j k} 

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/viewer/BallsRenderer.java
    trunk/Jmol/src/org/jmol/viewer/Eval.java
    trunk/Jmol/src/org/jmol/viewer/Frame.java
    trunk/Jmol/src/org/jmol/viewer/ModelManager.java
    trunk/Jmol/src/org/jmol/viewer/StateManager.java
    trunk/Jmol/src/org/jmol/viewer/SticksRenderer.java
    trunk/Jmol/src/org/jmol/viewer/TransformManager.java
    trunk/Jmol/src/org/jmol/viewer/TransformManager10.java
    trunk/Jmol/src/org/jmol/viewer/TransformManager11.java
    trunk/Jmol/src/org/jmol/viewer/Viewer.java

Modified: trunk/Jmol/src/org/jmol/viewer/BallsRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/BallsRenderer.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/BallsRenderer.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -30,13 +30,14 @@
 class BallsRenderer extends ShapeRenderer {
 
   int minX, maxX, minY, maxY, minZ, maxZ;
-  
+  boolean isNav;
   void render() {
     minX = rectClip.x;
     maxX = minX + rectClip.width;
     minY = rectClip.y;
     maxY = minY + rectClip.height;
     boolean slabbing = viewer.getSlabEnabled();
+    isNav = viewer.getNavigationMode();
     if (slabbing) {
       minZ = g3d.getSlab();
       maxZ = g3d.getDepth();
@@ -52,6 +53,11 @@
       if (slabbing) {
         if (g3d.isClippedZ(atom.screenZ)) {
           atom.clickabilityFlags = 0;
+          //note that in the case of navigation, 
+          //maxZ is set to Integer.MAX_VALUE.
+          
+          if (isNav)
+            continue;
           int r = atom.screenDiameter / 2;
           if (atom.screenZ < minZ - r || atom.screenZ > maxZ + r)
             continue;
@@ -91,7 +97,8 @@
   }
 
   void renderBall(Atom atom) {
-    g3d.fillSphereCentered(atom.colixAtom, atom.screenDiameter,
+    short colix = atom.colixAtom;
+    g3d.fillSphereCentered(colix, atom.screenDiameter,
                            atom.screenX, atom.screenY, atom.screenZ);
   }
 }

Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -1304,6 +1304,15 @@
       case Token.model:
         propertyValue = atom.getModelTagNumber();
         break;
+      case Token.atomX:
+        propertyValue = (int)(atom.x * 100);
+        break;
+      case Token.atomY:
+        propertyValue = (int)(atom.y * 100);
+        break;
+      case Token.atomZ:
+        propertyValue = (int)(atom.z * 100);
+        break;
       default:
         unrecognizedAtomProperty(property);
       }
@@ -1748,9 +1757,9 @@
     } else if (pt.z == 0) {
       pt3.set(pt1.x, 0, 1);
     }
-    viewer.convertFractionalCoordinates(pt1);
-    viewer.convertFractionalCoordinates(pt2);
-    viewer.convertFractionalCoordinates(pt3);
+    viewer.toCartesian(pt1);
+    viewer.toCartesian(pt2);
+    viewer.toCartesian(pt3);
     pt1.add(offset);
     pt2.add(offset);
     pt3.add(offset);
@@ -1931,7 +1940,7 @@
     if (getToken(++pcLastExpressionInstruction).tok != Token.rightbrace)
       coordinateExpected();
     if (coordinatesAreFractional && doConvert)
-      viewer.convertFractionalCoordinates(pt);
+      viewer.toCartesian(pt);
     return pt;
   }
 

Modified: trunk/Jmol/src/org/jmol/viewer/Frame.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Frame.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/Frame.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -2972,6 +2972,10 @@
       unitCell.toFractional(pt);
     }
     
+    void toUnitCell(Point3f pt, Point3f offset) {
+      unitCell.toUnitCell(pt, offset);  
+    }
+    
     void showInfo() {
       if (Logger.isActiveLevel(Logger.LEVEL_DEBUG))
         Logger.debug("cellInfos[" + modelIndex + "]:\n" + unitCell.dumpInfo(true));
@@ -2983,7 +2987,7 @@
     }
   }
   
-  void convertFractionalCoordinates(int modelIndex, Point3f pt) {
+  void toCartesian(int modelIndex, Point3f pt) {
     if (modelIndex < 0)
       modelIndex = 0;
     if (cellInfos == null || modelIndex >= cellInfos.length || cellInfos[modelIndex] == null)
@@ -2993,6 +2997,14 @@
     Logger.info(str + pt);
   }
 
+  void toUnitCell(int modelIndex, Point3f pt, Point3f offset) {
+    if (modelIndex < 0)
+      return;
+    if (cellInfos == null || modelIndex >= cellInfos.length || cellInfos[modelIndex] == null)
+      return;
+    cellInfos[modelIndex].toUnitCell(pt, offset);
+  }
+
   boolean reportFormalCharges = false;
   void setFormalCharges(BitSet bs, int formalCharge) {    
     for (int i = 0; i < atomCount; i++) 

Modified: trunk/Jmol/src/org/jmol/viewer/ModelManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ModelManager.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/ModelManager.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -1322,10 +1322,15 @@
     return false;
   }
 
