Revision: 21387
http://sourceforge.net/p/jmol/code/21387
Author: hansonr
Date: 2017-02-04 07:26:39 +0000 (Sat, 04 Feb 2017)
Log Message:
-----------
Jmol.___JmolVersion="14.8.2-beta-2017-02-03"
bug fix: NBO plugin fixes
noting undocumented
set fontscaling true; font label 10 arial plain 0.020
- last number is a fontscaling factor that allows one to set a font size for
- labels in angstroms. Roughly, this pointSize * factor is in Angstroms.
Modified Paths:
--------------
trunk/Jmol/src/org/gennbo/NBODialogView.java
trunk/Jmol/src/org/gennbo/NBOService.java
trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: trunk/Jmol/src/org/gennbo/NBODialogView.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBODialogView.java 2017-02-03 23:58:18 UTC
(rev 21386)
+++ trunk/Jmol/src/org/gennbo/NBODialogView.java 2017-02-04 07:26:39 UTC
(rev 21387)
@@ -62,6 +62,8 @@
import javax.swing.JTextField;
import javax.swing.ListCellRenderer;
import javax.swing.ScrollPaneConstants;
+import javax.swing.SwingUtilities;
+import javax.swing.Timer;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
@@ -149,8 +151,6 @@
protected final static int VIEW_STATE_VECTOR = 2;
protected final static int VIEW_STATE_CAMERA = 3;
- public static final int MAX_COLUMNS = 14; // orbitals
-
protected JPanel buildViewPanel() {
startingModelCount = vwr.ms.mc;
panel = new JPanel(new BorderLayout());
@@ -287,9 +287,7 @@
@Override
public void run() {
-
- if (alphaList != null)
- alphaList = betaList = null;
+ alphaList = betaList = null;
setNewBasis();
}
});
@@ -953,7 +951,7 @@
boolean isBeta = isOpenShell && !alphaSpin.isSelected();
DefaultListModel<String> list = (isBeta ? betaList : alphaList);
- if (list != null) {
+ if (list != null && list.size() > 0) {
orbitals.setModelList(list, false);
return;
}
@@ -964,6 +962,7 @@
alphaList = list;
if (!jmolOptionNONBO) {
+ logCmd("select " + comboBasis.getSelectedItem() + " " + (isBeta ?
"beta" : isOpenShell ? "alpha" : ""));
postNBO_v(getMetaHeader(true).append("CMD LABEL"),
NBOService.MODE_VIEW_LIST,
list, "Getting list", null, null);
}
@@ -1211,7 +1210,9 @@
showOrbital(findNextAtomicOrbital(atomno, list));
return;
}
- String[] tok2 = tok[1].split(" ");
+ tok = tok[1].split(" ");
+ String at1 = tok[2];
+ String at2 = tok[5];
switch (comboBasis.getSelectedIndex()) {
case BASIS_AO:
case BASIS_PNAO:
@@ -1220,13 +1221,13 @@
break;
case BASIS_PNHO:
case BASIS_NHO:
- showOrbital(selectOnNHO(tok2[2], tok2[5], list));
+ showOrbital(selectOnNHO(at1 + "(" + at2 + ")", at2 + "(" + at1 + ")",
list));
break;
case BASIS_PNBO:
case BASIS_NBO:
case BASIS_PNLMO:
case BASIS_NLMO:
- showOrbital(selectOnNBO(tok2[2], tok2[5], list));
+ showOrbital(selectOnNHO(at1 + "-" + at2, null, list));
break;
}
}
@@ -1256,38 +1257,47 @@
return curr;
}
- protected int selectOnNBO(String at1, String at2, DefaultListModel<String>
list) {
- String bond = at1 + "-" + at2;
- int curr = -1, size = list.getSize();
- if (currOrb.replace(" ", "").contains(bond))
- curr = list.indexOf(currOrb);
- for (int i = curr + 1; i < size + curr; i++) {
- String str = list.getElementAt(i % size).replace(" ", "");
- if (str.contains(bond)) {
- orbitals.setSelectedIndex(i % size);
- currOrb = list.get(i % size);
