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commanding.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:
#-* 
#-* 
#-*
#Z* -------------------------------------------------------------------

if __name__=='pymol.commanding':

   import thread
   import string
   import re
   import os
   import time
   import threading
   import traceback

   import cmd
   import pymol
   from cmd import _cmd,lock,unlock,Shortcut,QuietException
   from cmd import _feedback,fb_module,fb_mask,is_list

   def resume(fname):
      if os.path.exists(fname):
         if(re.search(r"\.py$|\.PY$|\.pym$|.PYM$",fname)):
            cmd.do("run %s"%fname)
         else:
            cmd.do("@%s"%fname)
      cmd.do("log_open %s,a"%fname)

   def log_open(fname='log.pml',mode='w'):
      try:
         try:
            if pymol._log_file!=None:
               pymol._log_file.close()
               del pymol._log_file
         except:
            pass
         pymol._log_file = open(fname,mode)
         if _feedback(fb_module.cmd,fb_mask.details): # redundant
            if mode!='a':
               print " Cmd: logging to '%s'."%fname
            else:
               print " Cmd: appending to '%s'."%fname            
         if mode=='a':
            pymol._log_file.write("\n") # always start on a new line
         if(re.search(r"\.py$|\.PY$|\.pym$|\.PYM$",fname)):
            cmd.set("logging",2,quiet=1)
         else:
            cmd.set("logging",1,quiet=1)
      except:
         print"Error: unable to open log file '%s'"%fname
         pymol._log_file = None
         cmd.set("logging",0,quiet=1)
         traceback.print_exc()

   def log(text,alt_text=None):
      if pymol._log_file!=None:
         mode = cmd.get_setting_legacy("logging")
         if mode:
            if mode==1:
               pymol._log_file.write(text)
            elif mode==2:
               if alt_text!=None:
                  pymol._log_file.write(alt_text)
               else:
                  pymol._log_file.write("cmd.do('''%s''')\n"%string.strip(text))
            pymol._log_file.flush()

   def log_close():
      if pymol._log_file!=None:
         pymol._log_file.close()
         del pymol._log_file
         cmd.set("logging",0,quiet=1)
         if _feedback(fb_module.cmd,fb_mask.details): # redundant
            print " Cmd: log closed."

   def cls(): 
      '''
DESCRIPTION

   "cls" clears the output buffer.

USAGE

   cls
   '''
      r = None
      try:
         lock()
         r = _cmd.cls()
      finally:
         unlock()
      return r

   def splash(mode=0):
      '''
DESCRIPTION

   "splash" shows the splash screen information.

USAGE

   splash
      '''
      r = None
      mode = int(mode)
      if mode == 1: # just show PNG
         png_path = os.path.expandvars("$PYMOL_PATH/data/pymol/splash.png")
         if os.path.exists(png_path):
            cmd.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
            r = 1
      else:
         if cmd.get_setting_legacy("internal_feedback")>0.1:
            cmd.set("text","1",quiet=1)
         print
         try:
            lock()
            r = _cmd.splash()
         finally:
            unlock()
      return r

   def reinitialize():
      '''
DESCRIPTION

   "reinitialize" reinitializes PyMOL

USAGE

   reinitialize
      '''
      try:
         lock()
         r = _cmd.reinitialize()
      finally:
         unlock()
      return r


   def sync(timeout=1.0,poll=0.05):
      '''
DESCRIPTION

   "sync" is an API-only function which waits until all current
   commmands have been executed before returning.  A timeout
   can be used to insure that this command eventually returns.

PYMOL API

   cmd.sync(float timeout=1.0,float poll=0.05)

SEE ALSO

   frame
   '''
      now = time.time()
      timeout = float(timeout)
      poll = float(poll)
      if _cmd.wait_queue(): # commands waiting to be executed?
         while 1:
            e = threading.Event() # using this for portable delay
            e.wait(poll)
            del e
            if not _cmd.wait_queue():
               break
            if (time.time()-now)>timeout:
               break


   def do(commands,log=1,echo=1):
      # WARNING: don't call this routine if you already have the API lock
      # use cmd._do instead
      '''
DESCRIPTION

   "do" makes it possible for python programs to issue simple PyMOL
   commands as if they were entered on the command line.

PYMOL API

   cmd.do( commands )

USAGE (PYTHON)

   from pymol import cmd
   cmd.do("load file.pdb")
      '''
      r = None
      log = int(log)
      if is_list(commands):
         cmmd_list = commands
      else:
         cmmd_list = [ commands ]
      for cmmd in cmmd_list:
         lst = string.split(string.replace(cmmd,chr(13),chr(10)),chr(10))
         if len(lst)<2:
            for a in lst:
               if(len(a)):
                  try:
                     lock()
                     r = _cmd.do(a,log,echo)
                  finally:
                     unlock()
         else:
            defer = cmd.get_setting_legacy("defer_updates")
            cmd.set('defer_updates',1)
            for a in lst:
               if(len(a)):
                  try:
                     lock()
                     r = _cmd.do(a,log,echo)
                  finally:
                     unlock()
            cmd.set('defer_updates',defer)
      return r


   def quit():
      '''
DESCRIPTION

   "quit" terminates the program. 

USAGE

   quit

PYMOL API

   cmd.quit()
      '''
      if thread.get_ident() == pymol.glutThread:
         cmd._quit()
      else:
         try:
            lock()
            _cmd.do("_ time.sleep(0.100);cmd._quit()",0,0)
            # allow time for a graceful exit from the calling thread
            thread.exit()
         finally:
            unlock()
      return None

   def delete(name):
      '''
DESCRIPTION

   "delete" removes an object or a selection. 

USAGE

   delete name  
   delete all   # deletes all objects

   name = name of object or selection

PYMOL API

   cmd.delete (string name = object-or-selection-name )

SEE ALSO

   remove
      '''
      try:
         lock()   
         r = _cmd.delete(str(name))
      finally:
         unlock()
      return r

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