def saveFavorite(self):
     """
     Writes the current favorite (selected in the combobox) to a file, any 
     where in the disk that 
     can be given to another NE1 user (i.e. as an email attachment).
     """
     
     cmd = greenmsg("Save Favorite File: ")
     env.history.message(greenmsg("Save Favorite File:"))
     current_favorite = self.favoritesComboBox.currentText()
     favfilepath = getFavoritePathFromBasename(current_favorite)
     
     formats = \
                 "Favorite (*.txt);;"\
                 "All Files (*.*)"
      
     
     fn = QFileDialog.getSaveFileName(
         self, 
         "Save Favorite As", # caption
         favfilepath, #where to save
         formats, # file format options
         QString("Favorite (*.txt)") # selectedFilter
         )
     if not fn:
         env.history.message(cmd + "Cancelled")
     
     else:
         saveFavoriteFile(str(fn), favfilepath)
     return

    def viewParallelTo(self):
        """
        Set view parallel to the vector defined by 2 selected atoms.
        """
        cmd = greenmsg("Set View Parallel To: ")

        atoms = self.assy.selatoms_list()

        if len(atoms) != 2:
            msg = redmsg("You must select 2 atoms.")
            env.history.message(cmd + msg)
            return

        v = norm(atoms[0].posn()-atoms[1].posn())

        if vlen(v) < 0.0001: # Atoms are on top of each other.
            info = 'The selected atoms are on top of each other.  No change in view.'
            env.history.message(cmd + info)
            return

        # If vec is pointing into the screen, negate (reverse) vec.
        if dot(v, self.glpane.lineOfSight) > 0:
            v = -v

        # Compute the destination quat (q2).
        q2 = Q(V(0,0,1), v)
        q2 = q2.conj()

        self.glpane.rotateView(q2)

        info = 'View set parallel to the vector defined by the 2 selected atoms.'
        env.history.message(cmd + info)

 def __init__(self, win):
     """
     @param win: the main window object
     """
     self.win = win
     self.pw = None # pw = part window. Its subclasses will create their
         # partwindow objects (and destroy them after Done)
         ###REVIEW: I think this (assignment or use of self.pw) does not
         # belong in this class [bruce 070615 comment]
         
     self.struct = None
     self.previousParams = None
     #bruce 060616 added the following kluge to make sure both cmdname and
     # cmd are set properly.
     if not self.cmdname and not self.cmd:
         self.cmdname = "Generate something"
     if self.cmd and not self.cmdname:
         # deprecated but common, as of 060616
         self.cmdname = self.cmd # fallback value; usually reassigned below
         try:
             cmdname = self.cmd.split('>')[1]
             cmdname = cmdname.split('<')[0]
             cmdname = cmdname.split(':')[0]
             self.cmdname = cmdname
         except:
             if debug_flags.atom_debug:
                 print "fyi: %r guessed wrong about format of self.cmd == %r" \
                       % (self, self.cmd,)
             pass
     elif self.cmdname and not self.cmd:
         # this is intended to be the usual situation, but isn't yet, as of
         # 060616
         self.cmd = greenmsg(self.cmdname + ": ")
     self.change_random_seed()
     return

    def makeAnchor(self):
        """
        Anchors the selected atoms so that they will not move
        during a minimization or simulation run.
        """
        cmd = greenmsg("Anchor: ")

        atoms = self.assy.selatoms_list()

        if not atoms:
            msg = "You must select at least one atom to create an Anchor."
            env.history.message(cmd + redmsg(msg))
            return

        # Print warning if over 200 atoms are selected.
        if atom_limit_exceeded_and_confirmed(self.assy.w,
                                             len(atoms),
                                             limit=200):
            return

        m = Anchor(self.assy, atoms)
        self.unpickall_in_GLPane()
        self.place_new_jig(m)

        env.history.message(cmd + "Anchor created")
        self.assy.w.win_update()

    def makeGridPlane(self):
        cmd = greenmsg("Grid Plane: ")

        atoms = self.assy.selatoms_list()

        if not atoms:
            msg = "You must select 3 or more atoms to create a Grid Plane."
            env.history.message(cmd + redmsg(msg))
            return