- return i % size;
- }
- }
- return curr;
- }
+// protected int selectOnNBO(String at1, String at2, DefaultListModel<String>
list) {
+// String bond = at1 + "-" + at2;
+// int curr = -1, size = list.getSize();
+// if (currOrb.replace(" ", "").contains(bond))
+// curr = list.indexOf(currOrb);
+// for (int i = curr + 1; i < size + curr; i++) {
+// String str = list.getElementAt(i % size).replace(" ", "");
+// if (str.contains(bond)) {
+// orbitals.setSelectedIndex(i % size);
+// currOrb = list.get(i % size);
+// return i % size;
+// }
+// }
+// return curr;
+// }
- protected int selectOnNHO(String at1, String at2, DefaultListModel<String>
list) {
- String bond = at1 + "(" + at2 + ")";
- String bond2 = at2 + "(" + at1 + ")";
+ protected int selectOnNHO(String b1, String b2, DefaultListModel<String>
list) {
int curr = -1, size = list.getSize();
- if (currOrb.replace(" ", "").contains(bond))
+ if (currOrb.replace(" ", "").contains(b1))
curr = list.indexOf(currOrb);
+ int n = orbitals.getVisibleRowCount();
for (int i = curr + 1; i < size + curr; i++) {
String str = list.getElementAt(i % size).replace(" ", "");
- if (str.contains(bond)) {
- orbitals.setSelectedIndex(i % size);
- currOrb = list.get(i % size);
+ if (str.contains(b1) || b2 != null && str.contains(b2)) {
+ final int ipt = i % size;
+ orbitals.setSelectedIndex(ipt);
+ currOrb = list.get(ipt);
+// BH: I cannot get this to work!
+// orbitals.setVisibleRowCount(n);
+// revalidate();
+// repaint();
+// SwingUtilities.invokeLater(new Runnable() {
+//
+// @Override
+// public void run() {
+// orbitals.ensureIndexIsVisible(ipt); // this does not work.
+//
+// }
+//
+// });
return i % size;
- } else if (str.contains(bond2)) {
- orbitals.setSelectedIndex(i % size);
- currOrb = list.get(i % size);
- return i % size;
}
}
return curr;
@@ -1360,16 +1370,18 @@
viewSettingsBox.setVisible(!jmolOptionNONBO);
// set list
-
- if (type.startsWith("P"))
+ DefaultListModel<String> list = (isBeta ? betaList : alphaList);
+ if (jmolOptionNONBO) {
+ if (type.startsWith("P"))
type = type.substring(1);
- if (type.equalsIgnoreCase("NLMO"))
+ if (type.equalsIgnoreCase("NLMO"))
type = "NBO";
- String[] a = ((Map<String, String[]>) moData.get("nboLabelMap"))
- .get((isBeta ? "beta_" : "") + type);
- DefaultListModel<String> list = (isBeta ? betaList : alphaList);
- for (int i = 0; i < a.length; i++)
- list.addElement((i + 1) + ". " + a[i] + " ");
+ String[] a = ((Map<String, String[]>) moData.get("nboLabelMap"))
+ .get((isBeta ? "beta_" : "") + type);
+ list.clear();
+ for (int i = 0; i < a.length; i++)
+ list.addElement((i + 1) + ". " + a[i] + " ");
+ }
orbitals.setModelList(list, true);
} catch (NullPointerException e) {
//not a problem? log(e.getMessage() + " reading file", 'r');
@@ -1422,7 +1434,7 @@
public OrbitalList() {
super();
setLayoutOrientation(JList.VERTICAL_WRAP);
- setVisibleRowCount(jmolOptionNONBO ? 15 : MAX_COLUMNS);
+ setVisibleRowCount(-1); // indicates to automatically calculate max
number of rows
setFont(nboFontLarge);
//setColorScheme();
setFont(listFont);
@@ -1460,6 +1472,7 @@
private JLabel cellLabel;
protected boolean myTurn;
+ private boolean toggled;
protected Component renderCell(int index) {
