Revision: 20241
http://sourceforge.net/p/jmol/code/20241
Author: hansonr
Date: 2015-01-24 23:03:41 +0000 (Sat, 24 Jan 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.12_2015.01.24"
new feature: load NBO CH3CH2CH3
-- retrieves the stucture of propane (in this case) from a local NBO server.
-- including inorganics. For example:
load nbo "Cr 3::acac"
load nbo "Cr 2:::Bz"
code: new interface for "services" that can provide valuable information to
Jmol
over ports or by running executable processes.
-- currently just NBO
bug fix: MOPAC reader loses two atoms in IRC calculation for MOPAC 2012
bug fix: _slabPlane and _depthPlane not set immediately when slab and depth are
set
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/simple/MopacReader.java
trunk/Jmol/src/org/jmol/c/CBK.java
trunk/Jmol/src/org/jmol/console/GenericConsole.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptEval.java
trunk/Jmol/src/org/jmol/util/GenericApplet.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StatusManager.java
trunk/Jmol/src/org/jmol/viewer/TransformManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/molecularplayground/MPJmolApp.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/NBODialog.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
Added Paths:
-----------
trunk/Jmol/src/org/openscience/jmol/app/nbo/
trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/simple/MopacReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/simple/MopacReader.java
2015-01-23 04:14:38 UTC (rev 20240)
+++ trunk/Jmol/src/org/jmol/adapter/readers/simple/MopacReader.java
2015-01-24 23:03:41 UTC (rev 20241)
@@ -165,7 +165,6 @@
* @throws Exception
*/
void processCoordinates() throws Exception {
- readLines(3);
if (!chargesFound) {
asc.newAtomSet();
baseAtomIndex = asc.ac;
@@ -174,7 +173,10 @@
}
Atom[] atoms = asc.atoms;
int atomNumber;
- while (rd() != null) {
+ while (rd().trim().length() == 0 || line.indexOf("ATOM") >= 0) {
+ // skip header lines
+ }
+ while (line != null) {
String[] tokens = getTokens();
if (tokens.length == 0
|| (atomNumber = parseIntStr(tokens[0])) == Integer.MIN_VALUE)
@@ -189,6 +191,7 @@
if (atno != Integer.MIN_VALUE)
elementSymbol = getElementSymbol(atno);
atom.elementSymbol = elementSymbol;
+ rd();
}
}
/**
Modified: trunk/Jmol/src/org/jmol/c/CBK.java
===================================================================
--- trunk/Jmol/src/org/jmol/c/CBK.java 2015-01-23 04:14:38 UTC (rev 20240)
+++ trunk/Jmol/src/org/jmol/c/CBK.java 2015-01-24 23:03:41 UTC (rev 20241)
@@ -42,6 +42,7 @@
MEASURE,
MESSAGE,
MINIMIZATION,
+ SERVICE,
PICK,
RESIZE,
SCRIPT,
Modified: trunk/Jmol/src/org/jmol/console/GenericConsole.java
===================================================================
--- trunk/Jmol/src/org/jmol/console/GenericConsole.java 2015-01-23 04:14:38 UTC
(rev 20240)
+++ trunk/Jmol/src/org/jmol/console/GenericConsole.java 2015-01-24 23:03:41 UTC
(rev 20241)
@@ -302,6 +302,7 @@
case HOVER:
case LOADSTRUCT:
case MINIMIZATION:
+ case SERVICE:
case RESIZE:
case SCRIPT:
case SYNC:
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-01-23 04:14:38 UTC
(rev 20240)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2015-01-24 23:03:41 UTC
(rev 20241)
@@ -1079,6 +1079,7 @@
case T.orientation:
case T.append:
case T.history:
+ case T.nbo:
if (nTokens != 1)
return ERROR;
//$FALL-THROUGH$
Modified: trunk/Jmol/src/org/jmol/script/ScriptEval.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-23 04:14:38 UTC
(rev 20240)
+++ trunk/Jmol/src/org/jmol/script/ScriptEval.java 2015-01-24 23:03:41 UTC
(rev 20241)
@@ -4110,17 +4110,32 @@
// load OCCUPANCY
// load PARTIALCHARGE
// load HISTORY
+ // load NBO
switch (tok) {
+ case T.nbo:
+ case T.history:
case T.menu:
String m = paramAsStr(checkLast(2));
- if (!chk)
- vwr.setMenu(m, true);
+ if (!chk) {
+ switch (tok) {
+ case T.nbo:
+ htParams.put("service", "nbo");
+ htParams.put("mode", Integer.valueOf(1)); // MODEL