-  void convertFractionalCoordinates(int modelIndex, Point3f pt) {
-    frame.convertFractionalCoordinates(modelIndex, pt);
+  void toCartesian(int modelIndex, Point3f pt) {
+    frame.toCartesian(modelIndex, pt);
     return;
   }
+
+  void toUnitCell(int modelIndex, Point3f pt, Point3f offset) {
+    frame.toUnitCell(modelIndex, pt, offset);
+    return;
+  }
   
   void clearBfactorRange(){
     frame.clearBfactorRange();

Modified: trunk/Jmol/src/org/jmol/viewer/StateManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateManager.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/StateManager.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -437,6 +437,7 @@
     boolean showMeasurements            = true;
     boolean frankOn                     = false;
     boolean centerPointer               = true;
+    boolean zShade                      = false;
     
     //atoms and bonds
 
@@ -479,9 +480,11 @@
     
     // window
     
-    int argbBackground = 0xFF000000;
-    String stereoState = null;
-    boolean navigationMode = false;
+    int argbBackground         = 0xFF000000;
+    String stereoState         = null;
+    boolean navigationMode     = false;
+    boolean navigationPeriodic = false;
+    boolean navigationCentered = false;
 
     String getWindowState() {
       StringBuffer str = new StringBuffer("# window state;\n# height " + viewer.getScreenHeight()

Modified: trunk/Jmol/src/org/jmol/viewer/SticksRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/SticksRenderer.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/SticksRenderer.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -53,7 +53,7 @@
   short madBond;
 
   void render() {
-    asBits = viewer.getTestFlag2();
+    asBits = false;//viewer.getTestFlag2();
     
     endcaps = Graphics3D.ENDCAPS_SPHERICAL;
     showMultipleBonds = viewer.getShowMultipleBonds();
@@ -63,7 +63,6 @@
     hbondsBackbone = viewer.getHbondsBackbone();
     bondsBackbone = hbondsBackbone | ssbondsBackbone;
     hbondsSolid = viewer.getHbondsSolid();
-
     Bond[] bonds = frame.bonds;
     for (int i = frame.bondCount; --i >= 0; ) {
       Bond bond = bonds[i];
@@ -198,9 +197,9 @@
       } else {
         if (lineBond)
           g3d.drawLine(colixA, colixB, xA, yA, zA, xB, yB, zB);
-        else if (asBits) // time test shows bitset method to be slower
-          g3d.fillCylinderBits(colixA, colixB, endcaps,
-              width, xA, yA, zA, xB, yB, zB);
+      //  else if (asBits) // time test shows bitset method to be slower
+        //  g3d.fillCylinderBits(colixA, colixB, endcaps,
+          //    width, xA, yA, zA, xB, yB, zB);
         else
           g3d.fillCylinder(colixA, colixB, endcaps,
                            width, xA, yA, zA, xB, yB, zB);

Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -29,6 +29,9 @@
 import javax.vecmath.Matrix4f;
 import javax.vecmath.Matrix3f;
 import javax.vecmath.AxisAngle4f;
+
+import org.jmol.util.Logger;
+
 import java.util.Hashtable;
 
 abstract class TransformManager {
@@ -56,6 +59,13 @@
   abstract protected void calcCameraFactors();
 
   /**
+   * calculate the perspective factor based on z
+   * @param z
+   * @return perspectiveFactor
+   */
+  abstract protected float getPerspectiveFactor(float z);
+
+  /**
    * sets slab and depth, possibly using visual range considerations
    * for setting the slab-clipping plane. (slab on; slab 0)
    *
@@ -90,6 +100,7 @@
     matrixRotate.setIdentity(); // no rotations
     setZoomEnabled(true);
     zoomToPercent(100);
+    zoomPercent = zoomPercentSetting;
     scaleFitToScreen();
     if (isNavigationMode)
       setNavigationMode(true);
@@ -552,20 +563,6 @@
     zoomToPercent(percent);
   }
 
-  protected float getPerspectiveFactor(float z) {
-    // all z's SHOULD be >= 0
-    // so the more positive z is, the smaller the screen scale
-    //new idea: phase out perspective depth when zoom is very large.
-    //zoomPercent 1000 or larger starts removing this effect
-    //we can go up to 200000
-    float factor = (z <= 0 ? perspectiveScale : perspectiveScale / z);
-    if (zoomPercent >= MAXIMUM_ZOOM_PERSPECTIVE_DEPTH)
-      factor += (zoomPercent - MAXIMUM_ZOOM_PERSPECTIVE_DEPTH)
-          / (MAXIMUM_ZOOM_PERCENTAGE - MAXIMUM_ZOOM_PERSPECTIVE_DEPTH)
-          * (1 - factor);
-    return factor;
-  }
-
   float getZoomPercentFloat() {
     return zoomPercent;
   }
@@ -843,7 +840,8 @@
    */
 
   protected boolean perspectiveDepth = true;
-  protected float cameraDepth = 3f;
+  protected float cameraDepth = Float.NaN;
+  protected float cameraDepthSetting = 3f;
   protected float visualRange = 5f;
   protected float observerOffset;
   protected float cameraDistance = 1000f; // prevent divide by zero on startup
@@ -866,10 +864,12 @@
    * @param percent
    */
   void setCameraDepthPercent(float percent) {
+    resetNavigationPoint();
     float screenMultiples = (percent < 0 ? -percent / 100 : percent);
     if (screenMultiples == 0)
       return;
-    cameraDepth = screenMultiples;
+    cameraDepthSetting = screenMultiples;
+    cameraDepth = Float.NaN;
   }
 
