Revision: 5219
Author: hansonr
Date: 2006-06-13 15:30:34 -0700 (Tue, 13 Jun 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5219&view=rev
Log Message:
-----------
bob200603 adds more isosurface functionality, including
isosurface functionXY
isosurface center
isosurface fixed
isosurface modelbased
and fixes isosurface visibility for correct multiple model/file display
deletes Geodesic3D2.Java
note - this adds one function to statusListener
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/api/JmolStatusListener.java
branches/bob200603/Jmol/src/org/jmol/applet/Jmol.java
branches/bob200603/Jmol/src/org/jmol/g3d/Geodesic3D.java
branches/bob200603/Jmol/src/org/jmol/viewer/Axes.java
branches/bob200603/Jmol/src/org/jmol/viewer/Draw.java
branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
branches/bob200603/Jmol/src/org/jmol/viewer/Mesh.java
branches/bob200603/Jmol/src/org/jmol/viewer/MeshRenderer.java
branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
branches/bob200603/Jmol/src/org/jmol/viewer/StatusManager.java
branches/bob200603/Jmol/src/org/jmol/viewer/Token.java
branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java
branches/bob200603/Jmol/src/org/openscience/jmol/app/Jmol.java
Removed Paths:
-------------
branches/bob200603/Jmol/src/org/jmol/g3d/Geodesic3D2.java
Modified: branches/bob200603/Jmol/src/org/jmol/api/JmolStatusListener.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/api/JmolStatusListener.java
2006-06-13 17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/api/JmolStatusListener.java
2006-06-13 22:30:34 UTC (rev 5219)
@@ -62,4 +62,5 @@
public void showConsole(boolean showConsole);
+ public float functionXY(int x, int y);
}
Modified: branches/bob200603/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/applet/Jmol.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/applet/Jmol.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -139,12 +139,11 @@
htmlName = getParameter("name");
String ms = getParameter("mayscript");
mayScript = (ms != null) && (!ms.equalsIgnoreCase("false"));
- appletRegistry = new JmolAppletRegistry(htmlName, mayScript,
appletWrapper);
-
+ appletRegistry = new JmolAppletRegistry(htmlName, mayScript,
appletWrapper);
initWindows();
initApplication();
}
-
+
String getParameter(String paramName) {
return appletWrapper.getParameter(paramName);
}
@@ -672,6 +671,10 @@
showStatusAndConsole(statusMessage);
}
+ public float functionXY(int x, int y) {
+ return ((Double) jsoWindow.call("functionXY", new Object[] { htmlName,
new Integer(x), new Integer(y)})).floatValue();
+ }
+
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) {
showStatusAndConsole(strMeasure);
}
Modified: branches/bob200603/Jmol/src/org/jmol/g3d/Geodesic3D.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/g3d/Geodesic3D.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/g3d/Geodesic3D.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -174,15 +174,16 @@
Geodesic3D(Graphics3D g3d) {
this.g3d = g3d;
- //String msg = "Geodesecs "+ System.currentTimeMillis();
- //System.out.println(msg+" 0");
- initialize();
- //System.out.println(msg+" 1");
+ String id = "Geodesecs "+ System.currentTimeMillis();
+ //System.out.println(id+" 0");
+ initialize(id);
+ //System.out.println(id+" 1");
}
- private static synchronized void initialize() {
+ private static synchronized void initialize(String id) {
if(vertexCounts != null)
return;
+ System.out.println(id + " initializing");
vertexCounts = new short[maxLevel];
neighborVertexesArrays = new short[maxLevel][];
faceVertexesArrays = new short[maxLevel][];
@@ -216,7 +217,7 @@
" edgeCount=" + getEdgeCount(i));
}
}
- System.out.println("geodesic initialization completed");
+ System.out.println(id+" initialization completed");
}
static int getVertexCount(int level) {
Deleted: branches/bob200603/Jmol/src/org/jmol/g3d/Geodesic3D2.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/g3d/Geodesic3D2.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/g3d/Geodesic3D2.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -1,432 +0,0 @@
-/* $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2005 Miguel, Jmol Development, www.jmol.org
- *
- * Contact: [EMAIL PROTECTED]
- *
- * This library is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public
- * License as published by the Free Software Foundation; either
- * version 2.1 of the License, or (at your option) any later version.
- *
- * This library is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this library; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- */
-
-package org.jmol.g3d;
-
-import javax.vecmath.Vector3f;
-import org.jmol.util.Int2IntHash;
-
- /**
- * Constructs a canonical geodesic sphere of unit radius.
- *<p>
- * The Normix3D code quantizes arbitrary vectors to the vectors
- * of this unit sphere. normix values are then used for
- * high performance surface normal lighting
- *<p>
- * The vertices of the geodesic sphere can be used for constructing
- * vanderWaals and Connolly dot surfaces.
- *<p>
- * One geodesic sphere is constructed. It is a unit sphere
- * with radius of 1.0
- *<p>
- * Many times a sphere is constructed with lines of latitude and
- * longitude. With this type of rendering, the atom has north and
- * south poles. And the faces are not regularly shaped ... at the
- * poles they are triangles but elsewhere they are quadrilaterals.
- *<p>
- * A geodesic sphere is more appropriate for this type
- * of application. The geodesic sphere does not have poles and
- * looks the same in all orientations ... as a sphere should. All
- * faces are triangles. Not equilateral, but close.
- *<p>
- * The geodesic sphere is constructed by starting with an icosohedron,
- * a platonic solid with 12 vertices and 20 equilateral triangles
- * for faces. The internal call to the private
- * method <code>quadruple</code> will
- * split each triangular face into 4 faces by creating a new vertex
- * at the midpoint of each edge. These midpoints are still in the
- * plane, so they are then 'pushed out' to the surface of the
- * enclosing sphere by normalizing their length back to 1.0
- *<p>
- * The sequence of vertex counts is 12, 42, 162, 642, 2562.
