Revision: 20131
http://sourceforge.net/p/jmol/code/20131
Author: hansonr
Date: 2014-11-25 18:16:57 +0000 (Tue, 25 Nov 2014)
Log Message:
-----------
Jmol.___JmolVersion="14.3.9_2014.11.26"
bug fix: hover OFF disables hover callback, but should not
bug fix: reading of JVXL file saved with noFill still does fill
bug fix: CASTEP DENSITY surface file reader does not do downsampling
new feature: VASP CHGCAR default cutoff set to 0.5
new feature: set edsUrlFormatDiff
-- specifies difference map location
new feature: isosurface "==1blu"
-- difference map fo-fc
-- defaults to sigma=3
-- automatically implements SIGN option
new feature: isosurface RMSD (same as SIGMA)
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/script/T.java
trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/script/T.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/T.java 2014-11-25 17:42:54 UTC (rev
20130)
+++ trunk/Jmol/src/org/jmol/script/T.java 2014-11-25 18:16:57 UTC (rev
20131)
@@ -843,11 +843,12 @@
public final static int defaultvdw = strparam | 35;
public final static int edsurlcutoff = strparam | 36;
public final static int edsurlformat = strparam | 37;
- public final static int energyunits = strparam | 38;
- public final static int filecachedirectory = strparam | 39;
- public final static int forcefield = strparam | 40;
- public final static int helppath = strparam | 41;
- public final static int hoverlabel = strparam | 42;
+ public final static int edsurlformatdiff = strparam | 38;
+ public final static int energyunits = strparam | 39;
+ public final static int filecachedirectory = strparam | 40;
+ public final static int forcefield = strparam | 41;
+ public final static int helppath = strparam | 42;
+ public final static int hoverlabel = strparam | 43;
public final static int language = strparam | 44;
public final static int loadformat = strparam | 45;
public final static int loadligandformat = strparam | 46;
@@ -2341,6 +2342,7 @@
"drawFontSize",
"edsUrlCutoff",
"edsUrlFormat",
+ "edsUrlFormatDiff",
"energyUnits",
"fileCacheDirectory",
"fontsize",
@@ -3361,6 +3363,7 @@
drawfontsize, // "drawFontSize"
edsurlcutoff, // "edsUrlCutoff"
edsurlformat, // "edsUrlFormat"
+ edsurlformatdiff, // "edsUrlFormatDiff"
energyunits, // "energyUnits"
filecachedirectory, // "fileCacheDirectory"
fontsize, // "fontsize"
Modified: trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2014-11-25 17:42:54 UTC
(rev 20130)
+++ trunk/Jmol/src/org/jmol/viewer/GlobalSettings.java 2014-11-25 18:16:57 UTC
(rev 20131)
@@ -271,6 +271,7 @@
setB("drawPicking", drawPicking);
setB("dsspCalculateHydrogenAlways", dsspCalcHydrogen);
setO("edsUrlFormat", edsUrlFormat);
+ setO("edsUrlFormatDiff", edsUrlFormatDiff);
//setParameterValue("edsUrlOptions", edsUrlOptions);
setO("edsUrlCutoff", edsUrlCutoff);
setB("ellipsoidArcs", ellipsoidArcs);
@@ -469,6 +470,7 @@
String loadFormat, loadLigandFormat, nmrUrlFormat, nmrPredictFormat,
smilesUrlFormat, nihResolverFormat, pubChemFormat;
String edsUrlFormat =
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.omap";;
+ String edsUrlFormatDiff =
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE_diff.omap";;
String edsUrlCutoff =
"http://eds.bmc.uu.se/eds/dfs/%LC13/%LCFILE/%LCFILE.sfdat";;
String edsUrlOptions = "within 2.0 {*}";
float minBondDistance = JC.DEFAULT_MIN_BOND_DISTANCE;
@@ -1066,6 +1068,7 @@
app(str, "#set nihResolverFormat " + PT.esc(nihResolverFormat));
app(str, "#set pubChemFormat " + PT.esc(pubChemFormat));
app(str, "#set edsUrlFormat " + PT.esc(edsUrlFormat));
+ app(str, "#set edsUrlFormatDiff " + PT.esc(edsUrlFormatDiff));
app(str, "#set edsUrlCutoff " + PT.esc(edsUrlCutoff));
// if (autoLoadOrientation)
// appendCmd(str, "set autoLoadOrientation true");
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-25 17:42:54 UTC
(rev 20130)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2014-11-25 18:16:57 UTC
(rev 20131)
@@ -18,18 +18,17 @@
Jmol.___JmolVersion="14.3.9_2014.11.26"
bug fix: hover OFF disables hover callback, but should not
-
-new feature: VASP CHGCAR default cutoff set to 0.5
-
-JmolVersion="14.3.9_2014.11.25"
-
bug fix: reading of JVXL file saved with noFill still does fill
bug fix: CASTEP DENSITY surface file reader does not do downsampling
+new feature: VASP CHGCAR default cutoff set to 0.5
+new feature: set edsUrlFormatDiff
+ -- specifies difference map location
+
new feature: isosurface "==1blu"
- -- difference map fo-fc
- -- defaults to sigma=3
- -- automatically implements SIGN option
+ -- difference map fo-fc
+ -- defaults to sigma=3
+ -- automatically implements SIGN option
new feature: isosurface RMSD (same as SIGMA)
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-11-25 17:42:54 UTC (rev
20130)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2014-11-25 18:16:57 UTC (rev
20131)
@@ -4307,24 +4307,16 @@
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)
+ boolean isDiff = f.startsWith("=");
+ if (isDiff)
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, diff };
+ String server = FileManager.fixFileNameVariables(isDiff ?
g.edsUrlFormatDiff : g.edsUrlFormat, f);
+ String strCutoff = (isDiff ? "" :
FileManager.fixFileNameVariables(g.edsUrlCutoff, f));
+ return new String[] { server, strCutoff, isDiff ? "diff" : null };
}
return f;
}
- public String[] getElectronDensityLoadInfo() {
- return new String[] { g.edsUrlFormat, g.edsUrlCutoff,
- g.edsUrlOptions };
- }
-
public String getStandardLabelFormat(int type) {
switch (type) {
default:
@@ -5612,6 +5604,17 @@
private void setStringPropertyTok(String key, int tok, String value) {
switch (tok) {
+ // 14.3.10 (forgot to add these earlier)
+ case T.edsurlcutoff:
+ g.edsUrlCutoff = value;
+ break;
+ case T.edsurlformat:
+ g.edsUrlFormat = value;
+ break;
+ // 14.3.10 new
+ case T.edsurlformatdiff:
+ g.edsUrlFormatDiff = value;
+ break;
// 13.3.6
case T.animationmode:
setAnimationMode(value);
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