Revision: 20123
http://sourceforge.net/p/jmol/code/20123
Author: hansonr
Date: 2014-11-25 02:53:08 +0000 (Tue, 25 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.9_2014.11.24"
new feature: isosurface "==1blu" -- difference map; defaults to sigma=3
Modified Paths:
--------------
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/VolumeFileReader.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2014-11-23 23:25:34 UTC
(rev 20122)
+++ trunk/Jmol/src/org/jmol/jvxl/data/JvxlData.java 2014-11-25 02:53:08 UTC
(rev 20123)
@@ -85,6 +85,7 @@
public JvxlData() {
}
+ public String msg = "";
public boolean wasJvxl;
public boolean wasCubic;
@@ -191,10 +192,11 @@
contourColors = null;
isSlabbable = false;
mapLattice = null;
- processLattice = null;
meshColor = null;
+ msg = "";
nPointsX = 0;
nVertexColors = 0;
+ processLattice = null;
slabInfo = null;
slabValue = Integer.MIN_VALUE;
thisSet = Integer.MIN_VALUE;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2014-11-23
23:25:34 UTC (rev 20122)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2014-11-25
02:53:08 UTC (rev 20123)
@@ -80,7 +80,7 @@
void init2JXR(SurfaceGenerator sg, BufferedReader br) {
init2VFR(sg, br);
jvxlData.wasJvxl = isJvxl = true;
- isXLowToHigh = false;
+ isXLowToHigh = canDownsample = false;
xr = new XmlReader(br);
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java 2014-11-23
23:25:34 UTC (rev 20122)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java 2014-11-25
02:53:08 UTC (rev 20123)
@@ -138,6 +138,8 @@
Logger.info("voxel grid origin:" + volumetricOrigin);
int downsampleFactor = params.downsampleFactor;
boolean downsampling = (canDownsample && downsampleFactor > 1);
+ if (downsampleFactor > 1 && !canDownsample)
+ jvxlData.msg += "\ncannot downsample this file type";
if (downsampling) {
downsampleRemainders = new int[3];
Logger.info("downsample factor = " + downsampleFactor);
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-11-23 23:25:34 UTC
(rev 20122)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2014-11-25 02:53:08 UTC
(rev 20123)
@@ -8299,7 +8299,7 @@
if (max == Float.MAX_VALUE)
ce.hi = max;
setShapeProperty(shapeType, "remapColor", ce);
- showString(getIsosurfaceDataRange(shapeType, ""));
+ showString(((String) getShapeProperty(JC.SHAPE_ISOSURFACE,
"dataRangeStr")).replace('\n',' '));
if (translucentLevel == Float.MAX_VALUE)
return;
} else if (max != Float.MAX_VALUE) {
@@ -8594,15 +8594,6 @@
return filename;
}
- public String getIsosurfaceDataRange(int iShape, String sep) {
- float[] dataRange = (float[]) getShapeProperty(iShape, "dataRange");
- return (dataRange != null && dataRange[0] != Float.MAX_VALUE
- && dataRange[0] != dataRange[1] ? sep + "isosurface"
- + " full data range " + dataRange[0] + " to " + dataRange[1]
- + " with color scheme spanning " + dataRange[2] + " to " + dataRange[3]
- : "");
- }
-
private P3[] getObjectBoundingBox(String id) {
Object[] data = new Object[] { id, null, null };
return (getShapePropertyData(JC.SHAPE_ISOSURFACE, "getBoundingBox", data)
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-23 23:25:34 UTC
(rev 20122)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2014-11-25 02:53:08 UTC
(rev 20123)
@@ -3191,8 +3191,8 @@
if (tokProperty != T.color) {
pt = new P3();
for (int iAtom = ac; --iAtom >= 0;)
- data[iAtom] = atoms[iAtom].atomPropertyFloat(vwr,
- tokProperty, pt);
+ data[iAtom] = atoms[iAtom].atomPropertyFloat(vwr, tokProperty,
+ pt);
}
}
if (tokProperty == T.color)
@@ -3870,10 +3870,9 @@
if (xyzdata.length != nX || xyzdata[0].length != nY