+ htParams.put("action", "load");
+ htParams.put("value", m);
+ htParams.put("sync", Boolean.TRUE);
+ vwr.sm.processService(htParams);
+ vwr.loadInline((String) htParams.get("ret"));
+ break;
+ case T.history:
+ vwr.setHistory(m);
+ break;
+ case T.menu:
+ vwr.setMenu(m, true);
+ break;
+ }
+ }
return;
- case T.history:
- String h = paramAsStr(checkLast(2));
- if (!chk)
- vwr.setHistory(h);
- return;
case T.data:
isData = true;
loadScript.append(" /*data*/ data");
Modified: trunk/Jmol/src/org/jmol/util/GenericApplet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/GenericApplet.java 2015-01-23 04:14:38 UTC
(rev 20240)
+++ trunk/Jmol/src/org/jmol/util/GenericApplet.java 2015-01-24 23:03:41 UTC
(rev 20241)
@@ -563,6 +563,8 @@
@Override
public boolean notifyEnabled(CBK type) {
switch (type) {
+ case SERVICE:
+ return false;
case ECHO:
case MESSAGE:
case MEASURE:
@@ -608,6 +610,7 @@
case EVAL:
case HOVER:
case MINIMIZATION:
+ case SERVICE:
case RESIZE:
case DRAGDROP:
// just send it
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-23 04:14:38 UTC
(rev 20240)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-01-24 23:03:41 UTC
(rev 20241)
@@ -17,8 +17,26 @@
TODO: add 2D graphics panel for Ramachandran and NBO-style 2D graphics -- send
to browser as data uri?
-Jmol.___JmolVersion="14.3.12_2015.01.22"
+Jmol.___JmolVersion="14.3.12_2015.01.24"
+new feature: load NBO CH3CH2CH3
+ -- retrieves the stucture of propane (in this case) from a local NBO server.
+ -- including inorganics. For example:
+
+ load nbo "Cr 3::acac"
+ load nbo "Cr 2:::Bz"
+
+code: new interface for "services" that can provide valuable information to
Jmol
+ over ports or by running executable processes.
+ -- currently just NBO
+
+
+bug fix: MOPAC reader loses two atoms in IRC calculation for MOPAC 2012
+bug fix: _slabPlane and _depthPlane not set immediately when slab and depth
are set
+
+JmolVersion="14.3.12_2015.01.22"
+released simultaneously with 14.2.12
+
bug fix: color rockets amino fails
bug fix: "color TRANSLUCENT -1" (screened translucency) restored;
-- had been removed in 14.3.12_2015.01.20 because broken in
jmol-11.7.27_02-27-09
Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2015-01-23 04:14:38 UTC
(rev 20240)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2015-01-24 23:03:41 UTC
(rev 20241)
@@ -613,6 +613,12 @@
new Object[] { null, Integer.valueOf(mode),
Integer.valueOf(atomIndex), Integer.valueOf(modelIndex), msg });
}
+ public void processService(Map<String, Object> info) {
+ if (notifyEnabled(CBK.SERVICE))
+ cbl.notifyCallback(CBK.SERVICE,
+ new Object[] { null, info });
+ }
+
public int getSyncMode() {
return (!isSynced ? SYNC_OFF : drivingSync ? SYNC_DRIVER : SYNC_SLAVE);
}
Modified: trunk/Jmol/src/org/jmol/viewer/TransformManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-01-23
04:14:38 UTC (rev 20240)
+++ trunk/Jmol/src/org/jmol/viewer/TransformManager.java 2015-01-24
23:03:41 UTC (rev 20241)
@@ -871,6 +871,7 @@
slabPlane = null;
setSlabEnabled(false);
setZShadeEnabled(false);
+ slabDepthChanged();
}
public int getSlabPercentSetting() {
@@ -888,6 +889,7 @@
private void slabDepthChanged() {
vwr.g.setI("slab", slabPercentSetting);
vwr.g.setI("depth", depthPercentSetting);
+ finalizeTransformParameters(); // also sets _slabPlane and _depthPlane
}
void depthByPercentagePoints(int percentage) {
@@ -944,6 +946,7 @@
slabPlane = plane;
slabPercentSetting = 100;
}
+ slabDepthChanged();
}
/**
@@ -952,7 +955,6 @@
* @param isDepth
*/
public void setSlabDepthInternal(boolean isDepth) {
- finalizeTransformParameters();
if (isDepth)
depthPlane = null;
else
@@ -960,7 +962,7 @@
slabInternal(getSlabDepthPlane(isDepth), isDepth);
}
- P4 getSlabDepthPlane(boolean isDepth) {
+ private P4 getSlabDepthPlane(boolean isDepth) {
// the third row of the matrix defines the Z coordinate, which is all we
need
// and, in fact, it defines the plane. How convenient!
