PMGApp.py

#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. 
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information. 
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-*
#-* NOTE: Based on code by John E. Grayson which was in turn 
#-* based on code written by Doug Hellmann. 
#Z* -------------------------------------------------------------------

import sys
import os
from glob import glob
import re
import string
import threading
import traceback
import Queue
import __builtin__
import types

# ensure that PyMOL seach path is used...

from Tkinter import *
from tkFileDialog import *
import tkMessageBox
import Pmw

00033 class PMGApp(Pmw.MegaWidget):

    def initOS(self):
         # Initialize platform-specific options
         if sys.platform == 'mac':
             self.initializeTk_mac()
         elif sys.platform[:3] == 'win':
             self.initializeTk_win32()
         elif sys.platform[:5] == 'linux':
             self.initializeTk_unix()
         else:
             self.initializeTk_unix()
#       self.root.tk.call('tk','scaling',1)

         # try to get the windows properly aligned...
         
         osFrame = { 'win32' : (4,60), 'irix'   : (0,41),
                     'darwin': (0,51), 'cygwin' : (0,60),
                     'linux' : (0,31), 'linux2' : (0,31) }

         if sys.platform in osFrame.keys():
             (self.frameXAdjust,self.frameYAdjust) = osFrame[sys.platform]
         else:
             self.frameYAdjust = 51
             self.frameXAdjust = 0
         
    def initializeTk_win32(self):
        self.root.option_add('*Font', 'Tahoma 8')
        self.pad = ' '
        
    def initializeTk_mac(self):
        pass
        
    def initializeTk_unix(self):
        pass

    def getLoadableFileTypes(self):
        return [("All Readable","*.pdb"),
                ("All Readable","*.pdb1"),                
                ("All Readable","*.ccp4"),
                ("All Readable","*.xplor"),
                ("All Readable","*.mol"),
                ("All Readable","*.mol2"),
                ("All Readable","*.sdf"),
                ("All Readable","*.xyz"),
                ("All Readable","*.r3d"),
                ("All Readable","*.cc1"),
                ("All Readable","*.cc2"), 
                ("All Readable","*.ent"),
                ("All Readable","*.dat"),
                ("All Readable","*.out"),
                ("All Readable","*.mmd"),
                ("All Readable","*.mmod"),
                ("All Readable","*.pse"),
                ("All Readable","*.psw"),
                ("All Readable","*.phi"),
                ("All Readable","*.fld"),
                ("All Readable","*.grd"),
                ("All Readable","*.o"),
                ("All Readable","*.omap"), 
                ("All Readable","*.brix"),
                ("All Readable","*.dx"),
                ("All Readable","*.pqr"),
                ("All Readable","*.p5m"),
                ("All Readable","*.p1m"),
                ("All Readable","*.cube"),
                ("All Readable","*.cif"),
                ("All Readable","*.moe"), # proprietary format
                ("All Readable","*.mae"), # proprietary format
                ("All Readable","*.fasta"),
                ("All Readable","*.aln"),
                ("All Readable","*.acnt"),
                #("All Readable","*.mtz"),                 
                ("PDB File","*.pdb"),
                ("PDB1 File","*.pdb1"),                
                ("All Files","*.*"),
                ("All Files","*"),  
                ("PDB File","*.ent"),
                ("PyMOL Session","*.pse"),
                ("PyMOL Show","*.psw"),
                ("CCP4 Map","*.ccp4"), 
                ("XPLOR Map","*.xplor"),
                ("MOL2/Multi-MOL2","*.mol2"),
                ("Macromodel File","*.dat"),
                ("Macromodel File","*.out"),
                ("Macromodel File","*.mmd"),
                ("Macromodel File","*.mmod"),
#                ("MTZ Reflection File","*.mtz"),
                ("BRIX/O Map","*.o"),
                ("BRIX/O Map","*.omap"),
                ("BRIX/O Map","*.brix"),
                ("CIF","*.cif"),
                ("Gaussian Cube Map","*.cube"),
                ("DX Map","*.dx"),     
                ("AVS (MEAD) Field","*.fld"),    
                ("MOL File","*.mol"),
                ("MOE File","*.moe"), # proprietary format
                ("MAE File","*.mae"), # proprietary format  
                ("ChemPy Model","*.pkl"),
                ("Raster3D Scene","*.r3d"),
                ("SDF File","*.sdf"),
                ("ChemDraw3D File","*.cc1"),
                ("ChemDraw3D File","*.cc2"),
                ("XYZ File","*.xyz"),
                ("Fasta File","*.fasta"),
                ("CLUSTAL file","*.aln"),
                ("ACNT Map","*.acnt"),                 
                ]

    def initializeTk_colors_common(self):
        #self.root.option_add('*background', 'grey')   #let system decide
        self.root.option_add('*foreground', 'black')
        self.root.option_add('*EntryField.Entry.background', 'white')
        self.root.option_add('*Entry.background', 'white')      
        self.root.option_add('*MessageBar.Entry.background', 'gray85')
        self.root.option_add('*Listbox*background', 'white')
        self.root.option_add('*Listbox*selectBackground', 'dark slate blue')
        self.root.option_add('*Listbox*selectForeground', 'white')
        
    def quit_app(self):
        self.pymol.cmd.log_close()
        self.pymol.cmd.quit()  # avoid logging this - it's inconvenient...