   void setVisualRange(float angstroms) {
@@ -967,7 +967,7 @@
   }
 
   short scaleToScreen(int z, int milliAngstroms) {
-    if (milliAngstroms == 0)
+    if (milliAngstroms == 0 || z < 2)
       return 0;
     int pixelSize = (int) scaleToPerspective(z, milliAngstroms * scalePixelsPerAngstrom / 1000);      
     return (short) (pixelSize > 0 ? pixelSize : 1);
@@ -1010,8 +1010,6 @@
   void setNavigationMode(boolean TF) {
     isNavigationMode = (TF && canNavigate());
     resetNavigationPoint();
-    if (isNavigationMode)
-      setPerspectiveDepth(true);
   }
 
   boolean getNavigating() {
@@ -1059,6 +1057,9 @@
 
     // note that the image is still centered at 0, 0 in the xy plane
 
+    if (Logger.isActiveLevel(Logger.LEVEL_DEBUG))
+      Logger.debug("modelCenterOffset + matrixTransform: " +modelCenterOffset+matrixTransform); 
+
   }
 
   void transformPoints(int count, Point3f[] angstroms, Point3i[] screens) {
@@ -1729,7 +1730,7 @@
     vibrationScale = 0;
   }
 
-  /*private*/ class VibrationThread extends Thread implements Runnable {
+  private class VibrationThread extends Thread implements Runnable {
 
     public void run() {
       long startTime = System.currentTimeMillis();

Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager10.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager10.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager10.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -45,6 +45,10 @@
     //(s) screen coordinates = (m) * screenPixelsPerAngstrom
     //(p) plane coordinates = (s) / screenPixelCount
     
+    if (Float.isNaN(cameraDepth)) {
+      cameraDepth = cameraDepthSetting;
+    }
+
     // distance from the front plane of the model at zoom=100, where p=0 
     cameraDistance = cameraDepth * screenPixelCount; //(s)
 
@@ -72,6 +76,20 @@
     observerOffset = 0; //(s)
   }
   
+  protected float getPerspectiveFactor(float z) {
+    // all z's SHOULD be >= 0
+    // so the more positive z is, the smaller the screen scale
+    //new idea: phase out perspective depth when zoom is very large.
+    //zoomPercent 1000 or larger starts removing this effect
+    //we can go up to 200000
+    float factor = (z <= 0 ? perspectiveScale : perspectiveScale / z);
+    if (zoomPercent >= MAXIMUM_ZOOM_PERSPECTIVE_DEPTH)
+      factor += (zoomPercent - MAXIMUM_ZOOM_PERSPECTIVE_DEPTH)
+          / (MAXIMUM_ZOOM_PERCENTAGE - MAXIMUM_ZOOM_PERSPECTIVE_DEPTH)
+          * (1 - factor);
+    return factor;
+  }
+
   protected void calcSlabAndDepthValues() {
     slabValue = 0;
     depthValue = Integer.MAX_VALUE;

Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager11.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager11.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager11.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -53,6 +53,11 @@
     //(s) screen coordinates = (m) * screenPixelsPerAngstrom
     //(p) plane coordinates = (s) / screenPixelCount
 
+    if (Float.isNaN(cameraDepth)) {
+      cameraDepth = cameraDepthSetting;
+      zoomFactor = Float.NaN;
+    }
+    
     // factor to apply as part of the transform (not used here)
     cameraScaleFactor = 1; //unitless
 
@@ -98,6 +103,10 @@
     }
   }
 
+  protected float getPerspectiveFactor(float z) {
+    return (z <= 0 ? perspectiveScale : perspectiveScale / z);
+  }
+
   protected void calcSlabAndDepthValues() {
     slabValue = 0;
     depthValue = Integer.MAX_VALUE;
@@ -106,9 +115,10 @@
       if (perspectiveDepth && visualRange > 0 && slabPercentSetting == 0) {
         slabValue = (int) observerOffset;
         depthValue = Integer.MAX_VALUE;
+        depthValue = (int)(radius + modelCenterOffset);
         if (Logger.isActiveLevel(Logger.LEVEL_DEBUG))
           Logger.debug("\n" + "\nperspectiveScale: " + perspectiveScale
-              + " screenPixelCount: " + screenPixelCount
+              + " screenPixelCount: " + screenPixelCount 
               + "\nmodelTrailingEdge: " + (modelCenterOffset + radius)
               + "\nmodelCenterOffset: " + modelCenterOffset + " radius: "
               + radius + "\nmodelLeadingEdge: " + (modelCenterOffset - radius)
@@ -212,12 +222,13 @@
     //no release from navigation mode if too far zoomed in!
     
