Revision: 20681
http://sourceforge.net/p/jmol/code/20681
Author: hansonr
Date: 2015-08-08 17:53:35 +0000 (Sat, 08 Aug 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.2.15_2015.08.08"
new feature: load "test.pdb" from write property atomno temperature now
restores values for atomno and temperature for points on plot
bug fix: "print stateVersion" not reporting as documented.
bug fix: write property atomno temperature "test.pdb" does not preserve long
residue names from CIF files or long atom names from other file types
Modified Paths:
--------------
branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
branches/v14_2/Jmol/src/org/jmol/viewer/GlobalSettings.java
branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
Modified: branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-08-07
18:05:21 UTC (rev 20680)
+++ branches/v14_2/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-08-08
17:53:35 UTC (rev 20681)
@@ -2892,13 +2892,14 @@
eval.iToken = pt0 + 1;
for (int i = 0; i < 3; i++) {
switch (tokAt(eval.iToken)) {
+ case T.nada:
case T.format:
case T.min:
case T.max:
i = 2;
continue;
}
- if (!T.tokAttr(propToks[i] = tokAt(eval.iToken), T.atomproperty))
+ if ((propToks[i] = tokAt(eval.iToken)) != T.property &&
!T.tokAttr(propToks[i], T.atomproperty))
invArg();
props[i] = getToken(eval.iToken).value.toString();
eval.iToken++;
@@ -2985,22 +2986,23 @@
// prepare data for property plotting
float[] dataX = null, dataY = null, dataZ = null;
+ String[] propData = new String[3];
if (tok == T.property) {
dataX = getBitsetPropertyFloat(bs, propToks[0] | T.selectedfloat,
propToks[0] == T.property? props[0] : null, (minXYZ == null ?
Float.NaN : minXYZ.x), (maxXYZ == null ? Float.NaN
: maxXYZ.x));
- props[0] = props[0] + " " + Escape.eAF(dataX);
+ propData[0] = props[0] + " " + Escape.eAF(dataX);
if (props[1] != null) {
dataY = getBitsetPropertyFloat(bs, propToks[1] | T.selectedfloat,
propToks[1] == T.property? props[1] : null, (minXYZ == null ?
Float.NaN : minXYZ.y),
(maxXYZ == null ? Float.NaN : maxXYZ.y));
- props[1] = props[1] + " " + Escape.eAF(dataY);
+ propData[1] = props[1] + " " + Escape.eAF(dataY);
}
if (props[2] != null) {
dataZ = getBitsetPropertyFloat(bs, propToks[2] | T.selectedfloat,
propToks[2] == T.property? props[2] : null, (minXYZ == null ?
Float.NaN : minXYZ.z),
(maxXYZ == null ? Float.NaN : maxXYZ.z));
- props[2] = props[2] + " " + Escape.eAF(dataZ);
+ propData[2] = props[2] + " " + Escape.eAF(dataZ);
}
if (minXYZ == null)
minXYZ = P3.new3(getPlotMinMax(dataX, false, propToks[0]),
@@ -3050,7 +3052,7 @@
dataZ[i] = (dataZ[i] - center.z) / factors.z;
}
parameters = new Object[] { bs, dataX, dataY, dataZ, minXYZ, maxXYZ,
- factors, center, format, props};
+ factors, center, format, propData};
}
// all set...
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-08-07
18:05:21 UTC (rev 20680)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/GlobalSettings.java 2015-08-08
17:53:35 UTC (rev 20681)
@@ -140,7 +140,7 @@
setI("spinFps", TransformManager.DEFAULT_SPIN_FPS);
setF("visualRange", TransformManager.DEFAULT_VISUAL_RANGE);
setI("stereoDegrees", TransformManager.DEFAULT_STEREO_DEGREES);
- setI("stateversion", 0); // only set by a saved state being recalled
+ //setI("stateversion", 0); // only set by a saved state being recalled
setB("syncScript", vwr.sm.syncingScripts);
setB("syncMouse", vwr.sm.syncingMouse);
setB("syncStereo", vwr.sm.stereoSync);
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-07
18:05:21 UTC (rev 20680)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-08
17:53:35 UTC (rev 20681)
@@ -6,11 +6,13 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.2.15_2015.08.07"
+Jmol.___JmolVersion="14.2.15_2015.08.08"
-bug fix: write property atomno temperature "test.pdb" preserves long residue
names from CIF files
-bug fix: load "test.pdb" from write property atomno temperature restores
values for atomno and temperature
+new feature: load "test.pdb" from write property atomno temperature now
restores values for atomno and temperature for points on plot
+bug fix: "print stateVersion" not reporting as documented.