    def flush_fifo_once(self):
        # flush the external GUI fifo command queue
        while not self.fifo.empty():
            try:
                cmmd = self.fifo.get(0)
                exec cmmd
            except:
                traceback.print_exc()
        
    def flush_fifo(self):
        self.flush_fifo_once()
        if self.allow_after:
            self.root.after(20,self.flush_fifo) # 50X a second
        
    def run(self,poll=0):
        # this call to mainloop needs to be replaced with something revocable
        self.flush_fifo_once()
        keep_alive = 1
        if poll:
            import time
            while keep_alive:
                self.root.update()
                time.sleep(0.05)
        else:
            self.root.mainloop()
            
        self.quit_app()

    def execute(self,cmmd):  
        self.fifo.put(cmmd)

    def installPlugin(self):
        plugdir = os.path.split(__file__)[0]
        path = os.path.join(plugdir, "startup", "check_writable")
        ok = 1
        try:
            f=open(path,'wb')
            f.close()
            os.unlink(path)
        except:
            ok = 0
            tkMessageBox.showinfo("Error",
 "Unable to write to the plugin directory.\nPerhaps you have insufficient privileges?  Please ensure that you have permission to write to:\n%s" % path)
        if ok:
            ofile = askopenfilename(title="Install Plugin",
                initialdir = os.getcwd(),
                filetypes=[ ("All Readable","*.py"),
                                ("All Readable","*.pyc"),                        
                                ])
            if len(ofile):
                initialdir, plugname = os.path.split(ofile)
                try:
                    f=open(ofile,'rb')
                    plugin = f.read()
                    f.close()
                    path = os.path.join(plugdir, "startup", plugname)
                    f=open(path,'wb')
                    f.write(plugin)
                    f.close()
                    tkMessageBox.showinfo("Success", 
                        "Plugin '%s' has been installed.\nPlease restart PyMOL to begin use." % plugname)
                except:
                    traceback.print_exc()
                    tkMessageBox.showinfo("Error", "unable to install plugin '%s'" % plugname)


    def my_show(self,win,center=1):
        if sys.platform!='linux2':
            win.show()
        else: # autocenter, deiconify, and run mainloop
            # this is a workaround for a bug in the
            # interaction between Tcl/Tk and common Linux
            # window managers (namely KDE/Gnome) which causes
            # an annoying 1-2 second delay in opening windows!
            if center:
                tw = win.winfo_reqwidth()+100
                th = win.winfo_reqheight()+100
                vw = win.winfo_vrootwidth()
                vh = win.winfo_vrootheight()
                x = max(0,(vw-tw)/2)
                y = max(0,(vh-th)/2)
                win.geometry(newGeometry="+%d+%d"%(x,y))
            win.deiconify()

    def my_withdraw(self,win):
        if sys.platform!='linux2':
            win.withdraw()
        else: 
            win.destroy()

    def removePlugin2(self,result):
        if result != 'OK':
            self.my_withdraw(self.dialog)
            self.dialog = None
        else:
            sels = self.dialog.getcurselection()
            if len(sels)!=0:
                startup_pattern = re.sub(r"[\/\\][^\/\\]*$","/startup/*.[Pp][Yy]*",__file__)
                removed = re.sub(r"[\/\\][^\/\\]*$","/startup/removed",__file__)
                if not os.path.isdir(removed):
                    try:
                        os.mkdir(removed,0775)
                    except:
                        pass
                raw_list = glob(startup_pattern)
                for a in raw_list:
                    prefix = re.sub(r".*[\/\\]|\.py.*$","",a)
                    if prefix in sels:
                        if a.lower()[-3:] == '.py':
                            try: # create backup copy
                                dest_path = os.path.join(removed,prefix+".py")
                                open(dest_path,'wb').write(open(a,'rb').read())
                            except:
                                traceback.print_exc()
                        os.unlink(a)
                tkMessageBox.showinfo("Success", 
                                      "One or more plugins have been removed.\nPlease restart PyMOL.")
            self.my_withdraw(self.dialog)
            del self.dialog
    
    def removePlugin(self):
        startup_pattern = re.sub(r"[\/\\][^\/\\]*$","/startup/*.py*",__file__)
        raw_list = glob(startup_pattern)
        unique = {}
        for a in raw_list:
            unique[re.sub(r".*[\/\\]|\.py.*$","",a)] = 1
        lst = unique.keys()
        lst = filter(lambda x:x!="__init__",lst)
        lst.sort()
        self.dialog = Pmw.SelectionDialog(self.root,title="Remove",
                                  buttons = ('OK', 'Cancel'),
                                              defaultbutton='Cancel',
                                  scrolledlist_labelpos=N,
                                  scrolledlist_listbox_selectmode=EXTENDED,
                                  label_text='Which plugin would you like to remove?',
                                  scrolledlist_items = lst,
                                  command = self.removePlugin2)
        if len(lst):
            listbox = self.dialog.component('scrolledlist')      
            listbox.selection_set(0)
        self.my_show(self.dialog)
        
