Revision: 21485
http://sourceforge.net/p/jmol/code/21485
Author: hansonr
Date: 2017-04-06 12:09:34 +0000 (Thu, 06 Apr 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.11.3" // 2017-04-06
bug fix: partial bond order for orders > 3 not working
-- for example: connect {_C} {_C} partial 5.3
bug fix: NBO MODEL loading with no file name goes to wrong directory
bug fix: NBO job names need to be cleaned and set if necessary
bug fix: some sort of bad build for DSSR
Modified Paths:
--------------
trunk/Jmol/src/org/gennbo/NBOFileHandler.java
trunk/Jmol/src/org/gennbo/NBOModel.java
trunk/Jmol/src/org/gennbo/NBORun.java
trunk/Jmol/src/org/jmol/render/SticksRenderer.java
trunk/Jmol/src/org/jmol/script/ScriptParam.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/gennbo/NBOFileHandler.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOFileHandler.java 2017-04-05 17:23:57 UTC
(rev 21484)
+++ trunk/Jmol/src/org/gennbo/NBOFileHandler.java 2017-04-06 12:09:34 UTC
(rev 21485)
@@ -356,6 +356,24 @@
return NBOUtil.newNBOFile(inputFile, filenum);
}
+ /**
+ * Fix a file name to be [A-Z0-9_]+
+ *
+ * @param name the name to fix, or if empty, the input file name truncated
to a maximum of 10 digits
+ * @return fixed name replacing not-allowed characters with '_'
+ */
+ public String fixJobName(String name) {
+ if (name == null || (name = name.trim()).length() == 0)
+ name = jobStem;
+ for (int i = name.length(); --i >= 0;) {
+ char ch = name.charAt(i);
+ if (!Character.isLetterOrDigit(ch) && ch != '_')
+ name = name.substring(0, i) + "_" + name.substring(i + 1);
+ }
+ return name;
+ }
+
+
public String[] update47File(String jobName, String keywords) {
if (!useExt.equals("47"))
return null;
@@ -405,5 +423,4 @@
return true;
}
-
}
Modified: trunk/Jmol/src/org/gennbo/NBOModel.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOModel.java 2017-04-05 17:23:57 UTC (rev
21484)
+++ trunk/Jmol/src/org/gennbo/NBOModel.java 2017-04-06 12:09:34 UTC (rev
21485)
@@ -297,14 +297,25 @@
@Override
protected boolean doFileBrowsePressed() {
String folder = tfDir.getText().trim();
- folder = NBOUtil.getWindowsFullNameFor(folder, tfName.getText(),
tfExt.getText());
+ String name = tfName.getText();
+ if (name.length() == 0)
+ name = "*";
+ String ext = tfExt.getText();
+ if (ext.length() == 0)
+ ext = "*";
+ folder = NBOUtil.getWindowsFullNameFor(folder, name, ext);
JFileChooser myChooser = new JFileChooser();
- if (useExt.contains(";"))
- myChooser.setFileFilter(new FileNameExtensionFilter(useExt, useExt
+ String filter = useExt;
+ if (name.equals("*") && !ext.equals("*"))
+ filter = ext;
+ if (filter.contains(";"))
+ myChooser.setFileFilter(new FileNameExtensionFilter(filter, filter
.split(";")));
else
- myChooser.setFileFilter(new FileNameExtensionFilter(useExt, useExt));
+ myChooser.setFileFilter(new FileNameExtensionFilter(filter, filter));
myChooser.setFileHidingEnabled(true);
+ if (folder.endsWith("/"))
+ folder = folder + "*.*";
if (!folder.equals(""))
myChooser.setSelectedFile(new File(folder));
int button = myChooser.showDialog(this, GT._("Select"));
Modified: trunk/Jmol/src/org/gennbo/NBORun.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBORun.java 2017-04-05 17:23:57 UTC (rev
21484)
+++ trunk/Jmol/src/org/gennbo/NBORun.java 2017-04-06 12:09:34 UTC (rev
21485)
@@ -326,7 +326,8 @@
tfJobName.setText(jobName);
}
}
- String name = tfJobName.getText();
+ String name = tfJobName.getText().trim();
+ name = dialog.inputFileHandler.fixJobName(name);
dialog.inputFileHandler.update47File(name, keywords);
addNBOKeylist();
tfJobName.setText(name);
@@ -694,8 +695,7 @@
// from another module
tfJobName.setText(dialog.inputFileHandler.jobStem);
}
- String jobName = (tfJobName == null ? dialog.inputFileHandler.jobStem
- : tfJobName.getText().trim());
+ String jobName = dialog.inputFileHandler.fixJobName(tfJobName == null ?
null : tfJobName.getText().trim());
// BH Q: Would it be reasonable if the NO option is chosen to put that
other job name in to the jobStem field, and also copy the .47 file to that? Or
use that?
// Or, would it be better to ask this question immediately upon file
loading so that it doesn't come up, and make it so that
Modified: trunk/Jmol/src/org/jmol/render/SticksRenderer.java
===================================================================
--- trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2017-04-05 17:23:57 UTC
(rev 21484)
+++ trunk/Jmol/src/org/jmol/render/SticksRenderer.java 2017-04-06 12:09:34 UTC
(rev 21485)
@@ -308,7 +308,7 @@
drawBond(mask);
bondsPerp = !bondsPerp;
bondOrder = 2;
- drawBond(mask);
+ drawBond(mask >> 2);
bondsPerp = !bondsPerp;
multipleBondSpacing = m;
}
@@ -325,7 +325,7 @@
bondsPerp = !bondsPerp;
bondOrder = 2;
multipleBondSpacing *= 1.5f;
- drawBond(mask);
+ drawBond(mask >> 3);
bondsPerp = !bondsPerp;
multipleBondSpacing = m;
}
@@ -342,7 +342,7 @@
bondsPerp = !bondsPerp;
bondOrder = 2;
multipleBondSpacing *= 1.5f;
- drawBond(mask);
+ drawBond(mask >> 4);
bondsPerp = !bondsPerp;
multipleBondSpacing = m;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptParam.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptParam.java 2017-04-05 17:23:57 UTC
(rev 21484)
+++ trunk/Jmol/src/org/jmol/script/ScriptParam.java 2017-04-06 12:09:34 UTC
(rev 21485)
@@ -982,7 +982,7 @@
}
/**
- * reads standard n.m float-as-integer n*1000000 + m and returns (n % 6) << 5
+ * reads standard n.m float-as-integer n*1000000 + m and returns (n % 7) << 5
* + (m % 0x1F)
*
* @param bondOrderInteger
@@ -989,7 +989,7 @@
* @return Bond order partial mask
*/
public static int getPartialBondOrderFromFloatEncodedInt(int
bondOrderInteger) {
- return (((bondOrderInteger / 1000000) % 6) << 5)
+ return (((bondOrderInteger / 1000000) % 7) << 5)
+ ((bondOrderInteger % 1000000) & 0x1F);
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-05 17:23:57 UTC
(rev 21484)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-04-06 12:09:34 UTC
(rev 21485)
@@ -49,8 +49,12 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.11.3" // 2017-04-05
+Jmol.___JmolVersion="14.11.3" // 2017-04-06
+bug fix: partial bond order for orders > 3 not working
+ -- for example: connect {_C} {_C} partial 5.3
+bug fix: NBO MODEL loading with no file name goes to wrong directory
+bug fix: NBO job names need to be cleaned and set if necessary
bug fix: some sort of bad build for DSSR
JmolVersion="14.11.2" // 2017-04-04
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