- * These are identified by 'levels', that run from 0 through 4;
- * The vertices
- * are stored so that when spheres are small they can choose to display
- * only the first n bits where n is one of the above vertex counts.
- *<code>
- * Faces + Vertices = Edges + 2
- * Faces: 20, 80, 320, 1280, 5120, 20480
- * start with 20 faces ... at each level multiply by 4
- * Edges: 30, 120, 480, 1920, 7680, 30720
- * start with 30 edges ... also multipy by 4 ... strange, but true
- * Vertices: 12, 42, 162, 642, 2562, 10242
- * start with 12 vertices and 30 edges.
- * when you subdivide, each edge contributes one vertex
- * 12 + 30 = 42 vertices at the next level
- * 80 faces + 42 vertices - 2 = 120 edges at the next level
- *</code>
- *<p>
- * The vertices of the 'one true canonical sphere' are rotated to the
- * current molecular rotation at the beginning of the repaint cycle.
- * That way,
- * individual atoms only need to scale the unit vector to the vdw
- * radius for that atom.
- *<p>
- *
- * Notes 27 Sep 2005 <br />
- * If I were to switch the representation to staring with
- * a tetrahedron instead of an icosohedron we would get:
- *<code>
- * Faces: 4, 16, 64, 256, 1024
- * Edges: 6, 24, 96, 384, 1536
- * Vertices: 4, 10, 34, 130, 514
- *</code>
- * If I switched to face-centered normixes then I could efficiently
- * Regardless, I think that face-centered normixes would also reduce
- * ambiguity and would speed up the normal to normix process.
- *
- * I could also start with an octahedron that placed one triangle
- * in each 3D cartesian octant. That would push to 512 faces instead
- * of 256 faces, leaving me with shorts. But, it would be easier to quantize
- * at the first level because it would be based upon sign. And perhaps
- * it would be easier to take advantage of symmetry in the process of
- * converting from normal to normix.
- *
- * Notes 11 Oct 2005 <br />
- * Using an octahedron, the counts come up as follows:
- * Faces: 8, 32, 128, 512
- * Edges: 12, 48, 192, 768
- * Vrtxs: 6, 18, 66, 258
- */
-
-class Geodesic3D2 {
-
- Graphics3D g3d;
-
- private final static boolean DUMP = true;
-
- final static float halfRoot5 = (float)(0.5 * Math.sqrt(5));
- final static float oneFifth = 2 * (float)Math.PI / 5;
- final static float oneTenth = oneFifth / 2;
-
- // miguel 2005 01 11
- // within the context of this code, the term 'vertex' is used
- // to refer to a short which is an index into the tables
- // of vertex information.
- final static short[] faceVertexesOctant = {
- 0, 1, 4,
- 0, 5, 1,
- 0, 3, 5,
- 0, 4, 3,
-
- 2, 1, 5,
- 2, 5, 3,
- 2, 3, 4,
- 2, 4, 1,
- };
-
- // every vertex has 6 neighbors ... except at the beginning of the world
- final static short[] neighborVertexesOctant = {
- 1, 4, 3, 5,-1,-1, // 0
- 0, 5, 2, 4,-1,-1, // 1
- 1, 5, 3, 4,-1,-1, // 2
- 0, 4, 2, 5,-1,-1, // 3
- 0, 1, 2, 3,-1,-1, // 4
- 0, 3, 2, 1,-1,-1, // 5
- };
-
- /**
- * 5 levels, 0 through 4
- */
- final static int maxLevel = 3;
- static short[] vertexCounts;
- static short[][] neighborVertexesArrays;
- static short[][] faceVertexesArrays;
- static Vector3f[][] faceVectorsArrays;
- static Vector3f[] vertexVectors = new Vector3f[] {
- new Vector3f( 0, 1, 0),
- new Vector3f( 0, 0, 1),
- new Vector3f( 0,-1, 0),
- new Vector3f( 0, 0,-1),
- new Vector3f( 1, 0, 0),
- new Vector3f(-1, 0, 0)
- };
-
-
-
- Geodesic3D2(Graphics3D g3d) {
- this.g3d = g3d;
- if (vertexCounts == null)
- initialize();
- if (DUMP) {
- System.out.println("vertexVectors.length=" + vertexVectors.length);
- for (int i = 0; i < vertexVectors.length; ++i)
- System.out.println("" + i + " : " + vertexVectors[i]);
- }
- }
-
- private synchronized void initialize() {
- if (vertexCounts != null)
- return;
- vertexCounts = new short[maxLevel];
- neighborVertexesArrays = new short[maxLevel][];
- faceVertexesArrays = new short[maxLevel][];
- faceVectorsArrays = new Vector3f[maxLevel][];
-
- faceVertexesArrays[0] = faceVertexesOctant;
- neighborVertexesArrays[0] = neighborVertexesOctant;
- vertexCounts[0] = 6;
-
- for (int i = 0; i < maxLevel - 1; ++i)
- quadruple(i);
-
- if (DUMP) {
- for (int i = 0; i < maxLevel; ++i) {
- System.out.println("geodesic level " + i +
- " vertexCount= " + getVertexCount(i) +
- " faceCount=" + getFaceCount(i) +
- " edgeCount=" + getEdgeCount(i));
- }
- }
- for (int i = 0; i < maxLevel; ++i)
- faceVectorsArrays[i] =
- buildFaceVectors(faceVertexesArrays[i], vertexVectors);
- }
-
- static int getVertexCount(int level) {
- return vertexCounts[level];
- }
-
- static Vector3f[] getVertexVectors() {
- return vertexVectors;
- }
-
- static int getFaceCount(int level) {
- return faceVertexesArrays[level].length / 3;
- }
-
- static int getEdgeCount(int level) {
