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Jmol

An interactive viewer for three-dimensional chemical structures.

Brought to you by: aherraez, egonw, hansonr, migueljmol, nicove

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[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/script Compiler.java,1.26,1.27 Eval.java,1.99,1.100

From: Michael T Howard <michaelthoward@us...> - 2004-02-29 21:36:15

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv27777/src/org/openscience/jmol/viewer/script

Modified Files:
	Compiler.java Eval.java 
Log Message:
many color changes


Index: Compiler.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Compiler.java,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- Compiler.java	28 Feb 2004 23:09:30 -0000	1.26
+++ Compiler.java	29 Feb 2004 21:17:54 -0000	1.27
@@ -211,7 +211,8 @@
               ltoken.removeAllElements();
               break;
             }
-            if ((token.tok & Token.setparam) == 0)
+            if ((token.tok & Token.setparam) == 0 &&
+                token.tok != Token.identifier)
               return cannotSet(ident);
           }
           break;

Index: Eval.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/script/Eval.java,v
retrieving revision 1.99
retrieving revision 1.100
diff -u -r1.99 -r1.100
--- Eval.java	29 Feb 2004 11:04:53 -0000	1.99
+++ Eval.java	29 Feb 2004 21:17:54 -0000	1.100
@@ -2186,6 +2186,9 @@
     case Token.write:
       notImplemented(1);
       break;
+    case Token.identifier:
+      viewer.setBooleanProperty((String)statement[1].value, getSetBoolean());
+      break;
     case Token.background:
     case Token.stereo:
       setspecialShouldNotBeHere();

[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/datamodel Atom.java,1.28,1.29

From: Michael T Howard <michaelthoward@us...> - 2004-02-29 21:36:15

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv27777/src/org/openscience/jmol/viewer/datamodel

Modified Files:
	Atom.java 
Log Message:
many color changes


Index: Atom.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/datamodel/Atom.java,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- Atom.java	25 Feb 2004 19:11:27 -0000	1.28
+++ Atom.java	29 Feb 2004 21:17:53 -0000	1.29
@@ -281,8 +281,10 @@
   public int getAtomno() {
     if (pdbAtom != null)
       return pdbAtom.getAtomSerial();
-    return atomIndex +
-      (frame.modelType == JmolConstants.MODEL_TYPE_XYZ ? 0 : 1);
+    if (frame.modelType == JmolConstants.MODEL_TYPE_XYZ &&
+        frame.viewer.getZeroBasedXyzRasmol())
+      return atomIndex;
+    return atomIndex + 1;
   }
 
   public Point3f getPoint3f() {

[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/viewer/managers ColorManager.java,1.30,1.31 StyleManager.java,1.19,1.20 TransformManager.java,1.22,1.23

From: Michael T Howard <michaelthoward@us...> - 2004-02-29 21:36:15

Update of /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/managers
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv27777/src/org/openscience/jmol/viewer/managers

Modified Files:
	ColorManager.java StyleManager.java TransformManager.java 
Log Message:
many color changes


Index: ColorManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/managers/ColorManager.java,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- ColorManager.java	29 Feb 2004 11:04:52 -0000	1.30
+++ ColorManager.java	29 Feb 2004 21:17:53 -0000	1.31
@@ -54,6 +54,10 @@
     System.out.println("setting color scheme to:" + colorScheme);
     if (colorScheme.equals("jmol")) {
       argbsCpk = JmolConstants.argbsCpk;
+      viewer.setColorBackground("snow");
+      viewer.setColorMeasurement(Color.black);
+      viewer.setColorLabel(Color.black);
+      viewer.setColorDots(null);
     } else if (colorScheme.equals("rasmol")) {
       int argb = JmolConstants.argbsCpkRasmol[0] | 0xFF000000;
       argbsCpk = new int[JmolConstants.argbsCpk.length];
@@ -66,6 +70,10 @@
         argbsCpk[atomNo] = argb;
         g3d.changeColixArgb((short)atomNo, argb);
       }
+      viewer.setColorBackground(Color.black);
+      viewer.setColorMeasurement(Color.white);
+      viewer.setColorLabel(null);
+      viewer.setColorDots(null);
     } else {
       System.out.println("unrecognized color scheme");
       return;
@@ -198,15 +206,15 @@
     colixBackground = g3d.getColix(colorBackground);
   }
 
-  public Color colorAxes = Color.gray;
-  public short colixAxes = Graphics3D.GRAY;
+  public Color colorAxes = new Color(128, 128, 0);
+  public short colixAxes = Graphics3D.OLIVE;
   public void setColorAxes(Color color) {
     colorAxes = color;
     colixAxes = g3d.getColix(color);
   }
 
