Revision: 21492
http://sourceforge.net/p/jmol/code/21492
Author: hansonr
Date: 2017-04-07 21:57:13 +0000 (Fri, 07 Apr 2017)
Log Message:
-----------
Modified Paths:
--------------
trunk/Jmol/src/org/gennbo/NBODialog.java
trunk/Jmol/src/org/gennbo/NBOModel.java
Modified: trunk/Jmol/src/org/gennbo/NBODialog.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialog.java 2017-04-07 02:55:42 UTC (rev
21491)
+++ trunk/Jmol/src/org/gennbo/NBODialog.java 2017-04-07 21:57:13 UTC (rev
21492)
@@ -1109,6 +1109,8 @@
}
protected void runScriptQueued(String script) {
+ if (script.indexOf("easure") >= 0)
+ System.out.println("TESTING NBOD");
logInfo("_$ " + PT.rep(script, "\n", "<br>"), Logger.LEVEL_DEBUG);
vwr.script(script);
}
Modified: trunk/Jmol/src/org/gennbo/NBOModel.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOModel.java 2017-04-07 02:55:42 UTC (rev
21491)
+++ trunk/Jmol/src/org/gennbo/NBOModel.java 2017-04-07 21:57:13 UTC (rev
21492)
@@ -85,6 +85,7 @@
private static final int MODEL_ACTION_REBOND = 9;
private static final int MODEL_ACTION_SYMMETRY = 10;
+ private final static int MODEL_ACTION_HBOND = 11;
static final int MODE_MODEL_EDIT = 21;
static final int MODE_MODEL_NEW = 31;
@@ -98,7 +99,7 @@
final static String[] MODEL_ACTIONS = {
"Alter", "Clip", "Fuse", "Link", "Mutate",
"Switch", "Twist", "Value", "3chb", "Rebond",
- "Symmetry?" };
+ "Symmetry?", "H-Bonds" };
private static final String[] EDIT_INFO = {
"Edit nuclear charge, bond length, bond angle, or dihedral angle",
@@ -111,7 +112,8 @@
"Value of nuclear charge, bond length, bond angle, and dihedral angle",
"Create 3-center linkage between two atoms and a ligand",
"Change bonding symmetry around transition metal",
- "Display point-group symmetry of current model"
+ "Display point-group symmetry of current model",
+ "Show NBOPro6-derived hydrogen bonds"
};
private final static int BOX_COUNT_4 = 4, BOX_COUNT_2 = 2, BOX_COUNT_1 = 1;
@@ -164,6 +166,8 @@
* Set to true each time a non-value option action is processed.
*/
private boolean resetOnAtomClick;
+ private Box innerLinkOptionBox;
+ private JRadioButton radLinkBond;
protected void setModelNotFromNBO() {
notFromNBO = true;
@@ -172,6 +176,7 @@
private void showComponents(boolean tf) {
editHeader.setVisible(tf);
editComponent.setVisible(tf);
+ innerLinkOptionBox.setVisible(false);
saveHeader.setVisible(tf);
saveComponent.setVisible(tf);
}
@@ -381,6 +386,7 @@
createInnerEditBox();
rightBox.add(this.innerEditBox);
Box lowBox = Box.createHorizontalBox();
+
JButton sym = new JButton(MODEL_ACTIONS[MODEL_ACTION_SYMMETRY]);
sym.setToolTipText(EDIT_INFO[MODEL_ACTION_SYMMETRY]);
sym.addActionListener(new ActionListener() {
@@ -401,6 +407,18 @@
}
});
lowBox.add(rebond);
+
+ JButton hbond = new JButton(MODEL_ACTIONS[MODEL_ACTION_HBOND]);
+ hbond.setToolTipText(EDIT_INFO[MODEL_ACTION_HBOND]);
+ hbond.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ doGetHBonds();
+ }
+ });
+ lowBox.add(hbond);
+
+
rightBox.add(lowBox);
editBox.add(rightBox);
@@ -513,7 +531,17 @@
});
innerEditBox.add(editValueTf).setVisible(false);
+ innerLinkOptionBox = Box.createHorizontalBox();
+ radLinkBond = new JRadioButton("Bond");
+ JRadioButton radLinkDotted = new JRadioButton("Dotted");
+ innerLinkOptionBox.add(radLinkBond);
+ innerLinkOptionBox.add(radLinkDotted);
+ ButtonGroup g = new ButtonGroup();
+ g.add(radLinkBond);
+ g.add(radLinkDotted);
+ innerEditBox.add(innerLinkOptionBox).setVisible(false);
+
Box lowBox = Box.createHorizontalBox();
jbClear = new JButton("Clear Selected");
jbClear.addActionListener(new ActionListener() {
@@ -535,6 +563,13 @@
}
+ protected void doLinkDotted() {
+ String atomList = modelEditGetSelected();
+ String[] atoms = PT.getTokens(atomList);
+ if (atoms.length == 2)