     if (zoomPercent < 5 && !isNavigationMode) {
-      isNavigationMode = true;
+      isNavigationMode = perspectiveDepth = true;
       return;
     }
     if (isNavigationMode) {
       navMode = NAV_MODE_RESET;
       slabPercentSetting = 0;
+      perspectiveDepth = true;
     } else {
       slabPercentSetting = 100;
     }
@@ -254,7 +265,7 @@
         navMode = NAV_MODE_NEWXYZ;
         break;
       }
-      navigationZOffset -= 5 * multiplier;
+      navigationZOffset -= 5 *(viewer.getNavigationPeriodic() ? 1 : multiplier);
       navMode = NAV_MODE_NEWZ;
       break;
     case KeyEvent.VK_DOWN:
@@ -268,7 +279,7 @@
         navMode = NAV_MODE_NEWXYZ;
         break;
       }
-      navigationZOffset += 5 * multiplier;
+      navigationZOffset += 5 *(viewer.getNavigationPeriodic() ? 1 : multiplier);
       navMode = NAV_MODE_NEWZ;
       break;
     case KeyEvent.VK_LEFT:
@@ -398,7 +409,7 @@
     case NAV_MODE_NONE:
       //update fixed rotation offset and find the new 3D navigation center
       fixedRotationOffset.set(fixedTranslation);
-      //fall through
+    //fall through
     case NAV_MODE_NEWXY:
       // redefine the navigation center based on its old screen position
       findCenterAt(fixedRotationCenter, navigationOffset, navigationCenter);
@@ -420,12 +431,39 @@
       unTransformPoint(navigationOffset, navigationCenter);
       break;
     }
+    if (viewer.getNavigationCentered()) {
+      fixedRotationOffset.set(navigationCenter);
+    }
     matrixTransform(navigationCenter, referenceOffset);
+    if (viewer.getNavigationPeriodic()) {
+      // but if periodic, then the navigationCenter may have to be moved back a notch
+      viewer.toUnitCell(navigationCenter, null);
+      if (pointT.distance(navigationCenter) > 0.01) {
+        matrixTransform(navigationCenter, pointT);
+        float dz = referenceOffset.z - pointT.z;
+        //the new navigation center determines the navigationZOffset
+        navigationZOffset += dz;
+        calcCameraFactors();
+        calcTransformMatrix();
+        matrixTransform(navigationCenter, referenceOffset);
+      }
+    }
     transformPoint(fixedRotationCenter, fixedTranslation);
+    /*
+    if (viewer.getNavigationCentered()) {
+      fixedRotationCenter.set(navigationCenter);
+      navigationZOffset -= referenceOffset.z;
+      calcCameraFactors();
+      calcTransformMatrix();
+      matrixTransform(navigationCenter, referenceOffset);
+      transformPoint(fixedRotationCenter, fixedTranslation);
+    }
+    */
     fixedRotationOffset.set(fixedTranslation);
     transformPoint(navigationCenter, navigationOffset);
     navigationOffset.z = observerOffset;
     navMode = NAV_MODE_NONE;
+
   }
 
   /**

Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java	2006-12-31 04:18:19 UTC (rev 6554)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java	2006-12-31 04:26:32 UTC (rev 6555)
@@ -310,6 +310,7 @@
     setSpecularPercent(global.specularPercent);
     setSpecularExponent(global.specularExponent);
     setSpecularPower(global.specularPower);
+    setZShade(false);
   }
 
   String listSavedStates() {
@@ -670,7 +671,7 @@
     //FrameRenderer
     transformManager.finalizeTransformParameters();
     g3d.setSlabAndDepthValues(transformManager.slabValue,
-        transformManager.depthValue);
+        transformManager.depthValue, global.zShade);
   }
 
   Point3i transformPoint(Point3f pointAngstroms) {
@@ -929,6 +930,14 @@
     return global.getSpecularState();
   }
   
+  private void setZShade(boolean TF) {
+    global.zShade = TF;
+  }
+  
+  boolean getZShade() {
+    return global.zShade;
+  }
+  
   private void setAmbientPercent(int ambientPercent) {
     //Eval
     colorManager.setAmbientPercent(ambientPercent);
@@ -1727,13 +1736,20 @@
     return modelManager.findAtomsInRectangle(rectRubberBand);
   }
 
-  void convertFractionalCoordinates(Point3f pt) {
+  void toCartesian(Point3f pt) {
     int modelIndex = getCurrentModelIndex();
     if (modelIndex < 0)
       return;
-    modelManager.convertFractionalCoordinates(modelIndex, pt);
+    modelManager.toCartesian(modelIndex, pt);
   }
 
+  void toUnitCell(Point3f pt, Point3f offset) {
+    int modelIndex = getCurrentModelIndex();
+    if (modelIndex < 0)
+      return;
+    modelManager.toUnitCell(modelIndex, pt, offset);
+  }
+
   public void setCenterSelected() {
     //depricated
     setCenterBitSet(selectionManager.bsSelection, true);
@@ -3420,6 +3436,18 @@
     boolean notFound = false;
     while (true) {
       ///11.1///
+      if (key.equalsIgnoreCase("navigationCentered")) {
+        setNavigationCentered(value);
+        break;
+      }
+      if (key.equalsIgnoreCase("navigationPeriodic")) {
+        setNavigationPeriodic(value);
+        break;
+      }
+      if (key.equalsIgnoreCase("zShade")) {
+        setZShade(value);
+        break;
+      }
       if (key.equalsIgnoreCase("drawHover")) {
         setDrawHover(value);
         break;
@@ -3960,6 +3988,22 @@
     global.hideNameInPopup = hideNameInPopup;
   }
 
+  private void setNavigationPeriodic(boolean TF) {
+    global.navigationPeriodic = TF;
+  }
+
+  boolean getNavigationPeriodic() {
+    return global.navigationPeriodic;
+  }
+  
+  private void setNavigationCentered(boolean TF) {
+    global.navigationCentered = TF;
+  }
+
+  boolean getNavigationCentered() {
+    return global.navigationCentered;
+  }
+  
   private void setNavigationMode(boolean TF) {
     global.navigationMode = TF;
     if (TF && !transformManager.canNavigate()) {