// eval "slab set"
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-23 04:14:38 UTC (rev
20240)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-01-24 23:03:41 UTC (rev
20241)
@@ -9172,4 +9172,5 @@
if (jmolpopup != null)
jmolpopup.jpiUpdateComputedMenus();
}
+
}
Modified: trunk/Jmol/src/org/molecularplayground/MPJmolApp.java
===================================================================
--- trunk/Jmol/src/org/molecularplayground/MPJmolApp.java 2015-01-23
04:14:38 UTC (rev 20240)
+++ trunk/Jmol/src/org/molecularplayground/MPJmolApp.java 2015-01-24
23:03:41 UTC (rev 20241)
@@ -267,12 +267,13 @@
case LOADSTRUCT:
case MEASURE:
case MINIMIZATION:
+ case SERVICE:
case PICK:
case RESIZE:
case SYNC:
case STRUCTUREMODIFIED:
case DRAGDROP:
- break;
+ return false;
}
return false;
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2015-01-23 04:14:38 UTC (rev 20240)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
2015-01-24 23:03:41 UTC (rev 20241)
@@ -38,6 +38,7 @@
import org.openscience.jmol.app.jsonkiosk.JsonNioClient;
import org.openscience.jmol.app.jsonkiosk.JsonNioServer;
import org.openscience.jmol.app.jsonkiosk.KioskFrame;
+import org.openscience.jmol.app.nbo.NBOService;
import org.openscience.jmol.app.surfacetool.SurfaceTool;
import org.jmol.script.T;
import org.jmol.util.Logger;
@@ -105,7 +106,7 @@
public class JmolPanel extends JPanel implements SplashInterface,
JsonNioClient {
- static HistoryFile historyFile;
+ public static HistoryFile historyFile;
public Viewer vwr;
@@ -114,6 +115,7 @@
StatusBar status;
int startupWidth, startupHeight;
JsonNioServer serverService;
+ public NBOService nboService;
protected String appletContext;
protected PropertyChangeSupport pcs = new PropertyChangeSupport(this);
@@ -1108,8 +1110,9 @@
@Override
public void actionPerformed(ActionEvent e) {
+ getNBOService();
if (nboDialog == null)
- nboDialog = new NBODialog(frame, vwr);
+ nboDialog = new NBODialog(frame, vwr, nboService);
else
nboDialog.setVisible(true);
}
@@ -1773,4 +1776,9 @@
vwr.syncScript(script, "~", 0);
}
+ public NBOService getNBOService() {
+ return (nboService == null ? (nboService = new NBOService(vwr))
+ : nboService);
+ }
+
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/NBODialog.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/NBODialog.java
2015-01-23 04:14:38 UTC (rev 20240)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/NBODialog.java
2015-01-24 23:03:41 UTC (rev 20241)
@@ -25,8 +25,7 @@
import org.jmol.viewer.Viewer;
import org.jmol.i18n.GT;
-import org.jmol.util.Logger;
-import org.openscience.jmol.app.jmolpanel.JmolPanel;
+import org.openscience.jmol.app.nbo.NBOService;
import java.awt.BorderLayout;
import java.awt.Component;
@@ -54,12 +53,15 @@
import javax.swing.event.ChangeListener;
import java.io.File;
-
+import java.util.Hashtable;
+import java.util.Map;
/**
* A dialog for interacting with NBO-Server (experimental)
*/
public class NBODialog extends JDialog implements ChangeListener {
+ private static final int MODEL = 1;
+
private transient Viewer vwr;
protected JButton nboPathButton;
@@ -72,11 +74,11 @@
private JTextField workingPathLabel;
- private JTextPane editArea1;
+ private JTextPane jmol_molfile;
private JScrollPane editPane1;
- private JTextPane editArea2;
+ private JTextPane nboOutput;
private JScrollPane editPane2;
@@ -88,45 +90,50 @@
private JTextField modelField;
-
+ private NBOService nboService;
+
/**
- * Creates a dialog for getting info related to output frames in
- * nbo format.
- * @param f The frame assosiated with the dialog
- * @param vwr The interacting display we are reproducing (source of view
angle info etc)
+ * Creates a dialog for getting info related to output frames in nbo format.