-  public Color colorAxesText = Color.gray;
-  public short colixAxesText = Graphics3D.GRAY;
+  public Color colorAxesText = colorAxes;
+  public short colixAxesText = Graphics3D.OLIVE;
   public void setColorAxesText(Color color) {
     colorAxesText = color;
     colixAxesText = g3d.getColix(color);

Index: StyleManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/managers/StyleManager.java,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- StyleManager.java	26 Feb 2004 21:35:22 -0000	1.19
+++ StyleManager.java	29 Feb 2004 21:17:53 -0000	1.20
@@ -107,6 +107,11 @@
     this.wireframeRotation = wireframeRotation;
   }
 
+  public boolean zeroBasedXyzRasmol = false;
+  public void setZeroBasedXyzRasmol(boolean zeroBasedXyzRasmol) {
+    this.zeroBasedXyzRasmol = zeroBasedXyzRasmol;
+  }
+
   void setCommonDefaults() {
     viewer.zoomToPercent(100);
     viewer.setPercentVdwAtom(20);
@@ -114,23 +119,23 @@
     viewer.setPerspectiveDepth(true);
     viewer.setBondTolerance(0.45f);
     viewer.setMinBondDistance(0.40f);
-    viewer.setMarBond((short)100);
+    viewer.setMarBond((short)150);
   }
 
   public void setJmolDefaults() {
     setCommonDefaults();
-    viewer.setColorBackground(Color.white);
-    viewer.setColorMeasurement(Color.black);
-    viewer.setColorLabel(Color.black);
+    viewer.setColorScheme("jmol");
+    viewer.setAxesOrientationRasmol(false);
+    setZeroBasedXyzRasmol(false);
   }
 
   public void setRasmolDefaults() {
     setCommonDefaults();
-    viewer.setColorBackground(Color.black);
-    viewer.setColorMeasurement(Color.white);
+    viewer.setColorScheme("rasmol");
+    viewer.setAxesOrientationRasmol(true);
+    setZeroBasedXyzRasmol(true);
     viewer.setPercentVdwAtom(0);
     viewer.setMarBondDefault((short)1);
-    viewer.setColorLabel(null);
   }
 
   public boolean showFrank;

Index: TransformManager.java
===================================================================
RCS file: /cvsroot/jmol/Jmol/src/org/openscience/jmol/viewer/managers/TransformManager.java,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- TransformManager.java	22 Feb 2004 01:11:38 -0000	1.22
+++ TransformManager.java	29 Feb 2004 21:17:53 -0000	1.23
@@ -100,13 +100,13 @@
     matrixRotate.mul(matrixTemp, matrixRotate);
   }
   public synchronized void rotateByY(float angleRadians) {
-    if (orientationRasMolChime)
+    if (axesOrientationRasmol)
       angleRadians = -angleRadians;
     matrixTemp.rotY(angleRadians);
     matrixRotate.mul(matrixTemp, matrixRotate);
   }
   public synchronized void rotateByZ(float angleRadians) {
-    if (orientationRasMolChime)
+    if (axesOrientationRasmol)
       angleRadians = -angleRadians;
     matrixTemp.rotZ(angleRadians);
     matrixRotate.mul(matrixTemp, matrixRotate);
@@ -436,9 +436,14 @@
   private final Vector3f vectorTemp = new Vector3f();
 
 
-  public boolean orientationRasMolChime = true;
-  public void setOrientationRasMolChime(boolean orientationRasMolChime) {
-    this.orientationRasMolChime = orientationRasMolChime;
+  /****************************************************************
+   * RasMol has the +Y axis pointing down
+   * And rotations about the y axis are left-handed
+   * setting this flag makes Jmol mimic this behavior
+   ****************************************************************/
+  public boolean axesOrientationRasmol = false;
+  public void setAxesOrientationRasmol(boolean axesOrientationRasmol) {
+    this.axesOrientationRasmol = axesOrientationRasmol;
   }
 
   public void calcTransformMatrices() {
@@ -483,7 +488,7 @@
       cameraDistanceFloat / scalePixelsPerAngstrom;
     matrixTemp.setZero();
     matrixTemp.setTranslation(vectorTemp);
-    if (orientationRasMolChime)
+    if (axesOrientationRasmol)
       matrixTransform.add(matrixTemp); // make all z positive
     else
       matrixTransform.sub(matrixTemp); // make all z negative
@@ -491,7 +496,7 @@
     // now scale to screen coordinates
     matrixTemp.setZero();
     matrixTemp.set(scalePixelsPerAngstrom);
-    if (! orientationRasMolChime) {
+    if (! axesOrientationRasmol) {
       // negate y (for screen) and z (for zbuf)
       matrixTemp.m11 = matrixTemp.m22 = -scalePixelsPerAngstrom;
     }

[Jmol-commits] CVS: Jmol/src/org/openscience/jmol/app PreferencesDialog.java,1.22,1.23