Revision: 18316
http://sourceforge.net/p/jmol/code/18316
Author: hansonr
Date: 2013-06-08 20:27:11 +0000 (Sat, 08 Jun 2013)
Log Message:
-----------
___JmolVersion="13.1.17_dev_2013.06.07"
TODO: PyMOL uniqueAtomSettings for transparency
-- will require by-vertex translucent option
bug fix: PyMOL volume map data saved from PyMOL 1.6 has slightly different data
structure
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
trunk/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java
trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java
trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/PyMOLMeshReader.java
trunk/Jmol/src/org/jmol/shapebio/BioShape.java
trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
trunk/Jmol/src/org/jmol/util/C.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-06-08 12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/adapter/readers/cifpdb/PdbReader.java
2013-06-08 20:27:11 UTC (rev 18316)
@@ -1795,9 +1795,6 @@
+ L[0][1] * xz - S[1][1] * x + S[2][2] * x + S[0][1] * y - S[0][2] * z;
anisou[6] = 12; // macromolecular Cartesian
anisou[7] = bresidual;
- if (Float.isNaN(bresidual))
- System.out.println("hmm");
-
if (tlsU == null)
tlsU = new Hashtable<Atom, float[]>();
tlsU.put(atom, anisou);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-08 12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2013-06-08 20:27:11 UTC (rev 18316)
@@ -230,6 +230,7 @@
case JC.SHAPE_CARTOON:
case JC.SHAPE_BACKBONE:
case JC.SHAPE_TRACE:
+ case JC.SHAPE_ISOSURFACE:
if (info instanceof Object[]) {
sm.loadShape(id);
sm.setShapePropertyBs(id, "params", info, bsAtoms);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2013-06-08 12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
2013-06-08 20:27:11 UTC (rev 18316)
@@ -369,7 +369,7 @@
if (doCheck && markCount >= 6 || markCount == 3 && inMovie)
return;
memo.put(Integer.valueOf(i), o);
- System.out.println("caching string " + o + " at " +
binaryDoc.getPosition());
+ //System.out.println("caching string " + o + " at " +
binaryDoc.getPosition());
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java 2013-06-08
12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java 2013-06-08
20:27:11 UTC (rev 18316)
@@ -6263,6 +6263,8 @@
Logger.info("PyMOL " + pymolVersion + " does not have setting " + i);
//$FALL-THROUGH$
case ellipsoid_transparency:
+ case ribbon_transparency:
+ case nonbonded_transparency:
return 0;
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-08 12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
2013-06-08 20:27:11 UTC (rev 18316)
@@ -44,16 +44,16 @@
// ellipsoid_scale
// label_color
// label_position
+// mesh_color
// nonbonded_transparency
// ribbon_color
// sphere_color
// sphere_scale
// sphere_transparency
+// surface_color
//
//TODO:
//
-// mesh_color
-// surface_color
// transparency (surface)
//
//special (probably) PyMOL-only:
@@ -900,7 +900,7 @@
float getUniqueFloatDef(int id, int key, float defaultValue) {
JmolList<Object> setting;
- if (id < 0
+ if (id <= 0
|| (setting = uniqueSettings.get(Integer.valueOf((id << 10) + key)))
== null)
return defaultValue;
float v = ((Number) setting.get(2)).floatValue();
@@ -912,7 +912,7 @@
@SuppressWarnings("unchecked")
P3 getUniquePoint(int id, int key, P3 pt) {
JmolList<Object> setting;
- if (id < 0
+ if (id <= 0
|| (setting = uniqueSettings.get(Integer.valueOf((id << 10) + key)))
== null)
return pt;
pt = new P3();
@@ -1397,6 +1397,25 @@
case PyMOL.REP_DOTS:
setUniqueObjects(JC.SHAPE_DOTS, bs, PyMOL.dot_color, dotColor, 0, 0,