+ *
+ * @param f
+ * The frame assosiated with the dialog
+ * @param vwr
+ * The interacting display we are reproducing (source of view angle
+ * info etc)
+ * @param nboService
*/
- public NBODialog(JFrame f, Viewer vwr) {
+ public NBODialog(JFrame f, Viewer vwr, NBOService nboService) {
super(f, GT._("NBO-Server Interface Setup"), false);
this.vwr = vwr;
-
-
-
+ this.nboService = nboService;
+ nboService.nboDialog = this;
JPanel container = new JPanel();
- container.setPreferredSize(new Dimension(700,500));
- container.setLayout(new BoxLayout(container,BoxLayout.Y_AXIS));
- JPanel leftPanel = buildLeftPanel();
+ container.setPreferredSize(new Dimension(700, 500));
+ container.setLayout(new BoxLayout(container, BoxLayout.Y_AXIS));
+ JPanel leftPanel = buildLeftPanel();
JPanel rightPanel = buildRightPanel();
JSplitPane splitPane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,
leftPanel, rightPanel);
- splitPane.setOneTouchExpandable(true);
+ splitPane.setOneTouchExpandable(true);
JPanel splitPanel = new JPanel(new BorderLayout());
splitPanel.add(splitPane, BorderLayout.CENTER);
container.add(splitPanel);
JPanel filePanel = buildFilePanel();
JPanel buttonPanel = buildButtonPanel();
-
+
JPanel gluePanel = new JPanel(new BorderLayout());
gluePanel.add(Box.createGlue(), BorderLayout.NORTH);
gluePanel.add(filePanel, BorderLayout.SOUTH);
container.add(gluePanel);
container.add(buttonPanel);
- getContentPane().add(container);
-
- getPathHistory();
+ getContentPane().add(container);
+
pack();
centerDialog();
+ getPathHistory();
+ loadArea1();
setVisible(true);
splitPane.setDividerLocation(0.5);
}
@@ -139,15 +146,24 @@
//GUI for panel with go, cancel and stop (etc) buttons
Box buttonBox = Box.createHorizontalBox();
buttonBox.add(Box.createGlue());
- JButton closeButton = new JButton("Close");
- closeButton.addActionListener(new ActionListener() {
+
+ JButton b = new JButton("Connect");
+ b.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ connectPressed();
+ }
+ });
+ buttonBox.add(b);
+ b = new JButton("Close");
+ b.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
closePressed();
}
});
- buttonBox.add(closeButton);
+ buttonBox.add(b);
buttonPanel.add(buttonBox);
return buttonPanel;
}
@@ -195,32 +211,36 @@
return filePanel;
}
+ private JPanel buildLeftPanel() {
+
+ JPanel showPanel = new JPanel(new BorderLayout());
+ inputTabs = new JTabbedPane();
+ inputTabs.addTab("Model", null, modelPanel = getModelPanel());
+ inputTabs.addTab("Run", null, runPanel = getRunPanel());
+ inputTabs.setSelectedComponent(modelPanel);
+ inputTabs.addChangeListener(this);
+ showPanel.add(inputTabs, BorderLayout.CENTER);
+ return showPanel;
+ }
+
private JPanel buildRightPanel() {
JPanel editPanel = new JPanel();
editPanel.setLayout(new BoxLayout(editPanel, BoxLayout.Y_AXIS));
TitledBorder editTitle =
- BorderFactory.createTitledBorder("NBO Working File (temp)");
+ BorderFactory.createTitledBorder("NBO Output");
editPanel.setBorder(editTitle);
- editArea1 = new JTextPane();
- editArea1.setContentType("text/plain");
- editArea1.setFont(new Font("Monospaced", Font.PLAIN, 10));
- editPane1 = new JScrollPane(editArea1);
+ jmol_molfile = new JTextPane();
+ jmol_molfile.setContentType("text/plain");
+ jmol_molfile.setFont(new Font("Monospaced", Font.PLAIN, 10));
+ editPane1 = new JScrollPane(jmol_molfile);
editPanel.add(editPane1);
- JButton goButton = new JButton("Execute");
- goButton.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- executeRaw();
- }
- });
- editPanel.add(goButton);
- editArea2 = new JTextPane();
- editArea2.setContentType("text/plain");
- editArea2.setFont(new Font("Monospaced", Font.PLAIN, 10));
- editPane2 = new JScrollPane(editArea2);
+ nboOutput = new JTextPane();
+ nboOutput.setContentType("text/plain");
+ nboOutput.setFont(new Font("Monospaced", Font.PLAIN, 10));
+ editPane2 = new JScrollPane(nboOutput);
//editPane2.setPreferredSize(new Dimension(500,100));
editPanel.add(editPane2);
@@ -228,23 +248,6 @@
return editPanel;