        
    def initializePlugins(self):
        # startup_pattern = /path/to/plugins/*.py*
        startup_pattern = re.sub(r"[\/\\][^\/\\]*$","/startup/*.py*",__file__)
        # startup_pattern = os.environ['PYMOL_PATH']+"/modules/pmg_tk/startup/*.py*"
        raw_list = glob(startup_pattern)
        unique = {}
        for a in raw_list:
            # strips the extension from the module name: foo.py -> foo
            unique[re.sub(r".*[\/\\]|\.py.*$","",a)] = 1
        for name in unique.keys():
            try:
                if name != "__init__":
                    module_context = string.join(string.split(__name__,'.')[0:-1])
                    # set the module name
                    mod_name = module_context+".startup."+name
                    # import the module by name, then
                    __builtin__.__import__(mod_name)
                    mod = sys.modules[mod_name]
                    # look it up and initialize it
                    if hasattr(mod,'__init_plugin__'):
                        mod.__init_plugin__(self)
                    elif hasattr(mod,'__init__'):
                        mod.__init__(self)
            except:
                suppress = 0
                # suppress error reporting when using old versions of Python
                if float(sys.version[0:3])<2.3:
                    if( name in ['apbs_tools' ]):
                        suppress = 1
                if not suppress:
                    print "Exception in plugin '%s' -- Traceback follows..."%name
                    traceback.print_exc()
                    print "Error: unable to initialize plugin '%s'."%name

    def addSkinMenuItems(self,menuBar,menuName):
        if not hasattr(self,'skinNameList'):
            # find installed skins
            skin_pattern = re.sub(r"[\/\\][^\/\\]*$","/skins/*/__init__.py*",__file__)
            raw_list = glob(skin_pattern)
            unique = {}
            for a in raw_list:
                key = re.sub(r"[\/\\]__init__\.py.*$","",a)
                unique[re.sub(r".*[\/\\]","",key)] = 1
            name_list = unique.keys()
            name_list.sort()
            self.skinNameList = name_list
        if hasattr(self,'skinNameList'):
            for name in self.skinNameList:
                caps_name = string.upper(name)[0:1]+string.lower(name)[1:]
                menuBar.addmenuitem(menuName, 'command', name,
                                    label=caps_name,
                                    command=lambda s=self,n=name:s.setSkin(n))

        
    def setSkin(self,skin,run=1):
        if isinstance(skin,types.StringType):
            inv = sys.modules.get("pymol.invocation",None)
            if inv!=None:
                module_path = inv.options.gui +".skins."+ skin
                __import__(inv.options.gui +".skins."+ skin)
                skin = sys.modules[module_path].__init__(self)
        if skin != self.skin:
            if self.skin != None:
                self.skin.takedown()
            self.skin = skin

        if run:
            self.runSkin()
            
    def runSkin(self):
        if self.skin != None:
            self.skin.setup()
    
    def __init__(self, pymol_instance, skin):

        self.allow_after = 1 # easy switch for troubleshooting threads

        self.pymol = pymol_instance
        
        if self.pymol._ext_gui != None:
        
            raise RuntimeError  # only one PMGApp should ever be instantiated
        
        else:

            # create a FIFO so that PyMOL can send code to be executed by the GUI thread
            
            self.fifo = Queue.Queue(0)

            # create a pymol global so that PyMOL can find the external GUI

            self.pymol._ext_gui = self

            self.skin = None
            
            # initialize Tcl/Tk

            self.root = Tk() # creates the root window for the application

            # color scheme

            self.initializeTk_colors_common()

             # operating-system dependencies

            self.initOS()

            # Python megawigit initialization

            Pmw.initialise(self.root)
            
            # Initialize the base class
            
            Pmw.MegaWidget.__init__(self, parent=self.root)

            # read the command line arguments regarding:
            # - the size of the root window
            # - the skin to use

            inv = sys.modules.get("pymol.invocation",None)
            if inv != None:
                if skin == None:
                    skin = inv.options.skin
                self.frameWidth = inv.options.win_x + 220
                self.frameXPos = inv.options.win_px - self.frameXAdjust
                self.frameHeight = inv.options.ext_y
                self.frameYPos = inv.options.win_py - (
                         self.frameHeight + self.frameYAdjust)
                self.setSkin(skin,run=0)
                
            # define the size of the root window
            
            self.root.geometry('%dx%d+%d+%d' % (
                self.frameWidth, self.frameHeight, self.frameXPos, self.frameYPos))
            
            # activate polling on the fifo

            if self.allow_after:
                self.root.after(1000,self.flush_fifo)

            # and let 'er rip

            self.runSkin()