PyMOL.sphere_scale, sphereScale, 1);
break;
+ case PyMOL.REP_SURFACE: // = 2;
+ // unique translucency here involves creating ghost surfaces
+ float withinDistance = floatSetting(PyMOL.surface_carve_cutoff);
+ jo = addJmolObject(T.isosurface, bs, new Object[] {
+ booleanSetting(PyMOL.two_sided_lighting) ? "FULLYLIT" : "FRONTLIT",
+ (surfaceMode == 3 || surfaceMode == 4) ? " only" : "",
+ bsCarve, Float.valueOf(withinDistance)});
+ jo.setSize(floatSetting(PyMOL.solvent_radius) * (solventAccessible ? -1
: 1));
+ jo.translucency = transparency;
+ if (surfaceColor >= 0)
+ jo.argb = PyMOL.getRGB(surfaceColor);
+ setUniqueObjects(JC.SHAPE_ISOSURFACE, bs, PyMOL.surface_color,
surfaceColor, PyMOL.transparency, transparency, 0, 0, 0);
+ break;
+ case PyMOL.REP_MESH: // = 8;
+ jo = addJmolObject(T.isosurface, bs, null);
+ jo.setSize(floatSetting(PyMOL.solvent_radius));
+ jo.translucency = transparency;
+ setUniqueObjects(JC.SHAPE_ISOSURFACE, bs, PyMOL.surface_color,
surfaceColor, PyMOL.transparency, transparency, 0, 0, 0);
+ break;
case PyMOL.REP_LABELS: // = 3;
bs.and(bsLabeled);
if (bs.isEmpty())
@@ -1434,55 +1453,37 @@
case PyMOL.REP_RIBBON: // backbone or trace, depending
createRibbonObject(bs);
break;
- case PyMOL.REP_SURFACE: // = 2;
- // unique translucency here involves creating ghost surfaces
- float withinDistance = floatSetting(PyMOL.surface_carve_cutoff);
- jo = addJmolObject(T.isosurface, bs, new Object[] {
- booleanSetting(PyMOL.two_sided_lighting) ? "FULLYLIT" : "FRONTLIT",
- (surfaceMode == 3 || surfaceMode == 4) ? " only" : "",
- bsCarve, Float.valueOf(withinDistance)});
- jo.setSize(floatSetting(PyMOL.solvent_radius) * (solventAccessible ? -1
: 1));
- jo.translucency = transparency;
- if (surfaceColor >= 0)
- jo.argb = PyMOL.getRGB(surfaceColor);
- break;
- case PyMOL.REP_MESH: // = 8;
- jo = addJmolObject(T.isosurface, bs, null);
- jo.setSize(floatSetting(PyMOL.solvent_radius));
- jo.translucency = transparency;
- break;
default:
Logger.error("Unprocessed representation type " + shapeID);
}
}
- private JmolObject setUniqueObjects(int shape, BS bs,
- int setColor, int color,
- int setTrans, float trans,
- int setSize, float size, float f) {
+ private JmolObject setUniqueObjects(int shape, BS bs, int setColor,
+ int color, int setTrans, float trans,
+ int setSize, float size, float f) {
int n = bs.cardinality();
short[] colixes = (setColor == 0 ? null : new short[n]);
float[] atrans = (setTrans == 0 ? null : new float[n]);
float[] sizes = new float[n];
- for (int pt=0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1),
pt++) {
- int id = (uniqueIDs == null ? -1 : uniqueIDs[i]);
+ for (int pt = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1),
pt++) {
+ int id = (reader == null ? uniqueIDs[i] : reader.getUniqueID(i));
if (colixes != null) {
int c = (int) getUniqueFloatDef(id, setColor, color);
if (c > 0)
colixes[pt] = getColix(c, 0);
}
if (atrans != null) {
- atrans[pt] = getUniqueFloatDef(id, setTrans, trans);
+ atrans[pt] = getUniqueFloatDef(id, setTrans, trans);
}
sizes[pt] = getUniqueFloatDef(id, setSize, size) * f;
}
- return addJmolObject(shape, bs, new Object[] {colixes, atrans, sizes});
+ return addJmolObject(shape, bs, new Object[] { colixes, atrans, sizes });
-// case PyMOL.REP_DOTS:
- // addJmolObject(JC.SHAPE_DOTS, bs, null).rd = new RadiusData(null,
+ // case PyMOL.REP_DOTS:
+ // addJmolObject(JC.SHAPE_DOTS, bs, null).rd = new RadiusData(null,
// value1, RadiusData.EnumType.FACTOR, EnumVdw.AUTO);