|| xyzdata[0][0].length != nZ) {
eval.iToken = ptX;
- eval.errorStr(ScriptError.ERROR_what, "xyzdata["
- + xyzdata.length + "][" + xyzdata[0].length + "]["
- + xyzdata[0][0].length + "] is not of size [" + nX + "]["
- + nY + "][" + nZ + "]");
+ eval.errorStr(ScriptError.ERROR_what, "xyzdata[" + xyzdata.length
+ + "][" + xyzdata[0].length + "][" + xyzdata[0][0].length
+ + "] is not of size [" + nX + "][" + nY + "][" + nZ + "]");
}
vxy.addLast(xyzdata); // (5) = float[][][] data
//if (!surfaceObjectSeen)
@@ -4135,18 +4134,22 @@
filename = info[0];
String strCutoff = (!firstPass || !Float.isNaN(cutoff) ? null
: info[1]);
+ String diff = info[2];
if (strCutoff != null && !chk) {
cutoff = Float.NaN;
+ String key = (diff == null ? "MAP_SIGMA_DENS" : "DIFF_SIGMA_DENS");
try {
- String sfdat = vwr.getFileAsString3(strCutoff, false, null);
- Logger.info(sfdat);
- sfdat = PT.split(sfdat, "MAP_SIGMA_DENS")[1];
- cutoff = PT.parseFloat(sfdat);
- showString("using cutoff = " + cutoff);
+ String sfdat = vwr.getFileAsString3(strCutoff, false, null);
+ Logger.info(sfdat);
+ sfdat = PT.split(sfdat, key)[1];
+ cutoff = PT.parseFloat(sfdat);
} catch (Exception e) {
- Logger.error("MAP_SIGMA_DENS -- could not read " + info[1]);
+ Logger.error(key + " -- could not read " + strCutoff);
}
if (cutoff > 0) {
+ if (diff != null && Float.isNaN(sigma))
+ sigma = 3;
+ showString("using cutoff = " + cutoff + (Float.isNaN(sigma) ? ""
: " sigma=" + sigma));
if (!Float.isNaN(sigma)) {
cutoff *= sigma;
sigma = Float.NaN;
@@ -4164,7 +4167,7 @@
if (bs.nextSetBit(0) >= 0) {
getWithinDistanceVector(propertyList, 2.0f, null, bs, false);
sbCommand.append(" within 2.0 ").append(Escape.eBS(bs));
- }
+ }
}
if (firstPass)
defaultMesh = true;
@@ -4281,7 +4284,7 @@
sbCommand.append(" true");
processLattice = true;
i++;
- }
+ }
}
break;
default:
@@ -4419,8 +4422,7 @@
if (doCalcVolume) {
volume = (doCalcVolume ? getShapeProperty(iShape, "volume") : null);
if (volume instanceof Float)
- vwr.setFloatProperty("isosurfaceVolume",
- ((Float) volume).floatValue());
+ vwr.setFloatProperty("isosurfaceVolume", ((Float)
volume).floatValue());
else
vwr.g.setUserVariable("isosurfaceVolume",
SV.getVariableAD((double[]) volume));
@@ -4440,18 +4442,9 @@
s = (String) getShapeProperty(iShape, "ID");
if (s != null && !eval.tQuiet) {
cutoff = ((Float) getShapeProperty(iShape, "cutoff")).floatValue();
- if (Float.isNaN(cutoff) && !Float.isNaN(sigma)) {
+ if (Float.isNaN(cutoff) && !Float.isNaN(sigma))
Logger.error("sigma not supported");
- }
- s += " created";
- if (isIsosurface)
- s += " with cutoff=" + cutoff;
- float[] minMax = (float[]) getShapeProperty(iShape, "minMaxInfo");
- if (minMax[0] != Float.MAX_VALUE)
- s += " min=" + minMax[0] + " max=" + minMax[1];
- s += "; " + JC.shapeClassBases[iShape].toLowerCase() + " count: "
- + getShapeProperty(iShape, "count");
- s += eval.getIsosurfaceDataRange(iShape, "\n");
+ s += " created " + getShapeProperty(iShape, "message");
}
}
String sarea, svol;
Modified: trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2014-11-23
23:25:34 UTC (rev 20122)
+++ trunk/Jmol/src/org/jmol/shapesurface/Isosurface.java 2014-11-25
02:53:08 UTC (rev 20123)
@@ -853,14 +853,26 @@
Object ret = getPropMC(property);
if (ret != null)
return ret;
+ if (property == "message") {
+ String s = "";
+ if (shapeID == JC.SHAPE_ISOSURFACE)
+ s += " with cutoff=" + jvxlData.cutoff;
+ if (jvxlData.dataMin != Float.MAX_VALUE)
+ s += " min=" + jvxlData.dataMin + " max=" + jvxlData.dataMax;
+ s += "; " + JC.shapeClassBases[shapeID].toLowerCase() + " count: "
