Revision: 18459
http://sourceforge.net/p/jmol/code/18459
Author: hansonr
Date: 2013-07-18 16:08:53 +0000 (Thu, 18 Jul 2013)
Log Message:
-----------
NMRCalculation should clear shift references whenever a new file is loaded.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java
trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-07-18 12:19:02 UTC
(rev 18458)
+++ trunk/Jmol/src/org/jmol/api/JmolNMRInterface.java 2013-07-18 16:08:53 UTC
(rev 18459)
@@ -7,6 +7,7 @@
import org.jmol.modelset.ModelSet;
import org.jmol.util.BS;
import org.jmol.util.JmolList;
+import org.jmol.util.SB;
import org.jmol.util.Tensor;
import org.jmol.util.V3;
import org.jmol.viewer.Viewer;
@@ -86,5 +87,7 @@
public JmolList<Object> getTensorInfo(String tensorType, String infoType, BS
bs);
public Map<String, Float> getMinDistances(MeasurementData md);
+
+ public boolean getState(SB sb);
}
Modified: trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java
===================================================================
--- trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-07-18 12:19:02 UTC
(rev 18458)
+++ trunk/Jmol/src/org/jmol/quantum/NMRCalculation.java 2013-07-18 16:08:53 UTC
(rev 18459)
@@ -41,6 +41,7 @@
import org.jmol.util.JmolList;
import org.jmol.util.Logger;
import org.jmol.util.Parser;
+import org.jmol.util.SB;
import org.jmol.util.Tensor;
import org.jmol.util.V3;
import org.jmol.viewer.Viewer;
@@ -347,7 +348,19 @@
private Map<String, Float> shiftRefsPPM = new Hashtable<String, Float>();
+ public boolean getState(SB sb) {
+ if (shiftRefsPPM.isEmpty())
+ return false;
+ for (Entry<String, Float> nuc : shiftRefsPPM.entrySet())
+ sb.append(" set shift_").append(nuc.getKey()).append("
").appendO(nuc.getValue()).append("\n");
+ return true;
+ }
+
public boolean setChemicalShiftReference(String element, float value) {
+ if (element == null) {
+ shiftRefsPPM.clear();
+ return false;
+ }
element = element.substring(0, 1).toUpperCase() + element.substring(1);
shiftRefsPPM.put(element, Float.valueOf(value));
return true;
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-18 12:19:02 UTC
(rev 18458)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-07-18 16:08:53 UTC
(rev 18459)
@@ -95,8 +95,6 @@
new feature: CASTEP reader filter option q=all
new feature: set picking DRAGLIGAND
-- won't move the protein
-new feature: isosurface SLAB TRANSLUCENT 0.x color
- -- inherits color of isosurface when color parameter is absent
new feature: CIF reader upgrade to allow multicharacter chain specs.
-- See 1bgl_1bgm.cif
-- automatically switches to chainCaseSensitive if multi-character
@@ -107,6 +105,9 @@
select chain="0123" OK
select :"0123" OK
select :"A*" or :"A'" or :'A"' or :"A\""
+
+---TODO DOCUMENTED BACK TO THIS POINT---
+
new feature: {atomset1}.distance.min({atomset2})
-- returns an array
-- minimum distance of each atom in atomset1 to any atom in atomset2
@@ -163,9 +164,9 @@
-- zoomHeight TRUE
-- measurementUnits ANGSTROMS
-new feature: color BALLS
- -- distinct from color ATOMS because it doesn't get inherited
- -- for PyMOL compatability with sphere_color
+ new feature: color BALLS
+ -- distinct from color ATOMS because it doesn't get inherited
+ -- for PyMOL compatability with sphere_color
new feature: restore SCENE "xxxx" nSec
@@ -812,7 +813,8 @@
-- load =1vif.cif filter "ASSEMBLY 1;!$C" # just label_asym_id values not C
new feature: LOAD "xxx.cif" APPEND "appendedData" @x
-- specifically for CIF files, reads a CIF file, appending string in variable
- -- feature particularly for PDB (John Westbrook), so, for example:
+ -- intentionally not documented.
+ -- feature particularly for RCSB (John Westbrook), so, for example:
Var x = load("test.txt")
load "1vif-early.cif" append "appendedData" @x FILTER "assembly
1;$A"
@@ -835,7 +837,8 @@
#
new feature: LOAD "xxx.cif" APPEND DATA "appendedData" .... end "appendedData"
- -- specifically for CIF files, reads a CIF file, appending string in lines
of script
+ -- specifically for CIF files, reads a CIF file, appending string in lines
of script
+ -- intentionally not documented
-- most important for saving the state:
load "1vif-early.cif" append data "appendedData"
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-18 12:19:02 UTC (rev
18458)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2013-07-18 16:08:53 UTC (rev
18459)
@@ -2784,6 +2784,9 @@
modelManager.zap();
if (scriptManager != null)
scriptManager.clear(false);
+ if (nmrCalculation != null)
+ getNMRCalculation().setChemicalShiftReference(null, 0);
+
if (haveDisplay) {
mouse.clear();
clearTimeouts();
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