        # Make sure only one atom is selected.
        if len(atoms) < 3:
            msg = "To create a Grid Plane, at least 3 atoms must be selected."
            env.history.message(cmd + redmsg(msg))
            return

        from model.jigs_planes import GridPlane
        m = GridPlane(self.assy, atoms)
        m.edit()
        if m.cancelled: # User hit 'Cancel' button in the jig dialog.
            env.history.message(cmd + "Cancelled")
            return

        self.unpickall_in_GLPane()
        self.place_new_jig(m)

        #After placing the jig, remove the atom list from the jig.
        m.atoms = []

        env.history.message(cmd + "Grid Plane created")
        self.assy.w.win_update()
        return

    def unselectConnected(self, atomlist=None):
        """
        Unselect any atom that can be reached from any currently
        selected atom through a sequence of bonds.
        If <atomlist> is supplied, use it instead of the currently selected atoms.
        """
        cmd = greenmsg("Unselect Connected: ")

        if atomlist is None and not self.selatoms:
            msg = redmsg("No atoms selected")
            env.history.message(cmd + msg)
            return

        if atomlist is None: # test for None since atomlist can be an empty list.
            atomlist = self.selatoms.values()

        catoms = self.getConnectedAtoms(atomlist)
        if not len(catoms): return

        natoms = 0
        for atom in catoms[:]:
            if atom.picked:
                atom.unpick()
                if not atom.picked:
                    # Just in case a selection filter was applied to this atom.
                    natoms += 1

        from platform_dependent.PlatformDependent import fix_plurals
        info = fix_plurals( "%d atom(s) unselected." % natoms)
        env.history.message( cmd + info)
        self.o.gl_update()

    def dispShowInvisAtoms(self):
        """
        Resets the display setting for each invisible atom in the selected
        chunks or atoms to Default display mode.
        """

        cmd = greenmsg("Show Invisible Atoms: ")

        if not self.assy.selmols and not self.assy.selatoms:
            msg = "No atoms or chunks selected."
            env.history.message(cmd + msg)
            return

        nia = 0 # nia = Number of Invisible Atoms

        if self.assy.selmols:
            nia = self.assy.showInvisibleAtoms()

        if self.assy.selectionContainsInvisibleAtoms():
            for a in self.assy.selatoms.itervalues(): #bruce 060707 itervalues
                if a.display == diINVISIBLE: 
                    a.setDisplay(diDEFAULT)
                    nia += 1

        msg = cmd + str(nia) + " invisible atoms found."
        env.history.message(msg)

    def selectDoubly(self):
        """
        Select any atom that can be reached from any currently
        selected atom through two or more non-overlapping sequences of
        bonds. Also select atoms that are connected to this group by
        one bond and have no other bonds.
        """
        ###@@@ same comment about interspace bonds as in selectConnected

        cmd = greenmsg("Select Doubly: ")

        if not self.selatoms:
            msg = redmsg("No atoms selected")
            env.history.message(cmd + msg)
            return

        alreadySelected = len(self.selatoms.values())
        from operations.op_select_doubly import select_doubly # new code, bruce 050520
        #e could also reload it now to speed devel!
        select_doubly(self.selatoms.values()) #e optim
        totalSelected = len(self.selatoms.values())

        from platform_dependent.PlatformDependent import fix_plurals
        info = fix_plurals("%d new atom(s) selected (besides the %d initially selected)." % \
                               (totalSelected - alreadySelected, alreadySelected) )
        env.history.message( cmd + info)

        if totalSelected > alreadySelected:
            ## otherwise, means nothing new selected. Am I right? ---Huaicai, not analyze the markdouble() algorithm yet
            #self.w.win_update()
            self.o.gl_update()
        return

    def makeESPImage(self):
        cmd = greenmsg("ESP Image: ")

        atoms = self.assy.selatoms_list()

        if len(atoms) < 3:
            msg = "You must select at least 3 atoms to create an ESP Image."
            env.history.message(cmd + redmsg(msg))
            return

        from analysis.ESP.ESPImage import ESPImage
        m = ESPImage(self.assy, atoms)
        m.edit()
        if m.cancelled: # User hit 'Cancel' button in the jig dialog.
            env.history.message(cmd + "Cancelled")
            return

        self.unpickall_in_GLPane()
        self.place_new_jig(m)