- return getVertexCount(level) + getFaceCount(level) - 2;
- }
-
- static short[] getNeighborVertexes(int level) {
- return neighborVertexesArrays[level];
- }
-
- static short[] getFaceVertexes(int level) {
- return faceVertexesArrays[level];
- }
-
- static Vector3f[] getFaceVectors(int level) {
- return faceVectorsArrays[level];
- }
-
-
- private static short vertexNext;
- private static Int2IntHash htVertex;
-
- private final static boolean VALIDATE = true;
-
- private static void quadruple(int level) {
- if (DUMP)
- System.out.println("quadruple(" + level + ")");
- htVertex = new Int2IntHash();
- int oldVertexCount = vertexVectors.length;
- short[] oldFaceVertexes = faceVertexesArrays[level];
- int oldFaceVertexesLength = oldFaceVertexes.length;
- int oldFaceCount = oldFaceVertexesLength / 3;
- int oldEdgesCount = oldVertexCount + oldFaceCount - 2;
- int newVertexCount = oldVertexCount + oldEdgesCount;
- int newFaceCount = 4 * oldFaceCount;
- Vector3f[] newVertexVectors = new Vector3f[newVertexCount];
- System.arraycopy(vertexVectors, 0, newVertexVectors, 0, oldVertexCount);
- vertexVectors = newVertexVectors;
-
- short[] newFacesVertexes = new short[3 * newFaceCount];
- faceVertexesArrays[level + 1] = newFacesVertexes;
- short[] neighborVertexes = new short[6 * newVertexCount];
- neighborVertexesArrays[level + 1] = neighborVertexes;
- for (int i = neighborVertexes.length; --i >= 0; )
- neighborVertexes[i] = -1;
-
- vertexCounts[level + 1] = (short)newVertexCount;
-
- if (DUMP)
- System.out.println("oldVertexCount=" + oldVertexCount +
- " newVertexCount=" + newVertexCount +
- " oldFaceCount=" + oldFaceCount +
- " newFaceCount=" + newFaceCount);
-
- vertexNext = (short)oldVertexCount;
-
- int iFaceNew = 0;
- for (int i = 0; i < oldFaceVertexesLength; ) {
- short iA = oldFaceVertexes[i++];
- short iB = oldFaceVertexes[i++];
- short iC = oldFaceVertexes[i++];
- short iAB = getVertex(iA, iB);
- short iBC = getVertex(iB, iC);
- short iCA = getVertex(iC, iA);
-
- newFacesVertexes[iFaceNew++] = iA;
- newFacesVertexes[iFaceNew++] = iAB;
- newFacesVertexes[iFaceNew++] = iCA;
-
- newFacesVertexes[iFaceNew++] = iB;
- newFacesVertexes[iFaceNew++] = iBC;
- newFacesVertexes[iFaceNew++] = iAB;
-
- newFacesVertexes[iFaceNew++] = iC;
- newFacesVertexes[iFaceNew++] = iCA;
- newFacesVertexes[iFaceNew++] = iBC;
-
- newFacesVertexes[iFaceNew++] = iCA;
- newFacesVertexes[iFaceNew++] = iAB;
- newFacesVertexes[iFaceNew++] = iBC;
-
- addNeighboringVertexes(neighborVertexes, iAB, iA);
- addNeighboringVertexes(neighborVertexes, iAB, iCA);
- addNeighboringVertexes(neighborVertexes, iAB, iBC);
- addNeighboringVertexes(neighborVertexes, iAB, iB);
-
- addNeighboringVertexes(neighborVertexes, iBC, iB);
- addNeighboringVertexes(neighborVertexes, iBC, iCA);
- addNeighboringVertexes(neighborVertexes, iBC, iC);
-
- addNeighboringVertexes(neighborVertexes, iCA, iC);
- addNeighboringVertexes(neighborVertexes, iCA, iA);
- }
- if (VALIDATE) {
- int vertexCount = vertexVectors.length;
- if (iFaceNew != newFacesVertexes.length)
- throw new NullPointerException();
- if (vertexNext != newVertexCount)
- throw new NullPointerException();
- for (int i = 0; i < 6; ++i) {
- for (int j = 0; j < 4; ++j) {
- int neighbor = neighborVertexes[i * 6 + j];
- if (neighbor < 0)
- throw new NullPointerException();
- if (neighbor >= vertexCount)
- throw new NullPointerException();
- }
- if (neighborVertexes[i * 6 + 4] != -1)
- throw new NullPointerException();
- if (neighborVertexes[i * 6 + 5] != -1)
- throw new NullPointerException();
- }
- for (int i = 6 * 6; i < neighborVertexes.length; ++i) {
- int neighbor = neighborVertexes[i];
- if (neighbor < 0)
- throw new NullPointerException();
- if (neighbor >= vertexCount)
- throw new NullPointerException();
- }
- for (int i = 0; i < newVertexCount; ++i) {
- int neighborCount = 0;
- for (int j = neighborVertexes.length; --j >= 0; )
- if (neighborVertexes[j] == i)
- ++neighborCount;
- if (i < 6) {
- if (neighborCount != 4)
- throw new NullPointerException();
- } else {
- if (neighborCount != 6)
- throw new NullPointerException();
- }
- int faceCount = 0;
- for (int j = newFacesVertexes.length; --j >= 0; )
- if (newFacesVertexes[j] == i)
- ++faceCount;
- if (i < 6) {
- if (faceCount != 4)
- throw new NullPointerException();
- } else {
- if (faceCount != 6)
- throw new NullPointerException();
- }
- }
- }
- htVertex = null;
- }
-
- private static void addNeighboringVertexes(short[] neighborVertexes,
- short v1, short v2) {
- //System.out.println("addNeighboringVertexes(...," + v1 + "," + v2 + ")");
- for (int i = v1 * 6, iMax = i + 6; i < iMax; ++i) {
- if (neighborVertexes[i] == v2)
- return;
- if (neighborVertexes[i] < 0) {
- neighborVertexes[i] = v2;