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[Jmol-commits] SF.net SVN: jmol: [6554] trunk/Jmol/src/org/jmol/viewer/Token.java

[<hansonr@us...>]

Revision: 6554
          http://svn.sourceforge.net/jmol/?rev=6554&view=rev
Author:   hansonr
Date:     2006-12-30 20:18:19 -0800 (Sat, 30 Dec 2006)

Log Message:
-----------
adds select atomX, atomY, atomZ comparison atom properties (tokens)

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

Modified: trunk/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Token.java	2006-12-31 04:17:41 UTC (rev 6553)
+++ trunk/Jmol/src/org/jmol/viewer/Token.java	2006-12-31 04:18:19 UTC (rev 6554)
@@ -354,6 +354,10 @@
   final static int psi             = atomproperty | 21;
   final static int partialCharge   = atomproperty | 22;
   
+  final static int atomX       = atomproperty | 23;
+  final static int atomY       = atomproperty | 24;
+  final static int atomZ       = atomproperty | 25;
+
   final static int opGT         = comparator |  0;
   final static int opGE         = comparator |  1;
   final static int opLE         = comparator |  2;
@@ -754,9 +758,9 @@
 
     "dash",         new Token(dash, "dash"),
     "user",         new Token(user, "user"),
-//    "x",            new Token(x, "x"),
-//    "y",            new Token(y, "y"),
-//    "z",            new Token(z, "z"),
+    "atomx",            new Token(atomX, "atomx"),
+    "atomy",            new Token(atomY, "atomy"),
+    "atomz",            new Token(atomZ, "atomz"),
     "*",            new Token(asterisk, "*"),
     "all",          tokenAll,
     "none",         new Token(none, "none"),


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[Jmol-commits] SF.net SVN: jmol: [6553] trunk/Jmol/src/org/jmol/viewer/Compiler.java

[<hansonr@us...>]

Revision: 6553
          http://svn.sourceforge.net/jmol/?rev=6553&view=rev
Author:   hansonr
Date:     2006-12-30 20:17:41 -0800 (Sat, 30 Dec 2006)

Log Message:
-----------
adds select atomX, atomY, atomZ comparison atom properties

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

Modified: trunk/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Compiler.java	2006-12-31 04:15:54 UTC (rev 6552)
+++ trunk/Jmol/src/org/jmol/viewer/Compiler.java	2006-12-31 04:17:41 UTC (rev 6553)
@@ -1291,6 +1291,9 @@
       case Token.phi:
       case Token.surfacedistance:
       case Token.temperature:
+      case Token.atomX:
+      case Token.atomY:
+      case Token.atomZ:
         // int = decimal here, but comparator has to use decmimal * 100
         val *= 100; 
         // fall through


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[Jmol-commits] SF.net SVN: jmol: [6552] trunk/Jmol/src/org/jmol

[<hansonr@us...>]

Revision: 6552
          http://svn.sourceforge.net/jmol/?rev=6552&view=rev
Author:   hansonr
Date:     2006-12-30 20:15:54 -0800 (Sat, 30 Dec 2006)

Log Message:
-----------
allows for wider range of unit cell loading and adds toUnitCell() method needed for periodic navigation

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
    trunk/Jmol/src/org/jmol/symmetry/UnitCell.java

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2006-12-31 04:14:04 UTC (rev 6551)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2006-12-31 04:15:54 UTC (rev 6552)
@@ -367,9 +367,12 @@
   
   void setLatticeCells(int[] latticeCells) {
     //set when unit cell is determined
-    //large numbers for x or y indicate that z is 0 (don't normalize) or 1 (normalize)
+    // x <= 555 and y >= 555 indicate a range of cells to load
+    // AROUND the central cell 555 and that
+    // we should normalize (z = 1) or not (z = 0)
     this.latticeCells = latticeCells;
-    doNormalize = (latticeCells[0] < 9 && latticeCells[1] < 9 || latticeCells[2] != 0);
+    isLatticeRange = (latticeCells[2] == 0 || latticeCells[2] == 1) && (latticeCells[0] <= 555  && latticeCells[1] >= 555);
+    doNormalize = (!isLatticeRange || latticeCells[2] == 1);
   }
   
   boolean setNotionalUnitCell(float[] info) {
@@ -412,6 +415,7 @@
    }
 
    boolean doNormalize = true;
+   boolean isLatticeRange = false;
    
    void applySymmetry(int maxX, int maxY, int maxZ) {
     if (!coordinatesAreFractional || spaceGroup == null)
@@ -426,7 +430,9 @@
     int minX = 0;
     int minY = 0;
     int minZ = 0;
-    if (maxX > 9 || maxY > 9) {
+    if (isLatticeRange) {
+      //alternative format for indicating a range of cells:
+      //{111 666}
       //555 --> {0 0 0}
       minX = (maxX / 100) - 5;
       minY = (maxX % 100) / 10 - 5;