if (cellLabel == null) {
@@ -1471,10 +1484,13 @@
}
};
+ cellLabel.setFont(listFont);
+ cellLabel.setMinimumSize(new Dimension(180, 20));
+ cellLabel.setPreferredSize(new Dimension(180, 20));
+ cellLabel.setMaximumSize(new Dimension(180, 20));
+ cellLabel.setOpaque(true);
}
- cellLabel.setFont(listFont);
cellLabel.setText(getModel().getElementAt(index));
- cellLabel.setOpaque(true);
myTurn = true;
Color bgcolor = (!bsOn.get(index) ? Color.WHITE
: bsNeg.get(index) ? orbColor2 : orbColor1);
@@ -1531,16 +1547,22 @@
script += updateBitSetFromModel();
else
updateModelFromBitSet();
+ logCmd("select...");
//System.out.println("update " + bsOn + " " + bsKnown + " " + iClicked);
- for (int i = model.getSize(); --i >= 0;) {
+ for (int i = 0, n = model.getSize(); i < n; i++) {
boolean isOn = bsOn.get(i);
if (i == iClicked || isOn && !bsKnown.get(i)
|| isSelectedIndex(i) != isOn) {
String id = "mo" + i;
- if (!isOn || bsKnown.get(i))
- bsOn.setBitTo(i, !isOn);
+ if (!isOn || bsKnown.get(i)) {
+ if (isOn && bsNeg.get(i)) {
+ bsKnown.clear(i);
+ bsNeg.clear(i);
+ }
+ bsOn.setBitTo(i, isOn = !isOn);
+ }
boolean isKnown = bsKnown.get(i);
- if (isKnown && !bsOn.get(i)) {
+ if (!bsOn.get(i)) {
// just turn it off
script += "isosurface mo" + i + " off;";
} else if (isKnown) {
@@ -1552,10 +1574,13 @@
script += getJmolIsosurfaceScript(id, type, i, isBeta,
bsNeg.get(i));
}
}
+ if (bsOn.get(i)) {
+ logCmd("...orbital " + orbitals.getModel().getElementAt(i) +
(bsNeg.get(i) ? " [-]" : ""));
+ }
}
updateModelFromBitSet();
runScriptQueued(script);
- // System.out.println("known" + bsKnown + " on" + bsOn + " neg" +
bsNeg + " " + script);
+ //System.out.println("known" + bsKnown + " on" + bsOn + " neg" + bsNeg +
" " + script);
}
private String updateBitSetFromModel() {
@@ -1611,6 +1636,9 @@
@Override
public void mousePressed(MouseEvent e) {
+ killMouseTimer();
+ mouseTimer = getMouseTimer();
+
// System.out.println("PRESS" + e);
// System.out.println("press " + PT.toJSON(null,
getSelectedIndices()) + e.getClickCount());
}
@@ -1619,22 +1647,50 @@
public void mouseReleased(MouseEvent e) {
// System.out.println("RELEASE" + e);
// System.out.println("release " + PT.toJSON(null,
getSelectedIndices()));
+ boolean toggled = this.toggled;
+ killMouseTimer();
+ int i = getSelectedIndex();
+// if (toggled)
+// this.toggleOrbitalNegation(i);
+ this.toggled = false;
+ updateIsosurfacesInJmol(i);
}
- private long lastTime = 0;
- private int lastPicked = 999;
- private final static long DBLCLICK_THRESHOLD_MS = 300;
+ private void killMouseTimer() {
+ if (mouseTimer != null)
+ mouseTimer.stop();
+ mouseTimer = null;
+ toggled = false;
+ }
+ private final static int DBLCLICK_THRESHOLD_MS = 300;
+
+ private Timer mouseTimer;
+
+
+ private Timer getMouseTimer() {
+ Timer t = new Timer(DBLCLICK_THRESHOLD_MS, new ActionListener() {
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ int i = getSelectedIndex();
+ if (bsOn.get(i)) {
+ toggled = true;
+ toggleOrbitalNegation(i);
+ repaint();
+ }
+
+ }
+ });
+
+ t.setRepeats(false);
+ t.start();
+ System.out.println("timer started");
+ return t;
+
+ }
@Override
public void mouseClicked(MouseEvent e) {
- int i = getSelectedIndex();
- if (e.getClickCount() > 1 || lastPicked == i