-// case PyMOL.REP_NONBONDED:
- // addJmolObject(JC.SHAPE_STARS, bs, null).rd = new RadiusData(null,
+ // case PyMOL.REP_NONBONDED:
+ // addJmolObject(JC.SHAPE_STARS, bs, null).rd = new RadiusData(null,
// f / 2, RadiusData.EnumType.FACTOR, EnumVdw.AUTO);
}
@@ -1701,9 +1702,12 @@
public void addMesh(int tok, JmolList<Object> obj, String objName, boolean
isMep) {
JmolObject jo = addJmolObject(tok, null, obj);
setSceneObject(objName, -1);
+ int meshColor = (int) floatSetting(PyMOL.mesh_color);
+ if (meshColor < 0)
+ meshColor = intAt(listAt(obj, 0), 2);
if (!isMep) {
jo.setSize(meshWidth);
- jo.argb = PyMOL.getRGB(intAt(listAt(obj, 0), 2));
+ jo.argb = PyMOL.getRGB(meshColor);
}
jo.translucency = transparency;
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-06-08 12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
2013-06-08 20:27:11 UTC (rev 18316)
@@ -1031,6 +1031,7 @@
public void setEllipsoids() {
if (!haveAnisou)
return;
+ getSymmetry();
int iAtomFirst = getLastAtomSetAtomIndex();
for (int i = iAtomFirst; i < atomCount; i++)
atoms[i].setEllipsoid(symmetry.getEllipsoid(atoms[i].anisoBorU));
Modified: trunk/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java 2013-06-08 12:30:43 UTC
(rev 18315)
+++ trunk/Jmol/src/org/jmol/jvxl/data/JvxlCoder.java 2013-06-08 20:27:11 UTC
(rev 18316)
@@ -166,7 +166,10 @@
jvxlEncodeContourData(jvxlData.vContours, data);
}
if (jvxlData.vertexColorMap != null) {
- XmlUtil.openTag(data, "jvxlVertexColorData");
+ if (jvxlData.baseColor == null)
+ XmlUtil.openTag(data, "jvxlVertexColorData");
+ else
+ XmlUtil.openTagAttr(data, "jvxlVertexColorData", new String[]
{"baseColor", jvxlData.baseColor});
for (Map.Entry<String, BS> entry : jvxlData.vertexColorMap.entrySet())
appendEncodedBitSetTag(data, "jvxlColorMap", entry.getValue(), -1, new
Object[] { "color", entry.getKey() });
jvxlData.vertexColorMap = null;
Modified: trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2013-06-08 12:30:43 UTC
(rev 18315)
+++ trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2013-06-08 20:27:11 UTC
(rev 18316)
@@ -171,6 +171,7 @@
public boolean allowVolumeRender;
public float voxelVolume;
public P3 mapLattice;
+ public String baseColor;
public void clear() {
allowVolumeRender = true;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2013-06-08
12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2013-06-08
20:27:11 UTC (rev 18316)
@@ -130,10 +130,13 @@
if (haveContourData)
jvxlDecodeContourData(jvxlData, xr.getXmlData("jvxlContourData", null,
false, false));
- if (jvxlData.nVertexColors > 0) {
+ if (jvxlDataIsColorMapped && jvxlData.nVertexColors > 0) {
jvxlData.vertexColorMap = new Hashtable<String, BS>();
+ String vdata = xr.getXmlData("jvxlVertexColorData", null, true, false);
+ String baseColor = XmlReader.getXmlAttrib(vdata, "baseColor");
+ jvxlData.baseColor = (baseColor.length() > 0 ? baseColor : null);
for (int i = 0; i < jvxlData.nVertexColors; i++) {
- String s = xr.getXmlData("jvxlColorMap", null, true, false);
+ String s = xr.getXmlData("jvxlColorMap", vdata, true, false);
String color = XmlReader.getXmlAttrib(s, "color");
BS bs = JvxlCoder.jvxlDecodeBitSet(xr.getXmlData("jvxlColorMap",
s, false, false));
@@ -352,37 +355,37 @@
}
protected void jvxlSetColorRanges(float dataMin, float dataMax, float red,
- float blue, boolean insideOut) {
+ float blue, boolean insideOut) {
if (jvxlDataIsColorMapped) {
- if (!Float.isNaN(dataMin) && !Float.isNaN(dataMax)) {
- if (dataMax == 0 && dataMin == 0) {