        # After placing the jig, remove the atom list from the jig.
        m.atoms = []

        env.history.message(cmd + "ESP Image created.")
        self.assy.w.win_update()
        return

 def calculate_energy(self):
     """
     Calculate energy.
     """
     
     cmd = greenmsg("Calculate Energy: ")
     
     errmsgs = ["GAMESS job aborted.",
                         "Error: GAMESS job failed."]
                         
     pset = self.pset
     runtyp = pset.ui.runtyp # Save runtyp (Calculate) setting to restore it later.
     pset.ui.runtyp = 0 # Energy calculation
     origCalType = self.gmsjob.Calculation
     self.gmsjob.Calculation = 'Energy'
     
     self.update_gamess_parms()
     
     # Run GAMESS job.  Return value r:
     # 0 = success
     # 1 = job aborted
     # 2 = job failed.
     r = self.gmsjob.launch()
     
     pset.ui.runtyp = runtyp # Restore to original value
     self.gmsjob.Calculation = origCalType
     
     if r: # Job was aborted or an error occurred.
         msg = redmsg(errmsgs[r-1])
         env.history.message( cmd + msg )
         return
         
     self.print_energy()

    def __CM_Align_to_chunk(self):
        """
        Rotary or Linear Motor context menu command: "Align to chunk"
        This uses the chunk connected to the first atom of the motor.
        """
        # I needed this when attempting to simulate the rotation of a long, skinny
        # chunk.  The axis computed from the attached atoms was not close to the axis
        # of the chunk.  I figured this would be a common feature that was easy to add.
        # 
        ##e it might be nice to dim this menu item if the chunk's axis hasn't moved since this motor was made or recentered;
        # first we'd need to extend the __CM_ API to make that possible. [mark 050717]

        cmd = greenmsg("Align to Chunk: ")

        chunk = self.atoms[0].molecule # Get the chunk attached to the motor's first atom.
        # wware 060116 bug 1330
        # The chunk's axis could have its direction exactly reversed and be equally valid.
        # We should choose between those two options for which one has the positive dot
        # product with the old axis, to avoid reversals of motor direction when going
        # between "align to chunk" and "recenter on atoms".
        #bruce 060116 modified this fix to avoid setting axis to V(0,0,0) if it's perpendicular to old axis.
        newAxis = chunk.getaxis()
        if dot(self.axis,newAxis) < 0:
            newAxis = - newAxis
        self.axis = newAxis
        self.assy.changed()   # wware 060116 bug 1331 - assembly changed when axis changed

        info = "Aligned motor [%s] on chunk [%s]" % (self.name, chunk.name) 
        env.history.message( cmd + info ) 
        self.assy.w.win_update()

        return

    def makethermo(self):
        """
        Attaches a thermometer to the single atom selected.
        """
        cmd = greenmsg("Thermometer: ")

        atoms = self.assy.selatoms_list()

        if not atoms:
            msg = "You must select an atom on the chunk you want to " \
                  "associate with a Thermometer."
            env.history.message(cmd + redmsg(msg))
            return

        # Make sure only one atom is selected.
        if len(atoms) != 1:
            msg = "To create a Thermometer, only one atom may be selected."
            env.history.message(cmd + redmsg(msg))
            return

        m = Thermo(self.assy, atoms)
        self.unpickall_in_GLPane()
        self.place_new_jig(m)

        env.history.message(cmd + "Thermometer created")
        self.assy.w.win_update()

    def merge(self):
        """
        Merges selected atoms into a single chunk, or merges the selected
        chunks into a single chunk.