}
- protected void executeRaw() {
- goPressed("raw");
-
- }
-
- private JPanel buildLeftPanel() {
-
- JPanel showPanel = new JPanel(new BorderLayout());
- inputTabs = new JTabbedPane();
- inputTabs.addTab("Model", null, modelPanel = getModelPanel());
- inputTabs.addTab("Run", null, runPanel = getRunPanel());
- inputTabs.setSelectedComponent(modelPanel);
- inputTabs.addChangeListener(this);
- showPanel.add(inputTabs, BorderLayout.CENTER);
- return showPanel;
- }
-
@Override
public void stateChanged(ChangeEvent event) {
if (event.getSource() == inputTabs) {
@@ -283,35 +286,26 @@
}
private Component getModelPanel() {
+ modelField = new JTextField("sh CH4");
+ modelField.setPreferredSize(new Dimension(100, 10));
+ modelField.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ modelCmd();
+ }}
+ );
JPanel showPanel = new JPanel(new BorderLayout());
Box a = Box.createVerticalBox();
Box b = Box.createHorizontalBox();
- b.add(newLabel("Formula"));
- b.add(modelField = new JTextField("CH4"));
+ b.add(newLabel("Model Command"));
+ b.add(modelField);
a.add(b);
a.add(Box.createVerticalGlue());
- b = Box.createHorizontalBox();
- b.add(Box.createHorizontalGlue());
- JButton goButton = new JButton("Load");
- goButton.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- loadModel();
- }
- });
- b.add(goButton);
- a.add(b);
-
showPanel.add(a, BorderLayout.NORTH);
//showPanel.add(Box.createGlue(), BorderLayout.CENTER);
return showPanel;
}
- protected void loadModel() {
- goPressed("model");
- vwr.loadInline(editArea2.getText());
- }
-
private Component newLabel(String label) {
JTextField t = new JTextField(label);
t.setEditable(false);
@@ -319,46 +313,52 @@
return t;
}
- private String lastText;
-
- void goPressed(String type) {
+ /////////////////////////////////////////////////////////
- String filename = "jmol_infile.txt";
- String workingPath = workingPathLabel.getText();
- File toNBOFile = new File(workingPath, filename);
- String s;
- if (type.equals("model")) {
- editArea1.setText(" 1 1 1\nsh " + modelField.getText());
- } else if (type.equals("raw")) {
+ public void nboReport(String s) {
+ nboOutput.setText(s == null ? "" : nboOutput.getText() + s + "\n");
+ }
+ protected void modelCmd() {
+ Map<String, Object> info = new Hashtable<String, Object>();
+ info.put("mode", Integer.valueOf(NBOService.MODEL));
+ info.put("sync", Boolean.FALSE);
+ String cmd = modelField.getText();
+ if (cmd.startsWith("sh ")) {
+ info.put("action", "load");
+ info.put("value", cmd.substring(3));
+ } else {
+ info.put("action", "run");
+ String fname = nboService.workingPath + File.separator + "jmol.orc";
+ String orcData = vwr.getData("*", "orc");
+ orcData = "%coords\ncoords" + orcData.substring(orcData.indexOf("\n\n")
+ 1) + "end\nend\n";
+ vwr.writeTextFile(fname, orcData);
+ cmd = "xxxuse.orc " + fname + "\n" + cmd;
}
- try {
- s = editArea1.getText();
- if (!s.equals(lastText)) {
- vwr.writeTextFile(toNBOFile.getAbsolutePath(), lastText = s);
- }
-
- String server = serverPathLabel.getText();
- File pathToExecutable = new File(server);
- ProcessBuilder builder = new ProcessBuilder(server);
- builder.directory(new File(pathToExecutable.getParent())); // this is
where you set the root folder for the executable to run with
- builder.redirectErrorStream(true);
- Process proc = builder.start();
- //Process proc = Runtime.getRuntime().exec(commandLineArgs);
- proc.waitFor();
- processResult();
- } catch (Exception e) {
- Logger.errorEx("Caught IOException in NBO-Server exec", e);
+ info.put("value", cmd.substring(3));
+ if (!nboService.processRequest(info)) {
+ clearInfo();
+ nboReport("You must connect first.");
}
- //saveHistory();
- //dispose();
- }
+ }
+
+ protected void connectPressed() {
+ nboService.closeProcess();
+ clearInfo();
+ String err = nboService.startProcess(true); // synchronous?
+ if (err == null) {
+ nboReport("listening...");
+ } else {
+ nboReport(err);
+ }
+ }
/**
* Responds to cancel being press- or equivalent eg window closed.