+ + getPropMC("count");
+ return s + getPropI("dataRangeStr") + jvxlData.msg;
+ }
if (property == "dataRange")
- return (thisMesh == null || jvxlData.jvxlPlane != null
- && thisMesh.colorEncoder == null
- ? null
- : new float[] {
- jvxlData.mappedDataMin, jvxlData.mappedDataMax,
- (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue :
jvxlData.valueMappedToRed),
- (jvxlData.isColorReversed ? jvxlData.valueMappedToRed :
jvxlData.valueMappedToBlue)});
+ return getDataRange();
+ if (property == "dataRangeStr") {
+ float[] dataRange = getDataRange();
+ return (dataRange != null && dataRange[0] != Float.MAX_VALUE
+ && dataRange[0] != dataRange[1] ? "\nisosurface"
+ + " full data range " + dataRange[0] + " to " + dataRange[1]
+ + " with color scheme spanning " + dataRange[2] + " to " +
dataRange[3]
+ : "");
+ }
if (property == "moNumber")
return Integer.valueOf(moNumber);
if (property == "moLinearCombination")
@@ -910,6 +922,17 @@
return null;
}
+ private float[] getDataRange() {
+ return (thisMesh == null || jvxlData.jvxlPlane != null
+ && thisMesh.colorEncoder == null ? null : new float[] {
+ jvxlData.mappedDataMin,
+ jvxlData.mappedDataMax,
+ (jvxlData.isColorReversed ? jvxlData.valueMappedToBlue
+ : jvxlData.valueMappedToRed),
+ (jvxlData.isColorReversed ? jvxlData.valueMappedToRed
+ : jvxlData.valueMappedToBlue) });
+ }
+
private Object calculateVolumeOrArea(boolean isArea) {
if (isArea) {
if (thisMesh.calculatedArea != null)
Modified: trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java
===================================================================
--- trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java 2014-11-23
23:25:34 UTC (rev 20122)
+++ trunk/Jmol/src/org/jmol/shapesurface/MolecularOrbital.java 2014-11-25
02:53:08 UTC (rev 20123)
@@ -320,7 +320,7 @@
if (propertyName.equals("list")) {
String s = (String) getPropI("list");
if (s.length() > 1)
- s += "cutoff = " + getPropI("cutoff") + "\n";
+ s += "cutoff = " + jvxlData.cutoff + "\n";
return vwr.getMoInfo(-1) + "\n" + s;
}
if (propertyName == "moNumber")
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-23 23:25:34 UTC
(rev 20122)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-25 02:53:08 UTC
(rev 20123)
@@ -15,8 +15,12 @@
TODO: design and implement sidechain mutation -- MUTATE command ?
TODO: remove HTML5 dependency on synchronous file loading (check SCRIPT
command for problems)
-Jmol.___JmolVersion="14.3.9_2014.11.23"
+Jmol.___JmolVersion="14.3.9_2014.11.24"
+new feature: isosurface "==1blu" -- difference map; defaults to sigma=3
+
+JmolVersion="14.3.9_2014.11.23"
+
bug fix: isosurface slab plane -xy not recognizing "-"
bug fix: PNGJ writing broken
bug fix: VASP CHGCAR reader not recognized for primitive cell
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-11-23 23:25:34 UTC (rev
20122)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-11-25 02:53:08 UTC (rev
20123)
@@ -4307,9 +4307,15 @@
return (withPrefix ? "MOL3D::" : "")
+ PT.formatStringS(format, "FILE", f);
case '_': // isosurface "=...", but we code that type as '_'
+ String diff = (f.startsWith("=") ? "_diff" : null);
+ if (diff != null)
+ f = f.substring(1);
String server = FileManager.fixFileNameVariables(g.edsUrlFormat, f);
+ if (diff != null)
+ server = PT.rep(server, ".omap", "_diff.omap");
+
String strCutoff = FileManager.fixFileNameVariables(g.edsUrlCutoff, f);
- return new String[] { server, strCutoff };
+ return new String[] { server, strCutoff, diff };
}
return f;
}
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