        @note: If the selected atoms belong to the same chunk, nothing happens.
        """
        #mark 050411 changed name from weld to merge (Bug 515)
        #bruce 050131 comment: might now be safe for clipboard items
        # since all selection is now forced to be in the same one;
        # this is mostly academic since there's no pleasing way to use it on them,
        # though it's theoretically possible (since Groups can be cut and maybe copied).

        cmd = greenmsg("Combine Chunks: ")

        if self.selatoms:
            self.makeChunkFromSelectedAtoms()
            return

        if len(self.selmols) < 2:
            msg = redmsg("Need two or more selected chunks to merge")
            env.history.message(cmd + msg)
            return
        self.changed() #bruce 050131 bugfix or precaution
        mol = self.selmols[0]
        for m in self.selmols[1:]:
            mol.merge(m)

    def modifyHydrogenate(self):
        """
        Add hydrogen atoms to bondpoints on selected chunks/atoms.
        """
        cmd = greenmsg("Hydrogenate: ")
        
        fixmols = {} # helps count modified mols for statusbar
        if self.selmols:
            counta = countm = 0
            for m in self.selmols:
                changed = m.Hydrogenate()
                if changed:
                    counta += changed
                    countm += 1
                    fixmols[id(m)] = m
            if counta:
                didwhat = "Added %d atom(s) to %d chunk(s)" \
                          % (counta, countm)
                if len(self.selmols) > countm:
                    didwhat += \
                        " (%d selected chunk(s) had no bondpoints)" \
                        % (len(self.selmols) - countm)
                didwhat = fix_plurals(didwhat)
            else:
                didwhat = "Selected chunks contain no bondpoints"    

        elif self.selatoms:
            count = 0
            for a in self.selatoms.values():
                ma = a.molecule
                for atm in a.neighbors():
                    matm = atm.molecule
                    changed = atm.Hydrogenate()
                    if changed:
                        count += 1
                        fixmols[id(ma)] = ma
                        fixmols[id(matm)] = matm
            if fixmols:
                didwhat = \
                    "Added %d atom(s) to %d chunk(s)" \
                    % (count, len(fixmols))
                didwhat = fix_plurals(didwhat)
                # Technically, we *should* say ", affected" instead of "from"
                # since the count includes mols of neighbors of
                # atoms we removed, not always only mols of atoms we removed.
                # Since that's rare, we word this assuming it didn't happen.
                # [#e needs low-pri fix to be accurate in that rare case;
                #  might as well deliver that as a warning, since that case is
                #  also "dangerous" in some sense.]
            else:
                didwhat = "No bondpoints on selected atoms"
        else:
            didwhat = redmsg("Nothing selected")

        if fixmols:
            self.changed()
            self.w.win_update()
        env.history.message(cmd + didwhat)
        return

 def viewRotate180(self):
     """
     Set view to the opposite of current view.
     """
     cmd = greenmsg("Opposite View: ")
     info = 'Current view opposite to the previous view'
     env.history.message(cmd + info)
     self.glpane.rotateView(self.glpane.quat + Q(V(0,1,0), math.pi))

 def setViewZoomToSelection(self):
     """
     Zoom to selection (Implemented for only selected jigs and chunks
     """
     cmd = greenmsg("Zoom To Selection:")
     info = ''
     env.history.message(cmd + info)
     self.glpane.setViewZoomToSelection()

 def setViewFitToWindow(self):
     """
     Fit to Window
     """
     cmd = greenmsg("Fit to Window: ")
     info = ''
     env.history.message(cmd + info)
     self.glpane.setViewFitToWindow()

 def movieInfo(self):
     """
     Prints information about the current movie to the history widget.
     """
     if not self.w.assy.current_movie:
         return
     env.history.message(greenmsg("Movie Information"))
     self.w.assy.current_movie._info()

 def viewRotateMinus90(self): # Added by Mark. 051013.
     """
     Decrement the current view by 90 degrees around the vertical axis.
     """
     cmd = greenmsg("Rotate View -90 : ")
     info = 'View decremented by 90 degrees'
     env.history.message(cmd + info)
     self.glpane.rotateView(self.glpane.quat + Q(V(0,1,0), -math.pi/2))

 def setViewHomeToCurrent(self):
     """
     Changes Home view of the model to the current view in the glpane.
     """
     cmd = greenmsg("Set Home View to Current View: ")
     info = 'Home'
     env.history.message(cmd + info)
     self.glpane.setViewHomeToCurrent()