*/
void closePressed() {
- saveHistory();
+ nboService.closeProcess();
+ nboService.saveHistory();
setVisible(false);
dispose();
}
@@ -380,15 +380,17 @@
int button = myChooser.showDialog(this, GT._("Select"));
if (button == JFileChooser.APPROVE_OPTION) {
File newFile = myChooser.getSelectedFile();
- String savePath;
+ String path;
if (newFile.isDirectory()) {
- savePath = newFile.toString();
+ path = newFile.toString();
} else {
- savePath = newFile.getParent();
+ path = newFile.getParent();
}
- workingPathLabel.setText(savePath);
+ workingPathLabel.setText(path);
loadArea1();
pack();
+ nboService.workingPath = path;
+ nboService.saveHistory();
}
}
@@ -403,19 +405,15 @@
int button = myChooser.showDialog(this, GT._("Select"));
if (button == JFileChooser.APPROVE_OPTION) {
File newFile = myChooser.getSelectedFile();
- serverPathLabel.setText(newFile.toString());
+ String path = newFile.toString();
+ serverPathLabel.setText(path);
pack();
+ nboService.serverPath = path;
+ nboService.saveHistory();
}
}
/**
- * Save INI file
- *
- * @return INI data
- */
-
-
- /**
* Centers the dialog on the screen.
*/
protected void centerDialog() {
@@ -435,65 +433,23 @@
* Just recovers the path settings from last session.
*/
private void getPathHistory() {
-
- java.util.Properties props = JmolPanel.historyFile.getProperties();
- if (serverPathLabel != null) {
- String nboPath = props.getProperty("nboServerPath",
- System.getProperty("user.home"));
- if (nboPath != null) {
- serverPathLabel.setText(nboPath);
- }
- }
- if (workingPathLabel != null) {
- String savePath = props.getProperty("nboWorkingPath",
- System.getProperty("user.home"));
- if (savePath != null) {
- workingPathLabel.setText(savePath);
- loadArea1();
- }
- }
+ serverPathLabel.setText(nboService.serverPath);
+ workingPathLabel.setText(nboService.workingPath);
}
- /**
- * Just saves the path settings from this session.
- */
- private void saveHistory() {
- java.util.Properties props = new java.util.Properties();
- props.setProperty("nboServerPath", serverPathLabel.getText());
- props.setProperty("nboWorkingPath", workingPathLabel.getText());
- JmolPanel.historyFile.addProperties(props);
+ void clearInfo() {
+ jmol_molfile.setText("");
+ nboOutput.setText("");
}
-
- String doubleQuoteIfContainsSpace(String str) {
- for (int i = str.length(); --i >= 0; )
- if (str.charAt(i) == ' ')
- return "\"" + str + "\"";
- return str;
- }
-
- String simpleQuoteIfContainsSpace(String str) {
- for (int i = str.length(); --i >= 0; )
- if (str.charAt(i) == ' ')
- return "\'" + str + "\'";
- return str;
- }
-
void loadArea1() {
String s = vwr.getFileAsString3(workingPathLabel.getText().replace('\\',
'/') + "/jmol_infile.txt", true, "nbodialog");
- editArea1.setText(s);
- lastText = s;
- editArea2.setText("");
+ jmol_molfile.setText(s);
+ nboOutput.setText("");
}
- void processResult() {
- loadArea1();
- loadArea2("jmol_molfile.txt");
+ public void setModel(String s) {
+ jmol_molfile.setText(s);
}
- private void loadArea2(String fname) {
- String s = vwr.getFileAsString3(workingPathLabel.getText().replace('\\',
'/') + "/" + fname, true, "nbodialog");
- editArea2.setText(s);
- }
-
-
+
}
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2015-01-23 04:14:38 UTC (rev 20240)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/StatusListener.java
2015-01-24 23:03:41 UTC (rev 20241)
@@ -96,6 +96,7 @@
case STRUCTUREMODIFIED:
case MEASURE:
case MESSAGE:
+ case SERVICE:
case PICK:
case SCRIPT:
case SYNC:
@@ -115,16 +116,18 @@
return false;
}
+ @SuppressWarnings("unchecked")
@Override
public void notifyCallback(CBK type, Object[] data) {
String strInfo = (data == null || data[1] == null ? null : data[1]
.toString());
+ Map<String, Object> info;
switch (type) {
case LOADSTRUCT:
notifyFileLoaded(strInfo, (String) data[2], (String) data[3],
(String) data[4], (Boolean) data[8]);
if (jmol.gaussianDialog != null)
- jmol.gaussianDialog.updateModel(-2);
+ jmol.gaussianDialog.updateModel(-2);
return;
case ANIMFRAME:
int[] iData = (int[]) data[1];
@@ -138,8 +141,8 @@