Modified: trunk/Jmol/src/org/jmol/symmetry/UnitCell.java
===================================================================
--- trunk/Jmol/src/org/jmol/symmetry/UnitCell.java	2006-12-31 04:14:04 UTC (rev 6551)
+++ trunk/Jmol/src/org/jmol/symmetry/UnitCell.java	2006-12-31 04:15:54 UTC (rev 6552)
@@ -73,6 +73,19 @@
     matrixCartesianToFractional.transform(pt);
   }
   
+  public final void toUnitCell(Point3f pt, Point3f offset) {
+    if (matrixCartesianToFractional == null)
+      return;
+    matrixCartesianToFractional.transform(pt);
+    pt.x = (float)(pt.x - Math.floor(pt.x));
+    pt.y = (float)(pt.y - Math.floor(pt.y));
+    pt.z = (float)(pt.z - Math.floor(pt.z));
+    if (offset == null)
+      offset = fractionalOffset;
+    pt.add(offset);
+    matrixFractionalToCartesian.transform(pt);
+  }
+  
   public void setOffset(Point3f pt) {
     // from "unitcell {i j k}" via uccage
     fractionalOffset.set(pt);


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[Jmol-commits] SF.net SVN: jmol: [6551] trunk/Jmol/src/org/jmol/g3d

[<hansonr@us...>]

Revision: 6551
          http://svn.sourceforge.net/jmol/?rev=6551&view=rev
Author:   hansonr
Date:     2006-12-30 20:14:04 -0800 (Sat, 30 Dec 2006)

Log Message:
-----------
adds g3d zShading capability (shadowy distant atoms)

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java
    trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
    trunk/Jmol/src/org/jmol/g3d/Sphere3D.java

Modified: trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java	2006-12-29 17:52:29 UTC (rev 6550)
+++ trunk/Jmol/src/org/jmol/g3d/Cylinder3D.java	2006-12-31 04:14:04 UTC (rev 6551)
@@ -68,6 +68,8 @@
   int sampleCount;
   boolean notClipped;
 
+  private int zShift;
+
   void render(short colixA, short colixB, byte endcaps, int diameter, int xA,
               int yA, int zA, int xB, int yB, int zB) {
     if (diameter > g3d.height * 3)
@@ -85,6 +87,8 @@
     dxB = xB - xA;
     dyB = yB - yA;
     dzB = zB - zA;
+    
+    zShift = g3d.getZShift((zA + zB) >> 1); 
 
     if (diameter <= 1) {
       line3d.plotLineDelta(g3d.getColixArgb(colixA), Graphics3D
@@ -96,12 +100,12 @@
     this.xA = xA;
     this.yA = yA;
     this.zA = zA;
-    this.shadesA = g3d.getShades(this.colixA = colixA);
-    this.shadesB = g3d.getShades(this.colixB = colixB);
-    this.isScreenedA = (colixA & Graphics3D.TRANSLUCENT_MASK) != 0;
-    this.isScreenedB = (colixB & Graphics3D.TRANSLUCENT_MASK) != 0;
+    this.endcaps = endcaps;
+    shadesA = g3d.getShades(this.colixA = colixA);
+    shadesB = g3d.getShades(this.colixB = colixB);
+    isScreenedA = (colixA & Graphics3D.TRANSLUCENT_MASK) != 0;
+    isScreenedB = (colixB & Graphics3D.TRANSLUCENT_MASK) != 0;
 
-    this.endcaps = endcaps;
     calcArgbEndcap(true);
 
     generateBaseEllipse();
@@ -175,7 +179,7 @@
   }
 
   private void plotRasterBits(int i) {
-    int fp8Up = fp8IntensityUp[i];
+    int fpz = fp8IntensityUp[i] >> (8 + zShift);
     int x = xRaster[i];
     int y = yRaster[i];
     int z = zRaster[i];
@@ -193,7 +197,7 @@
       }
     }
     line3d.plotLineDeltaBits(shadesA, isScreenedA, shadesB, isScreenedB,
-        fp8Up >> 8, xA + x, yA + y, zA - z, dxB, dyB, dzB, notClipped);
+        fpz, xA + x, yA + y, zA - z, dxB, dyB, dzB, notClipped);
     if (endcaps == Graphics3D.ENDCAPS_OPEN) {
       line3d.plotLineDelta(shadesA[0], isScreenedA, shadesB[0], isScreenedB, xA
           - x, yA - y, zA + z, dxB, dyB, dzB, notClipped);
@@ -219,9 +223,9 @@
     this.yTip = yTip;
     this.zTip = zTip;
 
-    this.colixA = colix;
-    this.shadesA = g3d.getShades(colix);
-    this.isScreenedA = (colixA & Graphics3D.TRANSLUCENT_MASK) != 0;
+    colixA = colix;
+    shadesA = g3d.getShades(colix);
+    isScreenedA = (colixA & Graphics3D.TRANSLUCENT_MASK) != 0;
     int intensityTip = Shade3D.calcIntensity(dxB, dyB, -dzB);
     g3d.plotPixelClipped(shadesA[intensityTip], isScreenedA, (int) xTip,
         (int) yTip, (int) zTip);
@@ -412,7 +416,7 @@
   }
 