- //set standard -1/1; bit of a hack
- dataMin = -1;
- dataMax = 1;
- }
- params.mappedDataMin = dataMin;
- params.mappedDataMax = dataMax;
- Logger.info("JVXL read: data_min/max " + params.mappedDataMin + "/"
- + params.mappedDataMax);
- }
- if (!params.rangeDefined)
- if (!Float.isNaN(red) && !Float.isNaN(blue)) {
- if (red == 0 && blue == 0) {
+ if (!Float.isNaN(dataMin) && !Float.isNaN(dataMax)) {
+ if (dataMax == 0 && dataMin == 0) {
//set standard -1/1; bit of a hack
- red = -1;
- blue = 1;
+ dataMin = -1;
+ dataMax = 1;
}
- params.valueMappedToRed = Math.min(red, blue);
- params.valueMappedToBlue = Math.max(red, blue);
- params.isColorReversed = (red > blue);
- params.rangeDefined = true;
- } else {
- params.valueMappedToRed = 0f;
- params.valueMappedToBlue = 1f;
- params.rangeDefined = true;
+ params.mappedDataMin = dataMin;
+ params.mappedDataMax = dataMax;
+ Logger.info("JVXL read: data_min/max " + params.mappedDataMin + "/"
+ + params.mappedDataMax);
}
- Logger.info("JVXL read: color red/blue: " + params.valueMappedToRed + "/"
- + params.valueMappedToBlue);
+ if (!params.rangeDefined)
+ if (!Float.isNaN(red) && !Float.isNaN(blue)) {
+ if (red == 0 && blue == 0) {
+ //set standard -1/1; bit of a hack
+ red = -1;
+ blue = 1;
+ }
+ params.valueMappedToRed = Math.min(red, blue);
+ params.valueMappedToBlue = Math.max(red, blue);
+ params.isColorReversed = (red > blue);
+ params.rangeDefined = true;
+ } else {
+ params.valueMappedToRed = 0f;
+ params.valueMappedToBlue = 1f;
+ params.rangeDefined = true;
+ }
+ Logger.info("JVXL read: color red/blue: " + params.valueMappedToRed + "/"
+ + params.valueMappedToBlue);
}
jvxlData.valueMappedToRed = params.valueMappedToRed;
jvxlData.valueMappedToBlue = params.valueMappedToBlue;
@@ -578,6 +581,8 @@
@Override
protected String readColorData() {
+ if (!jvxlDataIsColorMapped)
+ return "";
// overloads SurfaceReader
// standard jvxl file read for color
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PyMOLMeshReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PyMOLMeshReader.java 2013-06-08
12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PyMOLMeshReader.java 2013-06-08
20:27:11 UTC (rev 18316)
@@ -76,7 +76,7 @@
surfaceName = (String) data.get(data.size() - 1);
}
voxelList = getList(getList(getList(surfaceList, 14), 2), 6);
- System.out.println("Number of grid points = " + voxelList.size() + " " +
params.sigma);
+ System.out.println("Number of grid points = " + voxelList.size());
allowSigma = true;
}
@@ -95,11 +95,15 @@
jvxlFileHeaderBuffer.append(surfaceName + " (" + params.calculationType +
")\n");
// cell parameters
- t = getList(getList(surfaceList, 1), 0);
+ JmolList<Object> s = getList(surfaceList, 1);
+ t = getList(s, 0);
+ // change in format between PyMOL versions
+ if (t.size() < 3)
+ t = getList(s = getList(s, 0), 0);
a = getFloat(t, 0);
b = getFloat(t, 1);
c = getFloat(t, 2);
- t = getList(getList(surfaceList, 1), 1);
+ t = getList(s, 1);
alpha = getFloat(t, 0);
beta = getFloat(t, 1);
gamma = getFloat(t, 2);
Modified: trunk/Jmol/src/org/jmol/shapebio/BioShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/BioShape.java 2013-06-08 12:30:43 UTC
(rev 18315)
+++ trunk/Jmol/src/org/jmol/shapebio/BioShape.java 2013-06-08 20:27:11 UTC
(rev 18316)
@@ -313,15 +313,11 @@
}
}
- public void setParams(Object[] data, BS bsSelected) {
+ public void setParams(Object[] data, int[] atomMap, BS bsSelected) {
if (monomerCount == 0)
return;
// only implemented for simple colixes, really.