display.status.setStatus(1, menuName);
if (jmol.frame != null)
jmol.frame.setTitle(menuName);
-// if (jSpecViewFrame != null)
-// setJSpecView("", true);
+ // if (jSpecViewFrame != null)
+ // setJSpecView("", true);
}
return;
case SCRIPT:
@@ -164,17 +167,19 @@
break;
case MESSAGE:
break;
- // case CLICK:
- // x, y, action, int[] {action}
- // the fourth parameter allows an application to change the action
- // if (display.haveDisplay)
- // display.status
- // .setStatus(1, "(" + data[1] + "," + data[2] + ")");
- // break;
+ case SERVICE:
+ if (display == null)
+ return;
+ info = (Map<String, Object>) data[1];
+ String service = (String) info.get("service");
+ if ("nbo".equals(service)) {
+ display.jmolPanel.getNBOService().processRequest(info);
+ }
+ return;
case PICK:
notifyAtomPicked(strInfo);
if (jmol.gaussianDialog != null)
- jmol.gaussianDialog.updateModel(((Integer) data[2]).intValue());
+ jmol.gaussianDialog.updateModel(((Integer) data[2]).intValue());
break;
case STRUCTUREMODIFIED:
// 0 DONE; 1 in process
@@ -183,7 +188,7 @@
int modelIndexx = ((Integer) data[3]).intValue();
notifyStructureModified(atomIndex, modelIndexx, mode);
if (jmol.gaussianDialog != null)
- jmol.gaussianDialog.updateModel(-1);
+ jmol.gaussianDialog.updateModel(-1);
break;
case SYNC:
if (strInfo != null && strInfo.toLowerCase().startsWith("jspecview")) {
@@ -207,8 +212,8 @@
// cases that fail to return are sent to the console for processing
if (jmol.service != null)
jmol.service.scriptCallback(strInfo);
- JmolCallbackListener appConsole = (JmolCallbackListener) vwr
- .getProperty("DATA_API", "getAppConsole", null);
+ JmolCallbackListener appConsole = (JmolCallbackListener) vwr.getProperty(
+ "DATA_API", "getAppConsole", null);
if (appConsole != null)
appConsole.notifyCallback(type, data);
}
Added: trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
(rev 0)
+++ trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java 2015-01-24
23:03:41 UTC (rev 20241)
@@ -0,0 +1,275 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2014-12-13 22:43:17 -0600 (Sat, 13 Dec 2014) $
+ * $Revision: 20162 $
+ *
+ * Copyright (C) 2002-2005 The Jmol Development Team
+ *
+ * Contact: jmol-develop...@lists.sf.net
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.jmol.app.nbo;
+
+import org.jmol.viewer.Viewer;
+import org.openscience.jmol.app.jmolpanel.JmolPanel;
+import org.openscience.jmol.app.jmolpanel.NBODialog;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.PrintWriter;
+import java.util.Map;
+import java.util.Scanner;
+
+import javajs.util.SB;
+
+/**
+ * A service for interacting with NBOServe (experimental)
+ *
+ * TODO: figure out how to manage time-consuming asynchronous requests
+ *
+ */
+public class NBOService {
+
+ public static final int MODEL = 1; // do not change - referred to as "1" in
org.jmol.script.ScriptEval.cmdLoad
+
+ private transient Viewer vwr;
+
+ public NBODialog nboDialog;
+
+ private Process nboServer;
+ private Thread nboListener;
+ private InputStream stdout;
+ public Scanner nboScanner;
+ public BufferedReader nboReader;
+ private int nboMode;
+ private PrintWriter stdinWriter;
+
+ private SB sbRet;
+
+ private String nboAction;
+
+ /**
+ * Manage communication between Jmol and NBOServer
+ *
+ * @param vwr The interacting display we are reproducing (source of view
angle info etc)
+ */
+ public NBOService(Viewer vwr) {
+ this.vwr = vwr;
+ java.util.Properties props = JmolPanel.historyFile.getProperties();
+ serverPath = props.getProperty("nboServerPath",
+ System.getProperty("user.home"));
+ workingPath = props.getProperty("nboWorkingPath",
+ System.getProperty("user.home"));
+ }
+
+ public boolean processRequest(Map<String, Object> info) {
+ boolean ok = false;
+ boolean sync = (info.get("sync") == Boolean.TRUE);
+ sbRet = (sync ? new SB() : null);
+ closeProcess();
+ startProcess(sync);
+ nboMode = ((Integer) info.get("mode")).intValue();
+ if (stdinWriter == null) {
+ closeProcess();
+ sbRet.append("ERROR: Could not connect to NBOServe -- Use Tools...NBO...