- for (int j = v2 * 6, jMax = j + 6; j < jMax; ++j) {
- if (neighborVertexes[j] == v1)
- return;
- if (neighborVertexes[j] < 0) {
- neighborVertexes[j] = v1;
- return;
- }
- }
- }
- }
- throw new NullPointerException();
- }
-
- /*
- short getNeighborVertex(int level, short vertex, int neighborIndex) {
- short[] neighborVertexes = neighborVertexesArrays[level];
- int offset = vertex * 6 + neighborIndex;
- return neighborVertexes[offset];
- }
- */
-
- private static short getVertex(short v1, short v2) {
- if (v1 > v2) {
- short t = v1;
- v1 = v2;
- v2 = t;
- }
- int hashKey = (v1 << 16) + v2;
- int vertex = htVertex.get(hashKey);
- if (vertex != Integer.MIN_VALUE)
- return (short)vertex;
- Vector3f newVertexVector = vertexVectors[vertexNext] = new Vector3f();
- newVertexVector.add(vertexVectors[v1], vertexVectors[v2]);
- newVertexVector.normalize();
- htVertex.put(hashKey, vertexNext);
- return vertexNext++;
- }
-
- static boolean isNeighborVertex(short vertex1, short vertex2, int level) {
- short[] neighborVertexes = neighborVertexesArrays[level];
- int offset1 = vertex1 * 6;
- for (int i = offset1 + (vertex1 < 6 ? 4 : 6); --i >= offset1; )
- if (neighborVertexes[i] == vertex2)
- return true;
- return false;
- }
-
- private static Vector3f[] buildFaceVectors(short[] faceVertexes,
- Vector3f[] vertexVectors) {
- int faceCount = faceVertexes.length / 3;
- Vector3f faceVectors[] = new Vector3f[faceCount];
- for (int i = 0, j = 0; i < faceCount; ++i, j += 3) {
- Vector3f v = faceVectors[i] = new Vector3f();
- v.add(vertexVectors[faceVertexes[j]],
- vertexVectors[faceVertexes[j + 1]]);
- v.add(vertexVectors[faceVertexes[j + 2]]);
- v.normalize();
- }
- return faceVectors;
- }
-}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Axes.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Axes.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Axes.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -24,11 +24,22 @@
package org.jmol.viewer;
+import java.util.BitSet;
+
import javax.vecmath.Point3f;
import javax.vecmath.Vector3f;
class Axes extends SelectionIndependentShape {
+
+ void setProperty(String propertyName, Object value, BitSet bs) {
+ if ("scale" == propertyName) {
+ setScale(((Float)value).floatValue());
+ return;
+ }
+ super.setProperty(propertyName, value, bs);
+ }
+
final static Point3f[] unitAxisPoints = {
new Point3f( 1, 0, 0),
new Point3f( 0, 1, 0),
@@ -38,6 +49,8 @@
new Point3f( 0, 0,-1)
};
+ float scale = 1f;
+
final Point3f originPoint = new Point3f();
final Point3f[] axisPoints = new Point3f[6];
{
@@ -78,10 +91,15 @@
if (corner.z < MIN_AXIS_LEN)
corner.z = MIN_AXIS_LEN;
- axisPoint.x *= corner.x;
- axisPoint.y *= corner.y;
- axisPoint.z *= corner.z;
+ axisPoint.x *= corner.x * scale;
+ axisPoint.y *= corner.y * scale;
+ axisPoint.z *= corner.z * scale;
axisPoint.add(originPoint);
}
}
+
+ void setScale(float angstroms) {
+ scale = angstroms;
+ initShape();
+ }
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Draw.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Draw.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Draw.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -187,12 +187,12 @@
if (isFixed) {
currentMesh.setPolygonCount(1);
currentMesh.ptCenters = null;
- currentMesh.visibilityFlags = null;
+ currentMesh.modelFlags = null;
nPoly = setVerticesAndPolygons(-1, nPoly);
} else {
currentMesh.setPolygonCount(modelCount);
currentMesh.ptCenters = new Point3f[modelCount];
- currentMesh.visibilityFlags = new int[modelCount];
+ currentMesh.modelFlags = new int[modelCount];
for (int iModel = 0; iModel < modelCount; iModel++) {
// int n0 = currentMesh.vertexCount;
nPoly = setVerticesAndPolygons(iModel, nPoly);
@@ -216,7 +216,7 @@
addPoint(m.vertices[ipt]);
} else {
for (ipt = 0; ipt < m.drawVertexCount; ipt++) {
- System.out.println(nPoints +" "+m.meshID+ "
count="+m.drawVertexCount + " length=" + m.vertices.length);
+ //System.out.println(nPoints +" "+m.meshID+ "
count="+m.drawVertexCount + " length=" + m.vertices.length);
addPoint(m.vertices[ipt]);
}
@@ -274,10 +274,11 @@
*/
int modelCount = viewer.getModelCount();
for (int i = meshCount; --i >= 0;) {
- if (meshes[i].visibilityFlags == null)
+ meshes[i].visibilityFlags = myVisibilityFlag;
+ if (meshes[i].modelFlags == null)
continue;
for (int iModel = modelCount; --iModel >= 0;)
- meshes[i].visibilityFlags[iModel] = (bs.get(iModel) ? 1 : 0);
+ meshes[i].modelFlags[iModel] = (bs.get(iModel) ? 1 : 0);
}
}
@@ -294,7 +295,7 @@
mesh = meshes[i];
if (mesh.drawVertexCount == 2) {
for (int iModel = modelCount; --iModel >= 0;) {
- if (mesh.visibilityFlags != null && mesh.visibilityFlags[iModel] ==
0)
+ if (mesh.modelFlags != null && mesh.modelFlags[iModel] == 0)
continue;