- && System.currentTimeMillis() - lastTime < DBLCLICK_THRESHOLD_MS) {
- toggleOrbitalNegation(i);
- }
- updateIsosurfacesInJmol(i);
- lastTime = System.currentTimeMillis();
- lastPicked = i;
}
@Override
@@ -1724,6 +1780,7 @@
for (int i = 0; i < lines.length; i++) {
list.addElement(lines[i]);
}
+ orbitals.setModelList(list, true);
break;
case NBOService.MODE_VIEW_IMAGE:
String fname = inputFileHandler.inputFile.getParent() + "\\"
Modified: trunk/Jmol/src/org/gennbo/NBOService.java
===================================================================
--- trunk/Jmol/src/org/gennbo/NBOService.java 2017-02-03 23:58:18 UTC (rev
21386)
+++ trunk/Jmol/src/org/gennbo/NBOService.java 2017-02-04 07:26:39 UTC (rev
21387)
@@ -367,6 +367,7 @@
// we don't care
}
nboServer = null;
+ currentRequest = null;
}
/**
@@ -509,7 +510,6 @@
currentRequest = null;
clearQueue();
restart();
- setReady(true);
return true;
}
@@ -520,7 +520,6 @@
currentRequest = null;
clearQueue();
restart();
- setReady(true);
return true;
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
2017-02-03 23:58:18 UTC (rev 21386)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/GenNBOReader.java
2017-02-04 07:26:39 UTC (rev 21387)
@@ -123,7 +123,7 @@
isOK = readData31(line1);
}
if (!isOK)
- Logger.error("Unimplemented shell type -- no orbitals avaliable: " +
line);
+ Logger.error("Unimplemented shell type -- no orbitals available: " +
line);
if (isOutputFile)
return;
if (isOK)
@@ -159,18 +159,19 @@
discardLinesUntilContains("BETA");
filterMO();
}
- boolean isMO = !nboType.equals("AO");
+ boolean isAO = nboType.equals("AO");
+ boolean isNBO = !isAO && !nboType.equals("MO");
nOrbitals = orbitals.size();
if (nOrbitals == 0)
return;
line = null;
- if (!isMO)
+ if (!isNBO)
nOrbitals = nOrbitals0 + nAOs;
for (int i = nOrbitals0; i < nOrbitals; i++) {
Map<String, Object> mo = orbitals.get(i);
float[] coefs = new float[nAOs];
mo.put("coefficients", coefs);
- if (isMO) {
+ if (!isAO) {
if (line == null) {
while (rd() != null && Float.isNaN(parseFloatStr(line))) {
filterMO(); //switch a/b
@@ -539,6 +540,14 @@
type = "NBO";
tokens = map.get((betaOnly ? "beta_" : "") + type);
moData.put("nboLabelMap", map);
+ if (tokens == null) {
+ tokens = new String[nAOs];
+ for (int i = 0; i < nAOs; i++)
+ tokens[i] = nboType + (i + 1);
+ map.put(nboType, tokens);
+ if (isOpenShell)
+ map.put("beta_" + nboType, tokens);
+ }
moData.put("nboLabels", tokens);
boolean addBetaSet = (isOpenShell && !betaOnly && !isArchive);
if (addBetaSet)
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-02-03 23:58:18 UTC
(rev 21386)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2017-02-04 07:26:39 UTC
(rev 21387)
@@ -49,8 +49,17 @@
# 10. Run jmol/tools build-release.xml
#
-Jmol.___JmolVersion="14.8.2-beta-2017-02-02"
+Jmol.___JmolVersion="14.8.2-beta-2017-02-03"
+bug fix: NBO plugin fixes
+
+noting undocumented
+
+ set fontscaling true; font label 10 arial plain 0.020
+
+ - last number is a fontscaling factor that allows one to set a font size for
+ - labels in angstroms. Roughly, this pointSize * factor is in Angstroms.
+
bug fix: *.CA should pick up calcium in a PDB file
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