short[] c = (short[]) data[0];
- int n = bsSelected.length();
- int[] atomMap = new int[n];
- for (int pt = 0, i = bsSelected.nextSetBit(0); i >= 0; i =
bsSelected.nextSetBit(i + 1), pt++)
- atomMap[i] = pt;
// would have to do something like this here as well;
float[] atrans = (float[]) data[1];
//float[] sizes = (float[]) data[2];
@@ -329,6 +325,7 @@
isActive = true;
if (bsColixSet == null)
bsColixSet = new BS();
+ int n = atomMap.length;
for (int i = monomerCount; --i >= 0;) {
int atomIndex = leadAtomIndices[i];
if (bsSelected.get(atomIndex) && i < colixes.length && atomIndex < n) {
Modified: trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java 2013-06-08
12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/shapebio/BioShapeCollection.java 2013-06-08
20:27:11 UTC (rev 18316)
@@ -142,8 +142,12 @@
return;
}
if ("params" == propertyName) {
+ int n = bsSelected.length();
+ int[] atomMap = new int[n];
+ for (int pt = 0, i = bsSelected.nextSetBit(0); i >= 0; i =
bsSelected.nextSetBit(i + 1), pt++)
+ atomMap[i] = pt;
for (int i = bioShapes.length; --i >= 0;)
- bioShapes[i].setParams((Object[]) value, bsSelected);
+ bioShapes[i].setParams((Object[]) value, atomMap, bsSelected);
return;
}
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2013-06-08
12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2013-06-08
20:27:11 UTC (rev 18316)
@@ -92,21 +92,36 @@
package org.jmol.shapesurface;
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.Hashtable;
+import java.util.Map;
+
+import org.jmol.api.JmolDocument;
+import org.jmol.io.JmolBinary;
+import org.jmol.jvxl.api.MeshDataServer;
+import org.jmol.jvxl.data.JvxlCoder;
+import org.jmol.jvxl.data.JvxlData;
+import org.jmol.jvxl.data.MeshData;
+import org.jmol.jvxl.readers.Parameters;
+import org.jmol.jvxl.readers.SurfaceGenerator;
+import org.jmol.script.T;
import org.jmol.shape.Mesh;
import org.jmol.shape.MeshCollection;
import org.jmol.shape.Shape;
import org.jmol.util.Escape;
-
import org.jmol.util.AxisAngle4f;
import org.jmol.util.BS;
import org.jmol.util.C;
import org.jmol.util.ColorEncoder;
import org.jmol.util.ArrayUtil;
import org.jmol.util.ColorUtil;
+import org.jmol.util.JmolList;
import org.jmol.util.Logger;
import org.jmol.util.Matrix3f;
import org.jmol.util.Matrix4f;
-//import org.jmol.util.Measure;
import org.jmol.util.MeshSurface;
import org.jmol.util.Parser;
import org.jmol.util.P3;
@@ -118,30 +133,9 @@
import org.jmol.util.V3;
import org.jmol.viewer.ActionManager;
import org.jmol.viewer.JC;
-import org.jmol.script.T;
import org.jmol.viewer.Viewer;
-//import org.jmol.viewer.StateManager.Orientation;
-import java.io.BufferedInputStream;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.OutputStream;
-import org.jmol.util.JmolList;
-import java.util.Hashtable;
-
-import java.util.Map;
-
-
-import org.jmol.api.JmolDocument;
-import org.jmol.io.JmolBinary;
-import org.jmol.jvxl.api.MeshDataServer;
-import org.jmol.jvxl.data.JvxlCoder;
-import org.jmol.jvxl.data.JvxlData;
-import org.jmol.jvxl.data.MeshData;
-import org.jmol.jvxl.readers.Parameters;
-import org.jmol.jvxl.readers.SurfaceGenerator;
-
public class Isosurface extends MeshCollection implements MeshDataServer {
private IsosurfaceMesh[] isomeshes = new IsosurfaceMesh[4];
@@ -228,8 +222,9 @@
setPropI("modelIndex", Integer.valueOf(imodel), null);
setPropI("fileName", "cache://isosurface_" + id, null);
setPropI("readFile", null, null);