for (int iVertex = mesh.polygonIndexes[iModel].length; --iVertex >=
0;) {
int d2 = coordinateInRange(x, y,
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Eval.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -371,7 +371,7 @@
if (logMessages || viewer.getDebugScript())
logDebugScript();
Token token = statement[0];
- //System.out.println(token);
+ //System.out.println(token + " token/tok " + token.tok + " isosurface:"
+ Token.isosurface);
switch (token.tok) {
case Token.backbone:
proteinShape(JmolConstants.SHAPE_BACKBONE);
@@ -842,10 +842,18 @@
evalError("{ number number number } expected");
}
+ void coordinateOrNameOrExpressionRequired() throws ScriptException {
+ evalError(" {x y z} or $name or (atom expression) required");
+ }
+
void tooManyRotationPoints() throws ScriptException {
evalError("too many rotation points were specified");
}
+ void keywordRequired(String what) throws ScriptException {
+ evalError("keyword required: " + what);
+ }
+
void notImplemented(int itoken) {
notImplemented(statement[itoken]);
}
@@ -1580,8 +1588,6 @@
// color $ whatever green
String objectName = objectNameParameter(index);
int shapeType = viewer.getShapeIdFromObjectName(objectName);
- System.out.println("colorIdentifiedObject" + index + " " + shapeType + " "
- + objectName);
if (shapeType < 0)
objectNameExpected();
viewer.setShapeProperty(shapeType, "meshID", objectName);
@@ -3054,6 +3060,18 @@
}
void setAxes(int cmdPt) throws ScriptException {
+ if (statement.length == 1) {
+ viewer.setShapeSize(JmolConstants.SHAPE_AXES, 1);
+ return;
+ }
+ // set axes scale x.xxx
+ if (statement.length == cmdPt + 2
+ && statement[cmdPt].tok == Token.identifier
+ && ((String) statement[cmdPt].value).equalsIgnoreCase("scale")) {
+ viewer.setShapeProperty(JmolConstants.SHAPE_AXES, "scale", new Float(
+ floatParameter(cmdPt + 1)));
+ return;
+ }
viewer.setShapeSize(JmolConstants.SHAPE_AXES, getSetAxesTypeMad(cmdPt));
}
@@ -3980,10 +3998,8 @@
}
void isosurface() throws ScriptException {
- int fileIndexPt = 0;
int signPt = 0;
- int contourPt = 0;
- int orbitalPt = 0;
+ boolean isOrbital = false;
float[] nlmZR = new float[5];
viewer.loadShape(JmolConstants.SHAPE_ISOSURFACE);
viewer.setShapeProperty(JmolConstants.SHAPE_ISOSURFACE, "init", null);
@@ -3995,7 +4011,29 @@
String propertyName = null;
Object propertyValue = null;
Token token = statement[i];
+ System.out.println(i + " " + token);
switch (token.tok) {
+ case Token.center:
+ propertyName = "center";
+ switch (statement[++i].tok) {
+ case Token.dollarsign:
+ String id = objectNameParameter(++i);
+ propertyValue = viewer.getDrawObjectCenter(id);
+ if (propertyValue == null)
+ drawObjectNotDefined(id);
+ break;
+ case Token.expressionBegin:
+ propertyValue = viewer.getAtomSetCenter(expression(statement, i +
1));
+ i = pcLastExpressionInstruction;
+ break;
+ case Token.leftbrace:
+ propertyValue = getCoordinate(i, true);
+ i = pcLastExpressionInstruction;
+ break;
+ default:
+ coordinateOrNameOrExpressionRequired();
+ }
+ break;
case Token.leftbrace:
// {X, Y, Z, W}
propertyName = "plane";
@@ -4016,12 +4054,22 @@
colorRangeStage++;
break;
case Token.solvent:
- propertyName = "solvent";
- propertyValue = new Float(viewer.getSolventProbeRadius());
- System.out.println (propertyName+" "+propertyValue);
+ propertyName = "solvent";
+ propertyValue = new Float(viewer.getSolventProbeRadius());
break;
case Token.identifier:
String str = (String) token.value;
+ if (str.equalsIgnoreCase("FIXED")) {
+ propertyName = "fixed";
+ propertyValue = Boolean.TRUE;
+ break;
+ }
+ if (str.equalsIgnoreCase("MODELBASED")) {
+ propertyName = "fixed";
+ propertyValue = Boolean.FALSE;
+ break;
+ }
+
if (str.equalsIgnoreCase("sign")) {
signPt = i + 1;
propertyName = "sign";
@@ -4029,15 +4077,22 @@
colorRangeStage = 1;
break;
} else if (str.equalsIgnoreCase("phase")) {
- if (orbitalPt != 0) {
+ if (isOrbital) {
propertyName = "phase";
propertyValue = "_orb";
break;
}
colorByPhase = true;
break;
+ } else if (str.equalsIgnoreCase("functionXY")) {
+ propertyName = "functionXY";
+ break;
+ } else if (str.equalsIgnoreCase("insideOut")) {
+ propertyName = "insideOut";
+ break;
} else if (str.equalsIgnoreCase("fileIndex")) {
- fileIndexPt = i + 1;
+ propertyName = "fileIndex";
+ propertyValue = new Integer(intParameter(++i));
break;
} else if (str.equalsIgnoreCase("noBackground")) {
propertyName = "background";
@@ -4055,11 +4110,20 @@
propertyName = "gridPoints";
break;
} else if (str.equalsIgnoreCase("orbital")) {
- orbitalPt = i + nlmZR.length;
+ nlmZR[0] = intParameter(++i);
+ nlmZR[1] = intParameter(++i);
+ nlmZR[2] = intParameter(++i);
+ nlmZR[3] = (statement[i + 1].tok == Token.integer ?
floatParameter(++i)
+ : 6f);
+ nlmZR[4] = (statement[i + 1].tok == Token.integer ?