   private void plotRaster(int i) {
-    int fp8Up = fp8IntensityUp[i];
+    int fpz = fp8IntensityUp[i] >> (8 + zShift);
     int x = xRaster[i];
     int y = yRaster[i];
     int z = zRaster[i];
@@ -430,7 +434,7 @@
       }
     }
     line3d.plotLineDelta(shadesA, isScreenedA, shadesB, isScreenedB,
-        fp8Up >> 8, xA + x, yA + y, zA - z, dxB, dyB, dzB, notClipped);
+        fpz, xA + x, yA + y, zA - z, dxB, dyB, dzB, notClipped);
     if (endcaps == Graphics3D.ENDCAPS_OPEN) {
       line3d.plotLineDelta(shadesA[0], isScreenedA, shadesB[0], isScreenedB, xA
           - x, yA - y, zA + z, dxB, dyB, dzB, notClipped);
@@ -559,18 +563,18 @@
       g3d.plotPixelClipped(argbEndcap, isScreenedA, (int) xDn, (int) yDn,
           (int) zDn);
     }
-    int fp8Up = fp8IntensityUp[i];
+    int fpz = fp8IntensityUp[i] >> (8 + zShift);
 
     line3d.plotLineDelta(shadesA, isScreenedA, shadesA, isScreenedA,
-        fp8Up >> 8, (int) xUp, (int) yUp, (int) zUp, (int) Math
+        fpz, (int) xUp, (int) yUp, (int) zUp, (int) Math
             .ceil(xTip - xUp), (int) Math.ceil(yTip - yUp), (int) Math
             .ceil(zTip - zUp), false);
     line3d.plotLineDelta(shadesA, isScreenedA, shadesA, isScreenedA,
-        fp8Up >> 8, (int) xUp, (int) yUp + 1, (int) zUp, (int) Math.ceil(xTip
+        fpz, (int) xUp, (int) yUp + 1, (int) zUp, (int) Math.ceil(xTip
             - xUp), (int) Math.ceil(yTip - yUp) + 1, (int) Math
             .ceil(zTip - zUp), false);
     line3d.plotLineDelta(shadesA, isScreenedA, shadesA, isScreenedA,
-        fp8Up >> 8, (int) xUp + 1, (int) yUp, (int) zUp, (int) Math.ceil(xTip
+        fpz, (int) xUp + 1, (int) yUp, (int) zUp, (int) Math.ceil(xTip
             - xUp) + 1, (int) Math.ceil(yTip - yUp), (int) Math
             .ceil(zTip - zUp), false);
 

Modified: trunk/Jmol/src/org/jmol/g3d/Graphics3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Graphics3D.java	2006-12-29 17:52:29 UTC (rev 6550)
+++ trunk/Jmol/src/org/jmol/g3d/Graphics3D.java	2006-12-31 04:14:04 UTC (rev 6551)
@@ -71,6 +71,7 @@
   int width, height;
   int displayMinX, displayMaxX, displayMinY, displayMaxY;
   int slab, depth;
+  boolean zShade;
   int xLast, yLast;
   int[] pbuf;
   int[] zbuf;
@@ -222,16 +223,21 @@
    *<p>
    * @param slabValue front clipping percentage [0,100]
    * @param depthValue rear clipping percentage [0,100]
+   * @param zShade whether to shade along z front to back
    */
-  public void setSlabAndDepthValues(int slabValue, int depthValue) {
-    slab =
-      slabValue < 0 ? 0
-      : slabValue > ZBUFFER_BACKGROUND ? ZBUFFER_BACKGROUND : slabValue;
-    depth =
-      depthValue < 0 ? 0
-      : depthValue > ZBUFFER_BACKGROUND ? ZBUFFER_BACKGROUND : depthValue;
+  public void setSlabAndDepthValues(int slabValue, int depthValue,
+                                    boolean zShade) {
+    slab = slabValue < 0 ? 0
+        : slabValue > ZBUFFER_BACKGROUND ? ZBUFFER_BACKGROUND : slabValue;
+    depth = depthValue < 0 ? 0
+        : depthValue > ZBUFFER_BACKGROUND ? ZBUFFER_BACKGROUND : depthValue;
+    this.zShade = zShade;
   }
 
+  int getZShift(int z) {
+    return (zShade ? (z - slab) * 5 / (depth - slab): 0);
+  }
+  
   /**
    * used internally when oversampling is enabled
    */
@@ -345,6 +351,7 @@
     }
   }
 
+
   /**
    * fills a solid sphere
    *

Modified: trunk/Jmol/src/org/jmol/g3d/Sphere3D.java
===================================================================
--- trunk/Jmol/src/org/jmol/g3d/Sphere3D.java	2006-12-29 17:52:29 UTC (rev 6550)
+++ trunk/Jmol/src/org/jmol/g3d/Sphere3D.java	2006-12-31 04:14:04 UTC (rev 6551)
@@ -57,6 +57,8 @@
   private final static int maxSphereDiameter = 1000;
   private static int[][] sphereShapeCache = new int[maxSphereCache][];
 