- setPropI("finalize", "isosurface ID " + Escape.eS(id) + (imodel >= 0 ? "
modelIndex " + imodel : "")
- + " /*file*/" + Escape.eS("cache://isosurface_" + id), null);
+ setPropI("finalize", "isosurface ID " + Escape.eS(id)
+ + (imodel >= 0 ? " modelIndex " + imodel : "") + " /*file*/"
+ + Escape.eS("cache://isosurface_" + id), null);
setPropI("clear", null, null);
return;
}
@@ -263,39 +258,37 @@
return;
}
+ if ("params" == propertyName) {
+ if (thisMesh != null) {
+ ensureMeshSource();
+ thisMesh.checkAllocColixes();
+ Object[] data = (Object[]) value;
+ short[] colixes = (short[]) data[0];
+ int[] atomMap = null;
+ //float[] atrans = (float[]) data[1];
+ if (colixes != null) {
+ for (int i = 0; i < colixes.length; i++) {
+ short colix = colixes[i];
+ float f = 0;//(atrans == null ? 0 : atrans[pt]);
+ if (f > 0.01f)
+ colix = C.getColixTranslucent3(colix, true, f);
+ colixes[i] = colix;
+ }
+ atomMap = new int[bs.length()];
+ for (int pt = 0, i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i +
1), pt++)
+ atomMap[i] = pt;
+ }
+ thisMesh.setVertexColixesForAtoms(viewer, colixes, atomMap, bs);
+ thisMesh.setVertexColorMap();
+ }
+ return;
+ }
if ("atomcolor" == propertyName) {
// color $id red ({0:30 ....}) (atoms)
// color $id red [{0:30 ....}] (vertices)
if (thisMesh != null) {
- boolean haveColors = (thisMesh.vertexSource != null);
- if (haveColors)
- for (int i = thisMesh.vertexCount; --i >= 0;)
- if (thisMesh.vertexSource[i] < 0) {
- haveColors = false;
- break;
- }
- if (!haveColors) {
- int[] source = thisMesh.vertexSource;
- short[] vertexColixes = thisMesh.vertexColixes;
- short colix = (!thisMesh.isColorSolid ? 0 : thisMesh.colix);
- setProperty("init", null, null);
- setProperty("map", Boolean.FALSE, null);
- setProperty("property", new float[viewer.getAtomCount()], null);
- if (source == null) {
- if (colix != 0) {
- thisMesh.colorCommand = "color isosurface "
- + C.getHexCode(colix);
- setProperty("color", Integer.valueOf(C.getArgb(colix)), null);
- }
- } else {
- for (int i = thisMesh.vertexCount; --i >= 0;)
- if (source[i] < 0)
- source[i] = thisMesh.vertexSource[i];
- thisMesh.vertexSource = source;
- thisMesh.vertexColixes = vertexColixes;
- }
- }
- thisMesh.colorAtoms(C.getColixO(value), bs);
+ ensureMeshSource();
+ thisMesh.colorVertices(C.getColixO(value), bs, true);
}
return;
}
@@ -309,7 +302,7 @@
if ("vertexcolor" == propertyName) {
if (thisMesh != null) {
- thisMesh.colorVertices(C.getColixO(value), bs);
+ thisMesh.colorVertices(C.getColixO(value), bs, false);
}
return;
}
@@ -331,8 +324,10 @@
return;
}
if ("color" == propertyName) {
+ String color = C.getHexCode(C.getColixO(value));
if (thisMesh != null) {
// thisMesh.vertexColixes = null;
+ thisMesh.jvxlData.baseColor = color;
thisMesh.isColorSolid = true;
thisMesh.polygonColixes = null;
thisMesh.colorEncoder = null;
@@ -340,6 +335,7 @@
} else if (!TextFormat.isWild(previousMeshID)) {
for (int i = meshCount; --i >= 0;) {
// isomeshes[i].vertexColixes = null;
+ isomeshes[i].jvxlData.baseColor = color;
isomeshes[i].isColorSolid = true;
isomeshes[i].polygonColixes = null;
isomeshes[i].colorEncoder = null;
@@ -638,7 +634,7 @@
&& sg != null) {
sg.getParams().testFlags = (viewer.getTestFlag(2) ? 2 : 0);
} else if ("solvent" == propertyName) {
- sg.getParams().testFlags = (viewer.getTestFlag(1) ? 1 : 0);
+ sg.getParams().testFlags = (viewer.getTestFlag(1) ? 1 : 0);
}
// surface Export3D only (return TRUE) or shared (return FALSE)