floatParameter(++i)
+ : 10f);
+ propertyName = "orbital";
+ propertyValue = nlmZR;
+ isOrbital = true;
break;
} else if (str.equalsIgnoreCase("contour")) {
propertyName = "contour";
- contourPt = i + 1;
+ propertyValue = new Integer(intParameter(++i));
break;
}
propertyValue = token.value;
@@ -4091,41 +4155,13 @@
}
break;
case Token.decimal:
- if (colorRangeStage == 0 && orbitalPt <= 0) {
+ if (colorRangeStage == 0) {
propertyName = "cutoff";
propertyValue = token.value;
break;
}
// fall into
case Token.integer:
- if (orbitalPt > 0 && i <= orbitalPt) {
- int ipt = nlmZR.length - (orbitalPt - i) - 1;
- if (ipt < 3 && token.tok != Token.integer)
- integerExpected();
- // n l m Znuc ptsPerAngstrom
- nlmZR[ipt] = floatParameter(i);
- if (i != orbitalPt)
- break;
- propertyName = "orbital";
- propertyValue = nlmZR;
- orbitalPt = -999;
- break;
- }
- if (i == contourPt) {
- if (token.tok != Token.integer)
- integerExpected();
- propertyName = "contour";
- propertyValue = new Integer(token.intValue);
- contourPt = 0;
- break;
- }
- if (i == fileIndexPt) {
- if (token.tok != Token.integer)
- integerExpected();
- propertyName = "fileIndex";
- propertyValue = new Integer(token.intValue);
- break;
- }
if (colorRangeStage == 0 || colorRangeStage >= 3)
invalidArgument();
propertyName = colorRangeStage == 1 ? "red" : "blue";
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Isosurface.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -115,9 +115,11 @@
int colorPtr;
boolean colorByPhase;
int colorPhase;
+ boolean insideOut;
boolean isCalculation;
boolean isOrbital;
boolean isSolvent;
+ boolean isFunctionXY;
float solventRadius;
int edgeFractionBase;
@@ -156,10 +158,12 @@
boolean iDoContourPlane;
boolean dataIsJvxl2dContour;
+ Point3f center = new Point3f();
Point4f thePlane;
int nContours;
int thisContour;
boolean dotsOnly;
+ boolean isFixed;
BufferedReader br;
@@ -173,6 +177,8 @@
fileIndex = 1;
nBytes = 0;
nContours = 0;
+ insideOut = false;
+ isFixed = false;
thePlane = null;
iAddGridPoints = false;
associateNormals = true;
@@ -188,12 +194,19 @@
colorByPhase = false;
isOrbital = false;
isSolvent = false;
+ isFunctionXY = false;
isCalculation = false;
+ center.set(Float.MAX_VALUE, Float.MAX_VALUE, Float.MAX_VALUE);
cutoff = Float.MAX_VALUE;
super.setProperty("meshID", null, null);
return;
}
+ if ("center" == propertyName) {
+ center.set((Point3f) value);
+ return;
+ }
+
if ("sign" == propertyName) {
colorBySign = true;
colorPtr = 0;
@@ -227,6 +240,17 @@
return;
}
+ if ("insideOut" == propertyName) {
+ insideOut = true;
+ return;
+ }
+
+ if ("fixed" == propertyName) {
+ isFixed = ((Boolean) value).booleanValue();
+ setModelIndex();
+ return;
+ }
+
if ("contour" == propertyName) {
if (value instanceof Integer)
nContours = ((Integer) value).intValue();
@@ -274,13 +298,13 @@
return;
}
applyColorScale();
- if (currentMesh != null)
- currentMesh.visible = true;
+ setModelIndex();
return;
}
if ("solvent" == propertyName) {
isSolvent = isCalculation = true;
+ isOrbital = isFunctionXY = false;
solventRadius = ((Float) value).floatValue();
if (solventRadius < 0)
solventRadius = defaultSolventRadius;
@@ -292,6 +316,8 @@
if ("orbital" == propertyName) {
isOrbital = isCalculation = true;
+ isSolvent = isFunctionXY = false;
+
float[] nlmZR = (float[]) value;
psi_n = (int) nlmZR[0];
psi_l = (int) nlmZR[1];
@@ -307,6 +333,13 @@
}
propertyName = "bufferedReader";
}
+
+ if ("functionXY" == propertyName) {
+ isFunctionXY = true;
+ isSolvent = isOrbital = isCalculation = false;
+ return;
+ }
+
if ("bufferedReader" == propertyName) {
if (!isCalculation)
br = (BufferedReader) value;
@@ -321,12 +354,13 @@
currentMesh.nBytes = nBytes;
if (thePlane == null)
System.out.println("\n" + jvxlGetFile(currentMesh, jvxlFileMessage));
- currentMesh.visible = true;
+ setModelIndex();
return;
}
if ("colorReader" == propertyName) {
isSolvent = false;
isOrbital = false;
+ isFunctionXY = false;
System.out.println("mapping data...");
br = (BufferedReader) value;
checkFlags();
@@ -341,7 +375,7 @@
discardTempData(true);
currentMesh.nBytes = nBytes;
System.out.println("\n" + jvxlGetFile(currentMesh, jvxlFileMessage));