to set up NBOServe");
+ nboMode = 0;
+ }
+ nboAction = (String) info.get("action");
+ switch (nboMode) {
+ case MODEL:
+ String s = (String) info.get("value");
+ if (nboAction.equals("load")) {
+ s = "sh " + s;
+ } else if (nboAction.equals("run")) {
+ // ok as is
+ } else {
+ s = null;
+ }
+ if (s != null) {
+ sendToNBO(MODEL, s, sync);
+ if (sync) {
+ try {
+ nboServer.waitFor();
+ } catch (InterruptedException e) {
+ return false;
+ }
+ sbRet.append(getModel());
+ }
+ ok = true;
+ }
+ break;
+ default:
+ if (sync)
+ sbRet.append("unknown mode");
+ break;
+ }
+ if (sync) {
+ info.put("ret", sbRet.toString());
+ }
+ return ok;
+ }
+
+ /**
+ * temporary kludge to force exit
+ *
+ * @param mode
+ * @param s
+ * @param sync
+ */
+ private void sendToNBO(int mode, String s, boolean sync) {
+ stdinWriter.println(mode + "\n" + s + "\n" + (true || sync ?
"exit\nexit\n" : ""));
+ stdinWriter.flush();
+ }
+
+ public void nboReport(String nextLine) {
+ System.out.println(nextLine);
+ if (sbRet != null)
+ sbRet.append(nextLine + "\n");
+ try {
+ if (nboDialog != null)
+ nboDialog.nboReport(nextLine);
+ } catch (Throwable t) {
+ // ignore
+ }
+ }
+
+ public String serverPath;
+ public String workingPath;
+
+ public String startProcess(boolean sync) {
+ try {
+ File pathToExecutable = new File(serverPath);
+ ProcessBuilder builder = new ProcessBuilder(serverPath);
+ builder.directory(new File(pathToExecutable.getParent())); // this is
where you set the root folder for the executable to run with
+ builder.redirectErrorStream(true);
+ nboServer = builder.start();
+ stdout = nboServer.getInputStream();
+ nboReader = new BufferedReader(new InputStreamReader(stdout));
+ nboListener = null;
+ if (!sync) {
+ nboListener = new Thread(new Runnable() {
+ @Override
+ public void run() {
+ while (true) {
+ String line;
+ try {
+ while ((line = nboReader.readLine()) != null) {
+ nboReport(line);
+ }
+ asyncCallback();
+ } catch (Exception e1) {
+ }
+ break;
+ }
+ }
+ });
+ nboListener.start();
+ }
+ stdinWriter = new PrintWriter(nboServer.getOutputStream());
+ } catch (IOException e) {
+ System.out.println(e.getMessage());
+ return e.getMessage();
+ }
+ return null;
+ }
+
+ public void closeProcess() {
+// try {
+// stdout.close();
+// } catch (Exception e) {
+// }
+ stdout = null;
+ try {
+ stdinWriter.close();
+ } catch (Exception e) {
+ }
+ stdinWriter = null;
+ try {
+ nboScanner.close();
+ } catch (Exception e) {
+ }
+ nboScanner = null;
+ try {
+ nboReader.close();
+ } catch (Exception e) {
+ }
+ nboReader = null;
+ try {
+ nboListener.interrupt();
+ } catch (Exception e) {
+ }
+ nboListener = null;
+ try {
+ nboServer.destroy();
+ } catch (Exception e) {
+ }
+ nboServer = null;
+ }
+
+
+ /**
+ * process report from NBO -- asynchronous only
+ */
+ public void asyncCallback() {
+ switch (nboMode) {
+ case MODEL:
+ if (nboAction.equals("load")) {
+ String s = getModel();
+ nboDialog.setModel(s);
+ vwr.loadInline(s);
+ } else {
+ nboDialog.nboReport(null);
+ nboDialog.nboReport(getOutput());
+ }
+ }
+ }
+
+ /**
+ * temporary only
+ *
+ * @return model data
+ */
+ private String getModel() {
+ return getNBOFile("jmol_molfile.txt");
+ }
+
+ /**
+ * temporary only
+ *
+ * @return output data
+ */
+ private String getOutput() {
+ return getNBOFile("jmol_outfile.txt");
+ }
+
+ private String getNBOFile(String fname) {
+ return vwr.getFileAsString3(workingPath.replace('\\', '/') + "/" + fname,
true, "nbodialog");
+ }
+
+ /**
+ * Just saves the path settings from this session.
+ */
+ public void saveHistory() {
+ java.util.Properties props = new java.util.Properties();
+ props.setProperty("nboServerPath", serverPath);
+ props.setProperty("nboWorkingPath", workingPath);
+ JmolPanel.historyFile.addProperties(props);
+ }
+
+}
Property changes on: trunk/Jmol/src/org/openscience/jmol/app/nbo/NBOService.java
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+text/plain
\ No newline at end of property
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