Revision: 18525
http://sourceforge.net/p/jmol/code/18525
Author: hansonr
Date: 2013-08-08 04:26:38 +0000 (Thu, 08 Aug 2013)
Log Message:
-----------
___JmolVersion="13.2.4_dev_2013.08.07"
bug fix: shapeInfo not reporting visibility of isosurface
Modified Paths:
--------------
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
branches/v13_2/Jmol/src/org/jmol/script/ScriptEvaluator.java
branches/v13_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
branches/v13_2/Jmol/src/org/jmol/smiles/SmilesParser.java
branches/v13_2/Jmol/src/org/jmol/util/Parser.java
branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java
Modified:
branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-08-08 03:55:19 UTC (rev 18524)
+++ branches/v13_2/Jmol/src/org/jmol/adapter/readers/xtal/CrystalReader.java
2013-08-08 04:26:38 UTC (rev 18525)
@@ -33,6 +33,7 @@
import org.jmol.util.Logger;
import org.jmol.util.Matrix3f;
import org.jmol.util.P3;
+import org.jmol.util.Parser;
import org.jmol.util.Quaternion;
import org.jmol.util.SB;
import org.jmol.util.Tensor;
@@ -958,7 +959,7 @@
atomSetCollection.setAtomSetModelProperty("Ramanactivity", data[3]);
atomSetCollection.setAtomSetName((isLongMode ? "LO " : "") + data[0] + " "
+ TextFormat.formatDecimal(freq, 2) + " cm-1 ("
- + TextFormat.formatDecimal(Float.parseFloat(data[1]), 0)
+ + TextFormat.formatDecimal(Parser.fVal(data[1]), 0)
+ " km/Mole), " + activity);
}
Modified: branches/v13_2/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-08-08 03:55:19 UTC (rev 18524)
+++ branches/v13_2/Jmol/src/org/jmol/script/ScriptEvaluator.java
2013-08-08 04:26:38 UTC (rev 18525)
@@ -9294,8 +9294,8 @@
htParams.put("unitcell", fparams);
if (iGroup == Integer.MIN_VALUE)
iGroup = -1;
+ i = iToken + 1;
}
- i = iToken + 1;
if (iGroup != Integer.MIN_VALUE)
htParams.put("spaceGroupIndex", Integer.valueOf(iGroup));
}
Modified: branches/v13_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
2013-08-08 03:55:19 UTC (rev 18524)
+++ branches/v13_2/Jmol/src/org/jmol/shapesurface/Isosurface.java
2013-08-08 04:26:38 UTC (rev 18525)
@@ -1536,6 +1536,7 @@
protected void addMeshInfo(IsosurfaceMesh mesh, Map<String, Object> info) {
info.put("ID", (mesh.thisID == null ? "<noid>" : mesh.thisID));
+ info.put("visible", Boolean.valueOf(mesh.visible));
info.put("vertexCount", Integer.valueOf(mesh.vertexCount));
if (mesh.calculatedVolume != null)
info.put("volume", mesh.calculatedVolume);
Modified: branches/v13_2/Jmol/src/org/jmol/smiles/SmilesParser.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/smiles/SmilesParser.java 2013-08-08
03:55:19 UTC (rev 18524)
+++ branches/v13_2/Jmol/src/org/jmol/smiles/SmilesParser.java 2013-08-08
04:26:38 UTC (rev 18525)
@@ -641,9 +641,9 @@
isNot = true;
s = s.substring(1);
}
- float min = (pt + 1 == pt2 ? 0 : Float.parseFloat(s));
+ float min = (pt + 1 == pt2 ? 0 : Parser.fVal(s));
s = strMeasure.substring(pt2 + 1);
- float max = (s.length() == 0 ? Float.MAX_VALUE :
Float.parseFloat(s));
+ float max = (s.length() == 0 ? Float.MAX_VALUE : Parser.fVal(s));
m = new SmilesMeasure(molecule, index, type, min, max, isNot);
molecule.measures.addLast(m);
if (index > 0)
Modified: branches/v13_2/Jmol/src/org/jmol/util/Parser.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/util/Parser.java 2013-08-08 03:55:19 UTC
(rev 18524)
+++ branches/v13_2/Jmol/src/org/jmol/util/Parser.java 2013-08-08 04:26:38 UTC
(rev 18525)
@@ -358,10 +358,23 @@
}
private final static float[] decimalScale = { 0.1f, 0.01f, 0.001f, 0.0001f,
0.00001f,
- 0.000001f, 0.0000001f, 0.00000001f };
+ 0.000001f, 0.0000001f, 0.00000001f,
+ 0.000000001f, 0.0000000001f, 0.00000000001f,
+ 0.000000000001f, 0.000000000001f, 0.000000000001f,
+ };