- currentMesh.visible = true;
+ setModelIndex();
return;
}
@@ -526,6 +560,8 @@
System.out.println("cube axes vector:" + volumetricVectors[i]);
}
}
+ if (center.x != Float.MAX_VALUE)
+ offsetCenter();
setupMatrix(volumetricMatrix, volumetricVectors);
readAtoms();
return readExtraLine();
@@ -679,6 +715,8 @@
isJvxlColorMapped = false;
isJvxlColorPrecision = false;
thisInside = (!isJvxl || thePlane == null);
+ if(insideOut)
+ thisInside = !thisInside;
nDataPoints = 0;
voxelData = new float[nPointsX][][];
@@ -700,6 +738,8 @@
for (int y = 0; y < nPointsY; ++y) {
float[] strip = new float[nPointsZ];
plane[y] = strip;
+ if (isFunctionXY)
+ getValueZ(x, y);
for (int z = 0; z < nPointsZ; ++z) {
float voxelValue;
/*
@@ -714,6 +754,8 @@
voxelValue = getPsi2(x, y, z);
else if (isSolvent)
voxelValue = getSolventValue(x, y, z);
+ else if (isFunctionXY)
+ voxelValue = calcVoxelZDistance(x, y, z);
else if (isMapData || thePlane == null)
voxelValue = getNextVoxelValue();
else
@@ -2787,6 +2829,16 @@
return ptXyz;
}
+ void offsetCenter() {
+ Point3f ptXyz = new Point3f();
+ ptXyz.scaleAdd((voxelCounts[0] - 1) / 2f, volumetricVectors[0], ptXyz);
+ ptXyz.scaleAdd((voxelCounts[1] - 1) / 2f, volumetricVectors[1], ptXyz);
+ ptXyz.scaleAdd((voxelCounts[2] - 1) / 2f, volumetricVectors[2], ptXyz);
+ System.out.println("teset1 "+volumetricOrigin);
+ volumetricOrigin.sub(center, ptXyz);
+ System.out.println("teset2 "+volumetricOrigin);
+ }
+
Point3f pixelPtToXYZ(int x, int y) {
Point3f ptXyz = new Point3f();
ptXyz.scaleAdd(x, planarVectors[0], planarOrigin);
@@ -2896,7 +2948,7 @@
int lastFactorial = -1;
int psi_gridMax = 60;
- Point3f psiOrigin = new Point3f(0, 0, 0);
+ Point3f psiOrigin = new Point3f();
final static double A0 = 0.52918f; //x10^-10 meters
final static double ROOT2 = 1.414214;
int psi_n = 2;
@@ -2908,7 +2960,10 @@
void setupOrbital() {
psi_radiusAngstroms = autoScaleOrbital();
-
+ if (center.x == Float.MAX_VALUE)
+ psiOrigin.set(0,0,0);
+ else
+ psiOrigin.set(center);
for (int i = 0; i < 3; i++)
setVoxelRange(i, -psi_radiusAngstroms, psi_radiusAngstroms,
psi_ptsPerAngstrom, psi_gridMax);
@@ -3057,13 +3112,10 @@
jvxlFileHeader = "solvent accesible surface\nrange " + xyzMin + " to "
+ xyzMax + "\n";
- int maxGrid = solvent_gridMax / (iAtom > 50 ? 2 : 1);
- setVoxelRange(0, xyzMin.x, xyzMax.x, solvent_ptsPerAngstrom,
- maxGrid);
- setVoxelRange(1, xyzMin.y, xyzMax.y, solvent_ptsPerAngstrom,
- maxGrid);
- setVoxelRange(2, xyzMin.z, xyzMax.z, solvent_ptsPerAngstrom,
- maxGrid);
+ int maxGrid = solvent_gridMax / (iAtom > 50 ? 2 : 1);
+ setVoxelRange(0, xyzMin.x, xyzMax.x, solvent_ptsPerAngstrom, maxGrid);
+ setVoxelRange(1, xyzMin.y, xyzMax.y, solvent_ptsPerAngstrom, maxGrid);
+ setVoxelRange(2, xyzMin.z, xyzMax.z, solvent_ptsPerAngstrom, maxGrid);
jvxlFileHeader += jvxlGetVolumeHeader();
atomCount = 0;
@@ -3074,7 +3126,7 @@
solvent_voxel.setValue(x, y, z, Float.MAX_VALUE);
float rA, rB;
Point3f ptA, ptB;
- for (int i = 0; i < solvent_nAtoms && solvent_voxel.value >= -0.5; i++) {
+ for (int i = 0; i < solvent_nAtoms && solvent_voxel.value >= -0.5; i++) {
ptA = solvent_ptAtom[i];
rA = solvent_atomRadius[i];
float v = solvent_voxel.ptXyz.distance(ptA) - rA;
@@ -3199,4 +3251,44 @@
* Math.cos(angleBAS - angleVAB));
return dVS;
}
+
+ float zValue;
+
+ void getValueZ(int x, int y) {
+ zValue = viewer.functionXY(x, y);
+ }
+
+ float calcVoxelZDistance(int x, int y, int z) {
+ if (x < 2 && y < 2)
+ System.out.println(x + " " + y + " " + zValue + " " + (z - zValue));
+ return z - zValue;
+ }
+
+ void setModelIndex() {
+ if (currentMesh == null)
+ return;
+ currentMesh.visible = true;
+ int modelCount = viewer.getModelCount();
+ if (modelCount < 2)
+ isFixed = true;
+ if (isFixed) {
+ currentMesh.modelIndex = -1;
+ } else {
+ currentMesh.modelIndex = viewer.getDisplayModelIndex();
+ }
+ }
+
+ void setVisibilityFlags(BitSet bs) {
+ /*
+ * set all fixed objects visible; others based on model being displayed
+ *
+ */
+ for (int i = meshCount; --i >= 0;) {
+ Mesh mesh = meshes[i];
+ mesh.visibilityFlags =
+ (mesh.visible && (mesh.modelIndex < 0 || bs.get(mesh.modelIndex)) ?