+bug fix: write property atomno temperature "test.pdb" does not preserve long
residue names from CIF files or long atom names from other file types
+
JmolVersion="14.2.15_2015.08.06"
bug fix: stereo setting should not be saved in state.
Modified: branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
2015-08-07 18:05:21 UTC (rev 20680)
+++ branches/v14_2/Jmol/src/org/jmol/viewer/PropertyManager.java
2015-08-08 17:53:35 UTC (rev 20681)
@@ -1837,15 +1837,15 @@
);
else if (isHetero)
tokens = (leftJustify ? LabelToken.compile(vwr,
- "HETATM%5.-5i %-4.4a%1A%3.-3n %1c%4.-4R%1E _XYZ_"
+ "HETATM%5.-5i %-4.4a%1A%3.3n %1c%4.-4R%1E _XYZ_"
+ occTemp, '\0', null) : LabelToken.compile(vwr,
- "HETATM%5.-5i %-3.3a%1A%3.-3n %1c%4.-4R%1E _XYZ_"
+ "HETATM%5.-5i %-3.3a%1A%3.3n %1c%4.-4R%1E _XYZ_"
+ occTemp, '\0', null));
else
tokens = (leftJustify ? LabelToken.compile(vwr,
- "ATOM %5.-5i %-4.4a%1A%3.-3n %1c%4.-4R%1E _XYZ_"
+ "ATOM %5.-5i %-4.4a%1A%3.3n %1c%4.-4R%1E _XYZ_"
+ occTemp, '\0', null) : LabelToken.compile(vwr,
- "ATOM %5.-5i %-3.3a%1A%3.-3n %1c%4.-4R%1E _XYZ_"
+ "ATOM %5.-5i %-3.3a%1A%3.3n %1c%4.-4R%1E _XYZ_"
+ occTemp, '\0', null));
String XX = a.getElementSymbolIso(false).toUpperCase();
XX = pdbKey(a.group.getBioPolymerIndexInModel())
@@ -1960,19 +1960,22 @@
}
}
+//
+// /**
+// * PDB line sorter
+// * @param s1
+// * @param s2
+// * @return -1, 0, or 1
+// */
+// public int compare(String s1, String s2) {
+// int atA = PT.parseInt(s1.substring(10, 16));
+// int atB = PT.parseInt(s2.substring(10, 16));
+// int resA = PT.parseInt(s1.substring(26, 30));
+// int resB = PT.parseInt(s2.substring(26, 30));
+// return (resA < resB ? -1 : resA > resB ? 1 : atA < atB ? -1
+// : atA > atB ? 1 : 0);
+// }
- /**
- * PDB line sorter
- */
- public int compare(String s1, String s2) {
- int atA = PT.parseInt(s1.substring(10, 16));
- int atB = PT.parseInt(s2.substring(10, 16));
- int resA = PT.parseInt(s1.substring(26, 30));
- int resB = PT.parseInt(s2.substring(26, 30));
- return (resA < resB ? -1 : resA > resB ? 1 : atA < atB ? -1
- : atA > atB ? 1 : 0);
- }
-
/* **********************
*
* Jmol Data Frame methods
@@ -2024,12 +2027,27 @@
Atom[] atoms = vwr.ms.at;
if (isPDBFormat) {
out.append("REMARK 6 Jmol PDB-encoded data: ").append(type)
- .append(";\n");
+ .append("; ").append(Viewer.getJmolVersion()).append(";
").append(vwr.apiPlatform.getDateFormat(null)).append("\n");
out.append("REMARK 6 Jmol data").append(" min = ")
.append(Escape.eP(minXYZ)).append(" max = ")
.append(Escape.eP(maxXYZ)).append(" unScaledXyz = xyz * ")
.append(Escape.eP(factors)).append(" + ").append(Escape.eP(center))
.append(";\n");
+ String atomNames = null;
+ for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms
+ .nextSetBit(i + 1)) {
+ String name = "" + atoms[i].getAtomName();
+ if (atomNames != null || name.length() > 4) {
+ if (atomNames == null) {
+ atomNames = "";
+ i = -1;
+ continue;
+ }
+ atomNames += " " + name;
+ }
+ }
+ if (atomNames != null)
+ out.append("REMARK 6 Jmol atom
names").append(atomNames).append("\n");
String resNames = null;
for (int i = bsAtoms.nextSetBit(0); i >= 0; i = bsAtoms
.nextSetBit(i + 1)) {
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