private final static float[] tensScale = { 10, 100, 1000, 10000, 100000,
1000000 };
+ /**
+ * A float parser that is 30% faster than Float.parseFloat(x) and
+ * also accepts x.yD+-n
+ *
+ * @param str
+ * @param ichMax
+ * @param next pointer; incremented
+ * @param isStrict
+ * @return value or Float.NaN
+ */
private static float parseFloatChecked(String str, int ichMax, int[] next,
boolean isStrict) {
boolean digitSeen = false;
float value = 0;
@@ -376,27 +389,31 @@
negative = true;
}
char ch = 0;
+ int ival = 0;
while (ich < ichMax && (ch = str.charAt(ich)) >= '0' && ch <= '9') {
- value = value * 10 + (ch - '0');
+ ival = (ival << 3) + (ival << 1) + (ch - '0');
++ich;
digitSeen = true;
}
boolean isDecimal = false;
+ int ival2 = 0;
+ int iscale = 0;
if (ch == '.') {
isDecimal = true;
- int iscale = 0;
while (++ich < ichMax && (ch = str.charAt(ich)) >= '0' && ch <= '9') {
- if (iscale < decimalScale.length)
- value += (ch - '0') * decimalScale[iscale];
- ++iscale;
+ if (iscale < decimalScale.length) {
+ ival2 = (ival2 << 3) + (ival2 << 1) + (ch - '0');
+ iscale++;
+ }
digitSeen = true;
}
}
+ value = ival;
+ if (ival2 != 0)
+ value += ival2 * decimalScale[iscale - 1];
boolean isExponent = false;
if (!digitSeen)
value = Float.NaN;
- else if (negative)
- value = -value;
if (ich < ichMax && (ch == 'E' || ch == 'e' || ch == 'D')) {
isExponent = true;
if (++ich >= ichMax)
@@ -408,18 +425,18 @@
int exponent = parseIntChecked(str, ichMax, next);
if (exponent == Integer.MIN_VALUE)
return Float.NaN;
- if (exponent > 0)
- value *= ((exponent < tensScale.length) ? tensScale[exponent - 1]
- : Math.pow(10, exponent));
- else if (exponent < 0)
- value *= ((-exponent < decimalScale.length) ? decimalScale[-exponent -
1]
- : Math.pow(10, exponent));
+ if (exponent > 0 && exponent <= tensScale.length)
+ value *= tensScale[exponent - 1];
+ else if (exponent < 0 && -exponent <= decimalScale.length)
+ value *= decimalScale[-exponent - 1];
+ else if (exponent != 0)
+ value *= Math.pow(10, exponent);
} else {
next[0] = ich; // the exponent code finds its own ichNextParse
}
- if (value == Float.NEGATIVE_INFINITY)
- value = -Float.MAX_VALUE;
- else if (value == Float.POSITIVE_INFINITY)
+ if (negative)
+ value = -value;
+ if (value == Float.POSITIVE_INFINITY)
value= Float.MAX_VALUE;
return (!isStrict
|| (!isExponent || isDecimal) && checkTrailingText(str, next[0],
ichMax)
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-08
03:55:19 UTC (rev 18524)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/Jmol.properties 2013-08-08
04:26:38 UTC (rev 18525)
@@ -9,8 +9,12 @@
# Don't use ___ in your text, as that is the key for stripping out
# the information saved in the JAR version of this file.
-___JmolVersion="13.2.4_dev_2013.07.30"
+___JmolVersion="13.2.4_dev_2013.08.07"
+bug fix: shapeInfo not reporting visibility of isosurface
+code: Even faster float parsing
+bug fix: filter lost after CENTROID or PACKED load option
+bug fix: set rangeSelected not functional
bug fix: minimization can fail after MMFF switches to UFF.
bug fix: CIF reader fix for no element given "phenyl1" in ZjzxlegN.cif
Modified: branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-08 03:55:19 UTC
(rev 18524)
+++ branches/v13_2/Jmol/src/org/jmol/viewer/Viewer.java 2013-08-08 04:26:38 UTC
(rev 18525)
@@ -3473,7 +3473,7 @@
public void setCurrentColorRange(String label) {
float[] data = getDataFloat(label);
BS bs = (data == null ? null : (BS) (dataManager.getData(label))[2]);
- if (bs != null && getBoolean(T.rangeselected))
+ if (bs != null && global.rangeSelected)
bs.and(getSelectionSet(false));
setCurrentColorRangeData(data, bs);
}
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