@@ -717,6 +713,36 @@
setPropertySuper(propertyName, value, bs);
}
+ private void ensureMeshSource() {
+ boolean haveColors = (thisMesh.vertexSource != null);
+ if (haveColors)
+ for (int i = thisMesh.vertexCount; --i >= 0;)
+ if (thisMesh.vertexSource[i] < 0) {
+ haveColors = false;
+ break;
+ }
+ if (!haveColors) {
+ int[] source = thisMesh.vertexSource;
+ short[] vertexColixes = thisMesh.vertexColixes;
+ short colix = (thisMesh.isColorSolid ? thisMesh.colix : 0);
+ setProperty("init", null, null);
+ setProperty("map", Boolean.FALSE, null);
+ setProperty("property", new float[viewer.getAtomCount()], null);
+ if (colix != 0) {
+ thisMesh.colorCommand = "color isosurface "
+ + C.getHexCode(colix);
+ setProperty("color", Integer.valueOf(C.getArgb(colix)), null);
+ }
+ if (source != null) {
+ for (int i = thisMesh.vertexCount; --i >= 0;)
+ if (source[i] < 0)
+ source[i] = thisMesh.vertexSource[i];
+ thisMesh.vertexSource = source;
+ thisMesh.vertexColixes = vertexColixes;
+ }
+ }
+ }
+
protected void slabPolygons(Object[] slabInfo) {
thisMesh.slabPolygons(slabInfo, false);
thisMesh.reinitializeLightingAndColor(viewer);
Modified: trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2013-06-08
12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/shapesurface/IsosurfaceMesh.java 2013-06-08
20:27:11 UTC (rev 18316)
@@ -487,24 +487,40 @@
jvxlData.vContours = null;
}
- /**
- * color a specific set of vertices based on a set of atoms
- *
- * @param colix
- * @param bs
- */
- void colorAtoms(short colix, BS bs) {
- colorVertices2(colix, bs, true);
+ void setVertexColorMap() {
+ vertexColorMap = new Hashtable<String, BS>();
+ short lastColix = -999;
+ BS bs = null;
+ for (int i = vertexCount; --i >= 0;) {
+ short c = vertexColixes[i];
+ if (c != lastColix) {
+ String color = C.getHexCode(lastColix = c);
+ bs = vertexColorMap.get(color);
+ if (bs == null)
+ vertexColorMap.put(color, bs = new BS());
+ }
+ bs.set(i);
+ }
}
- /**
- * color a specific set of vertices
- *
- * @param colix
- * @param bs
- */
- void colorVertices(short colix, BS bs) {
- colorVertices2(colix, bs, false);
+ void setVertexColixesForAtoms(Viewer viewer, short[] colixes, int[] atomMap,
+ BS bs) {
+ jvxlData.vertexDataOnly = true;
+ jvxlData.vertexColors = new int[vertexCount];
+ jvxlData.nVertexColors = vertexCount;
+ Atom[] atoms = viewer.modelSet.atoms;
+ for (int i = mergeVertexCount0; i < vertexCount; i++) {
+ int iAtom = vertexSource[i];
+ if (iAtom < 0 || !bs.get(iAtom))
+ continue;
+ jvxlData.vertexColors[i] = viewer.getColorArgbOrGray(vertexColixes[i] = C
+ .copyColixTranslucency(colix, atoms[iAtom].getColix()));
+
+ short colix = (colixes == null ? C.INHERIT_ALL :
colixes[atomMap[iAtom]]);
+ if (colix == C.INHERIT_ALL)
+ colix = atoms[iAtom].getColix();
+ vertexColixes[i] = C.copyColixTranslucency(this.colix, colix);
+ }
}
/**
@@ -514,17 +530,12 @@
* @param bs
* @param isAtoms
*/
- private void colorVertices2(short colix, BS bs, boolean isAtoms) {
+ void colorVertices(short colix, BS bs, boolean isAtoms) {
if (vertexSource == null)
return;
colix = C.copyColixTranslucency(this.colix, colix);
BS bsVertices = (isAtoms ? new BS() : bs);
- if (vertexColixes == null || vertexColorMap == null && isColorSolid) {
- vertexColixes = new short[vertexCount];
- for (int i = 0; i < vertexCount; i++)
- vertexColixes[i] = this.colix;
- }
- isColorSolid = false;
+ checkAllocColixes();
// TODO: color translucency?