+ processHBonds("1 " + atomList);
+ }
+
protected void doAtomNumBoxFocus(boolean isGained, int num) {
if (!isGained) {
int atnum = PT.parseInt(atomNumBoxes[num].getText());
@@ -624,6 +659,9 @@
if (actionID == MODEL_ACTION_ALTER || actionID == MODEL_ACTION_TWIST &&
cnt == 4) {
postActionToNBO(MODEL_ACTION_VALUE);
}
+ if (actionID == MODEL_ACTION_LINK) {
+ script = "";
+ }
dialog.runScriptQueued(script);
editValueTf.setText("");
editValueTf.setEnabled(selected.length() > 0);
@@ -806,9 +844,11 @@
boxCount = BOX_COUNT_1;
setEditBox(null);
break;
+ case MODEL_ACTION_LINK:
+ innerLinkOptionBox.setVisible(true);
+ //$FALL-THROUGH$
case MODEL_ACTION_CLIP:
case MODEL_ACTION_FUSE:
- case MODEL_ACTION_LINK:
case MODEL_ACTION_SWITCH:
case MODEL_ACTION_3CHB:
boxCount = BOX_COUNT_2;
@@ -891,7 +931,6 @@
*
*/
protected void clearSelected(boolean andShow) {
- System.out.println("clearing all boxes");
for (int i = 0; i < boxCount; i++) {
atomNumBoxes[i].setText("");
}
@@ -916,6 +955,10 @@
*
*/
protected void postActionToNBO(int actionID) {
+ if (actionID == MODEL_ACTION_LINK && !radLinkBond.isSelected()) {
+ doLinkDotted();
+ return;
+ }
SB sb = new SB();
String selected = modelEditGetSelected();
String cmd = MODEL_ACTIONS[actionID].toLowerCase() + " " + selected + " ";
@@ -934,14 +977,15 @@
}
if (actionID == MODEL_ACTION_REBOND) {
currentRebondSymOp = jcSymOps.getSelectedIndex();
- cmd += jcSymOps.getSelectedItem().toString();
}
-// dialog.runScriptNow("save orientation o2");
+
+ // dialog.runScriptNow("save orientation o2");
NBOUtil.postAddCmd(sb, cmd);
dialog.logCmd(cmd);
jbApply.setEnabled(false);
resetOnAtomClick = (actionID != MODEL_ACTION_VALUE);
- postNBO(sb, actionID, (actionID == MODEL_ACTION_VALUE ? "Checking value":
"Editing model"), null, null);
+ postNBO(sb, actionID, (actionID == MODEL_ACTION_VALUE ? "Checking value"
+ : "Editing model"), null, null);
}
/**
@@ -954,6 +998,15 @@
}
/**
+ * Post a request for a point group symmetry check.
+ */
+ protected void doGetHBonds() {
+ String cmd = "hbond";
+ dialog.logCmd(cmd);
+ postNBO(NBOUtil.postAddCmd(new SB(), cmd), MODEL_ACTION_HBOND, "Getting
Hydrogen Bonds", null, null);
+ }
+
+ /**
* clipped in?
*
* @param textBox
@@ -967,6 +1020,10 @@
saveFileHandler.setInput(null, "", "");
clearSelected(false);
if (textBox == jtNIHInput) {
+ if (model.startsWith("!")) {
+ dialog.runScriptQueued(model.substring(1));
+ return;
+ }
dialog.modelOrigin = NBODialog.ORIGIN_NIH;
notFromNBO = true;
if ("$:=".indexOf(model.charAt(0)) < 0)
@@ -1220,7 +1277,7 @@
.length() > 4);
if (actionID == MODEL_ACTION_MUTATE) {
doModelAction(actionID);
- } else if (actionID == MODEL_ACTION_REBOND && serverMode !=
MODEL_ACTION_SYMMETRY)
+ } // else if (actionID == MODEL_ACTION_REBOND && serverMode !=
MODEL_ACTION_SYMMETRY)
//doGetSymmetry();
if (showSelectedOnFileLoad) {
updateSelected(false);
@@ -1319,6 +1376,12 @@
dialog.logValue(sval);
setCurrentValue(sval);
break;
+ case MODEL_ACTION_HBOND:
+ dialog.logValue("testing HBOND: " + s);
+ if (s.length() < 3)
+ s = "1\n1\n4";
+ processHBonds(s);
+ break;
case MODEL_ACTION_SYMMETRY:
// do not reorient the return in this case
String symmetry = s.substring(0, s.indexOf("\n"));
@@ -1333,4 +1396,22 @@
}
}
+ /**
+ * first number is number of bonds
+ *
+ * @param s
+ */
+ private void processHBonds(String s) {
+ float[] atomList = PT.parseFloatArray(s);
+ if (atomList.length == 0 || atomList[0] == 0)
+ return;
+ String script = "";
+ for (int i = atomList.length%2; i < atomList.length;) {
+ script += "measure ID m" + ("" + Math.random()).substring(2) + " @"
+ + (int) atomList[i++] + " @" + (int) atomList[i++]
+ + " radius 0.1 ' '";
+ }
+ dialog.runScriptQueued(script);
+ }
+
}
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