myVisibilityFlag : 0);
+ }
+ }
+
+
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
2006-06-13 17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
2006-06-13 22:30:34 UTC (rev 5219)
@@ -39,7 +39,7 @@
// for now, just update this by hand
// perhaps use ant filter later ... but mth doesn't like it :-(
public final static String copyright = "(C) 2006 Jmol Development";
- public final static String version = "10.x.11(branch bob200603)";
+ public final static String version = "10.x.11c(branch bob200603)";
public final static String cvsDate = "$Date$";
public final static String date = cvsDate.substring(7, 23);
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Mesh.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Mesh.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Mesh.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -27,7 +27,6 @@
import org.jmol.g3d.*;
-import javax.vecmath.Point3i;
import javax.vecmath.Point3f;
import javax.vecmath.Point4f;
import javax.vecmath.Vector3f;
@@ -73,9 +72,10 @@
Vector3f axes[];
String meshType = null;
String drawType = null;
+ int modelIndex = -1; // for Isosurface
+ int visibilityFlags;
+ int[] modelFlags = null; //one per POLYGON for DRAW
- int[] visibilityFlags = null;
-
boolean showPoints = false;
boolean drawTriangles = false;
boolean fillTriangles = true;
@@ -155,7 +155,7 @@
}
void setPolygonCount(int polygonCount) {
- System.out.println("Mesh setPolygonCount" + polygonCount);
+ //System.out.println("Mesh setPolygonCount" + polygonCount);
this.polygonCount = polygonCount;
if (polygonIndexes == null || polygonCount > polygonIndexes.length)
polygonIndexes = new int[polygonCount][];
@@ -185,6 +185,7 @@
}
void checkForDuplicatePoints(float cutoff) {
+ //not implemented
float cutoff2 = cutoff * cutoff;
for (int i = vertexCount; --i >= 0; )
for (int j = i; --j >= 0; ) {
@@ -202,8 +203,8 @@
}
final boolean isPolygonDisplayable(int index) {
- return (visibilityFlags == null ||
- visibilityFlags[index] != 0);
+ return (modelFlags == null ||
+ modelFlags[index] != 0);
}
final int setPolygon(Point3f[] ptList, int nVertices, int nPoly,
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/MeshRenderer.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/MeshRenderer.java
2006-06-13 17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/MeshRenderer.java
2006-06-13 22:30:34 UTC (rev 5219)
@@ -35,7 +35,7 @@
short backgroundColix;
void render1(Mesh mesh) {
- if (!mesh.visible)
+ if (mesh.visibilityFlags == 0)
return;
int vertexCount = mesh.vertexCount;
if (vertexCount == 0)
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
2006-06-13 17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/ModelManager.java
2006-06-13 22:30:34 UTC (rev 5219)
@@ -1282,6 +1282,8 @@
boolean showHydrogens = viewer.getShowHydrogens();
int ballVisibilityFlag =
viewer.getShapeVisibilityFlag(JmolConstants.SHAPE_BALLS);
int haloVisibilityFlag =
viewer.getShapeVisibilityFlag(JmolConstants.SHAPE_HALO);
+
+ //the three isosurface-related objects must be set individually
BitSet bs = viewer.getVisibleFramesBitSet();
Draw draw = (Draw) frame.shapes[JmolConstants.SHAPE_DRAW];
if (draw != null)
@@ -1289,6 +1291,10 @@
Polyhedra p = (Polyhedra) frame.shapes[JmolConstants.SHAPE_POLYHEDRA];
if (p != null)
p.setVisibilityFlags(bs);
+ Isosurface surf = (Isosurface)
frame.shapes[JmolConstants.SHAPE_ISOSURFACE];
+ if (surf != null)
+ surf.setVisibilityFlags(bs);
+
for (int i = frame.atomCount; --i >= 0; ) {
Atom atom = atoms[i];
atom.shapeVisibilityFlags &= (
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/StatusManager.java
2006-06-13 17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/StatusManager.java
2006-06-13 22:30:34 UTC (rev 5219)
@@ -304,5 +304,9 @@
return msgList;
}
+ float functionXY(int x, int y) {
+ return (jmolStatusListener == null ? 0 :
+ jmolStatusListener.functionXY(x, y));
+ }
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Token.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Token.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Token.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -181,7 +181,7 @@
final static int pmesh = command | 91;
final static int polyhedra = command | 92 | embeddedExpression;
final static int centerAt = command | 93;
- final static int isosurface = command | 94 | negnums | showparam |
colorparam;
+ final static int isosurface = command | 94 | negnums | showparam |
colorparam | embeddedExpression;
final static int draw = command | 95 | embeddedExpression;
final static int getproperty = command | 96;
final static int dipole = command | 97 | embeddedExpression;
@@ -546,7 +546,7 @@
// setparams
"ambient", new Token(ambient, "ambient"),
- "axes", new Token(axes, onDefault1, "axes"),
+ "axes", new Token(axes, varArgCount, "axes"),
"backfade", new Token(backfade, "backfade"),
"bondmode", new Token(bondmode, "bondmode"),
"bonds", new Token(bonds, "bonds"),
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java 2006-06-13
17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Viewer.java 2006-06-13
22:30:34 UTC (rev 5219)
@@ -3212,5 +3212,8 @@
public void setAtomCoordRelative(int atomIndex, float x, float y, float z) {
modelManager.setAtomCoordRelative(atomIndex,x,y,z);
}
-
+
+ float functionXY(int x, int y) {
+ return statusManager.functionXY(x, y);
+ }
}
Modified: branches/bob200603/Jmol/src/org/openscience/jmol/app/Jmol.java
===================================================================
--- branches/bob200603/Jmol/src/org/openscience/jmol/app/Jmol.java
2006-06-13 17:57:57 UTC (rev 5218)
+++ branches/bob200603/Jmol/src/org/openscience/jmol/app/Jmol.java
2006-06-13 22:30:34 UTC (rev 5219)
@@ -1439,6 +1439,10 @@
scriptWindow.hide();
}
+ public float functionXY(int x, int y) {
+ return 0; // for user-defined isosurface functions (testing only -- bob
hanson)
+ }
+
}
class ExecuteScriptAction extends AbstractAction {
@@ -1450,4 +1454,5 @@
viewer.evalStringQuiet(e.getActionCommand());
}
}
+
}
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