if (isAtoms)
for (int i = 0; i < vertexCount; i++) {
@@ -533,7 +544,8 @@
continue;
if (bs.get(pt)) {
vertexColixes[i] = colix;
- bsVertices.set(i);
+ if (bsVertices != null)
+ bsVertices.set(i);
}
}
else
@@ -552,6 +564,12 @@
addColorToMap(vertexColorMap, color, bs);
}
+ void checkAllocColixes() {
+ if (vertexColixes == null || vertexColorMap == null && isColorSolid)
+ allocVertexColixes();
+ isColorSolid = false;
+ }
+
/**
* adds a set of specifically-colored vertices to the map,
* ensuring that no vertex is in two maps.
@@ -674,6 +692,10 @@
remapColors(null, null, Float.NaN);
}
} else {
+ if (jvxlData.baseColor != null) {
+ for (int i = vertexCount; --i >= 0;)
+ vertexColixes[i] = colix;
+ }
for (Map.Entry<String, BS> entry : jvxlData.vertexColorMap.entrySet())
{
BS bsMap = entry.getValue();
short colix = C.copyColixTranslucency(this.colix, C.getColixS(entry
@@ -718,11 +740,12 @@
boolean inherit = (vertexSource != null && ce.currentPalette ==
ColorEncoder.INHERIT);
vertexColorMap = null;
polygonColixes = null;
+ jvxlData.baseColor = null;
jvxlData.vertexCount = vertexCount;
if (vertexValues == null || jvxlData.vertexCount == 0)
return;
if (vertexColixes == null || vertexColixes.length != vertexCount)
- vertexColixes = new short[vertexCount];
+ allocVertexColixes();
if (inherit) {
jvxlData.vertexDataOnly = true;
jvxlData.vertexColors = new int[vertexCount];
Modified: trunk/Jmol/src/org/jmol/util/C.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/C.java 2013-06-08 12:30:43 UTC (rev 18315)
+++ trunk/Jmol/src/org/jmol/util/C.java 2013-06-08 20:27:11 UTC (rev 18316)
@@ -110,7 +110,7 @@
*/
- public final static short INHERIT_ALL = 0;
+ public final static short INHERIT_ALL = 0; // do not change this from 0; new
colix[n] must be this
public final static short INHERIT_COLOR = 1;
public final static short USE_PALETTE = 2;
public final static short RAW_RGB = 3;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-08 12:30:43 UTC
(rev 18315)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-06-08 20:27:11 UTC
(rev 18316)
@@ -11,10 +11,10 @@
___JmolVersion="13.1.17_dev_2013.06.07"
-TODO: PyMOL EDM data saved from PyMOL 1.6?
-TODO: PyMOL uniqueAtomSettings for mesh_color, surface_color, and transparency
- -- color isosurface {xxxx} red translucent 0.5 ??
+TODO: PyMOL uniqueAtomSettings for transparency
+ -- will require by-vertex translucent option
+bug fix: PyMOL volume map data saved from PyMOL 1.6 has slightly different
data structure
bug fix: jvxl reader ignores jvxlVertexColorData
bug fix: ellipsoid rendering problems
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