+  private int zShift;
+  
   static void flushImageCache() {
     sphereShapeCache = new int[maxSphereCache][];
   }
@@ -77,6 +79,7 @@
     int minZ = z - radius, maxZ = z + radius;
     if (maxZ < g3d.slab || minZ > g3d.depth)
       return;
+    zShift = g3d.getZShift(z);
     if (diameter >= maxSphereCache) {
       if (diameter > maxSphereDiameter)
         return;
@@ -97,6 +100,7 @@
     int[] pbuf = g3d.pbuf;
     int[] zbuf = g3d.zbuf;
     int offsetSphere = 0;
+    
     int width = g3d.width;
     int evenSizeCorrection = 1 - (diameter & 1);
     int offsetSouthCenter = width * y + x;
@@ -114,19 +118,19 @@
           int zPixel = z - (packed & 0x7F);
           if (zPixel < zbuf[offsetSE]) {
             zbuf[offsetSE] = zPixel;
-            pbuf[offsetSE] = shades[(packed >> 7) & 0x3F];
+            pbuf[offsetSE] = shades[((packed >> 7) & 0x3F) >> zShift];
           }
           if (zPixel < zbuf[offsetSW]) {
             zbuf[offsetSW] = zPixel;
-            pbuf[offsetSW] = shades[(packed >> 13) & 0x3F];
+            pbuf[offsetSW] = shades[((packed >> 13) & 0x3F) >> zShift];
           }
           if (zPixel < zbuf[offsetNE]) {
             zbuf[offsetNE] = zPixel;
-            pbuf[offsetNE] = shades[(packed >> 19) & 0x3F];
+            pbuf[offsetNE] = shades[((packed >> 19) & 0x3F) >> zShift];
           }
           if (zPixel < zbuf[offsetNW]) {
             zbuf[offsetNW] = zPixel;
-            pbuf[offsetNW] = shades[(packed >> 25) & 0x3F];
+            pbuf[offsetNW] = shades[((packed >> 25) & 0x3F) >> zShift];
           }
           ++offsetSE;
           --offsetSW;
@@ -158,19 +162,19 @@
         int zPixel = z - (packed & 0x7F);
         if ((flipflops & 1) != 0 && zPixel < zbuf[offsetSE]) {
           zbuf[offsetSE] = zPixel;
-          pbuf[offsetSE] = shades[(packed >> 7) & 0x3F];
+          pbuf[offsetSE] = shades[((packed >> 7) & 0x3F)>>zShift];
         }
         if ((flipflops & 2) != 0 && zPixel < zbuf[offsetSW]) {
           zbuf[offsetSW] = zPixel;
-          pbuf[offsetSW] = shades[(packed >> 13) & 0x3F];
+          pbuf[offsetSW] = shades[((packed >> 13) & 0x3F)>>zShift];
         }
         if ((flipflops & 4) != 0 && zPixel < zbuf[offsetNE]) {
           zbuf[offsetNE] = zPixel;
-          pbuf[offsetNE] = shades[(packed >> 19) & 0x3F];
+          pbuf[offsetNE] = shades[((packed >> 19) & 0x3F)>>zShift];
         }
         if ((flipflops & 8) != 0 && zPixel < zbuf[offsetNW]) {
           zbuf[offsetNW] = zPixel;
-          pbuf[offsetNW] = shades[(packed >> 25) & 0x3F];
+          pbuf[offsetNW] = shades[((packed >> 25) & 0x3F)>>zShift];
         }
         ++offsetSE;
         --offsetSW;
@@ -244,7 +248,7 @@
               int i = (packed >> 7) & 0x3F;
               if (isCore)
                 i = SHADE_SLAB_CLIPPED - 3 + ((randu >> 7) & 0x07);
-              pbuf[offsetSE] = shades[i];
+              pbuf[offsetSE] = shades[i >> zShift];
             }
             if (tWestVisible && (!tScreened || (flipflops & 2) != 0) &&
                 zPixel < zbuf[offsetSW]) {
@@ -252,7 +256,7 @@
               int i = (packed >> 13) & 0x3F;
               if (isCore)
                 i = SHADE_SLAB_CLIPPED - 3 + ((randu >> 13) & 0x07);
-              pbuf[offsetSW] = shades[i];
+              pbuf[offsetSW] = shades[i >> zShift];
             }
           }
           if (tNorthVisible) {
@@ -262,7 +266,7 @@
               int i = (packed >> 19) & 0x3F;
               if (isCore)
                 i = SHADE_SLAB_CLIPPED - 3 + ((randu >> 19) & 0x07);
-              pbuf[offsetNE] = shades[i];
+              pbuf[offsetNE] = shades[i >> zShift];
             }
             if (tWestVisible && (!tScreened || (flipflops & 8) != 0) &&
                 zPixel < zbuf[offsetNW]) {
@@ -270,7 +274,7 @@
               int i = (packed >> 25) & 0x3F;
               if (isCore)
                 i = SHADE_SLAB_CLIPPED - 3 + ((randu >> 25) & 0x07);
-              pbuf[offsetNW] = shades[i];
+              pbuf[offsetNW] = shades[i >> zShift];
             }
           }
         }
@@ -462,7 +466,7 @@
           if (zbuf[offsetPbuf] <= z0)
             continue;
           int x8 = ((j * xSign + radius) << 8) / dDivisor;
-          pbuf[offsetPbuf] = shades[sphereIntensities[(y8 << 8) + x8]];
+          pbuf[offsetPbuf] = shades[sphereIntensities[((y8 << 8) + x8) >> zShift]];
           zbuf[offsetPbuf] = z0;
         }
       }
@@ -544,7 +548,7 @@
           int x8 = ((j * xSign + radius) << 8) / dDivisor;
           s = sphereIntensities[(y8 << 8) + x8];
         }
-        pbuf[offsetPbuf] = shades[s];
+        pbuf[offsetPbuf] = shades[s >> zShift];
         zbuf[offsetPbuf] =  zPixel;
       }
       // randu is failing me and generating moire patterns :-(


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