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cmd.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* -------------------------------------------------------------------

# cmd.py 
# Python interface module for PyMol
#
# **This is the only module which should be/need be imported by 
# ** PyMol API Based Programs

# NOTE: this cmd module has grown absurdly huge, therefore expect this
# file to be broken down sometime after the 0.51 release into more
# manageable pieces.  Note that cmd.<whatever> will still work -- the
# symbols will be mapped into this namespace even after the code modules
# are separated.

# NEW CALL RETURN CONVENTIONS for _cmd.so C-layer
#
# (1) Calls into C (_cmd) should return results/status and print errors
#     and feedback (according to mask) BUT NEVER RAISE EXCEPTIONS.
## (2) In the absence of an expected return value, truth applies:
#        Success is 1, true 
#        Failure is 0, false. None, NULL
#
#     NOTE: if you need more informative failure, then code and
#           document an exception to this rule for your functions!
#
# (3) If _cmd produces a specific return result, be sure to include an
#     error result as one of the possibilities outside the range of the
#     expected return value.  For example, a negative distance or count
#
# (4) cmd.py API wrappers can then raise exceptions based on truth
#     and should return truth for success or None for failure
#     (if no exception was raised)
#
#
# NOTE: Output tweaking via the "quiet" parameter of API functions.
#
# Many PyMOL API functions have a "quiet" parameter which is used to
# customize output depending on when and where the routine was called.
#
# As defined, quiet should be 1.  Called from an external module, output
# to the console should be minimal.
#
# However, when a command is run through the parser (often manually) the
# user expects a little more feedback.  The parser will automatically
# set "quiet" to zero
#
# In rare cases, certain nonserious error or warning output should
# also be suppressed.  Set "quiet" to 2 for this behavior.

if __name__=='pymol.cmd':

   import traceback
   import sys
   
   try:
      
      import re
      import _cmd
      import string
      import thread
      import threading
      import types
      import pymol
      import os
      import parsing
      import __main__
      import time
      import urllib
      
      from shortcut import Shortcut

      from chempy import io

      #######################################################################
      # symbols for early export
      #######################################################################

      file_ext_re= re.compile(string.join([
         "\.pdb$|\.pdb1$|\.ent$|\.mol$|\.p5m$|",
         r"\.PDB$|\.pdb1$|\.ENT$|\.MOL$|\.P5M$|",
         r"\.mmod$|\.mmd$|\.dat$|\.out$|\.mol2$|",
         r"\.MMOD$|\.MMD$|\.DAT$|\.OUT$|\.MOL2$|",
         r"\.xplor$|\.pkl$|\.sdf$|\.pqr|", 
         r"\.XPLOR$|\.PKL$|\.SDF$|\.PQR|",                        
         r"\.r3d$|\.xyz$|\.xyz_[0-9]*$|", 
         r"\.R3D$|\.XYZ$|\.XYZ_[0-9]*$|",
         r"\.cc1$|\.cc2$|", # ChemDraw 3D
         r"\.CC1$|\.CC2$|",
         r"\.DX$|\.dx$|", # DX files (APBS)
         r"\.pse$|\.PSE$|", # PyMOL session (pickled dictionary)
         r"\.pmo$|", # Experimental molecular object format
         r"\.PMO$|",
         r"\.ccp4$|\.CCP4$|", # CCP4
         r"\.top$|\.TOP$|", # AMBER Topology
         r"\.trj$|\.TRJ$|", # AMBER Trajectory
         r"\.crd$|\.CRD$|", # AMBER coordinate file
         r"\.rst$|\.RST$|", # AMBER restart
         r"\.cex$|\.CEX$|", # CEX format (used by metaphorics)
         r"\.phi$|\.PHI$|", # PHI format (delphi)
         r"\.fld$|\.FLD$|", # FLD format (AVS)
         r"\.o$|\.O$|\.omap$|\.OMAP$|\.dsn6$|\.DSN6$|\.brix$|\.BRIX$", # BRIX/O format
         r"|\.grd$|\.GRD$", # InsightII Grid format
         ],''))

      reaper = None
      safe_oname_re = re.compile(r"\ |\+|\(|\)|\||\&|\!|\,")  # quash reserved characters
      sanitize_list_re = re.compile(r"[^0-9\.\-\[\]\,]+")
      sanitize_alpha_list_re = re.compile(r"[^a-zA-Z0-9\'\"\.\-\[\]\,]+")

      def safe_list_eval(st):
         return eval(sanitize_list_re.sub('',st))

      def safe_alpha_list_eval(st):
         return eval(sanitize_alpha_list_re.sub('',st))

      QuietException = parsing.QuietException

      #--------------------------------------------------------------------
      # shortcuts...

      toggle_dict = {'on':1,'off':0,'1':1,'0':0}
      toggle_sc = Shortcut(toggle_dict.keys())

      stereo_dict = {'on':1,'off':0,'1':1,'0':0,'swap':-1,
                     'crosseye':2,'quadbuffer':3,'walleye':4}
      stereo_sc = Shortcut(stereo_dict.keys())

      space_sc = Shortcut(['cmyk','rgb','pymol'])

      window_dict = { 'show' : 1, 'hide' : 0 }
      window_sc = Shortcut(window_dict.keys())

      repres = {
         'everything'    : -1,
         'sticks'        : 0,
         'spheres'       : 1,
         'surface'       : 2,
         'labels'        : 3,
         'nb_spheres'    : 4,
         'cartoon'       : 5,
         'ribbon'        : 6,
         'lines'         : 7,
         'mesh'          : 8,
         'dots'          : 9,
         'dashes'        :10,
         'nonbonded'     :11,
         'cell'          :12,
         'cgo'           :13,
         'callback'      :14,
         'extent'        :15,
         'slice'         :16,
         'angles'        :17,
         'dihedrals'     :18,         
      }
      repres_sc = Shortcut(repres.keys())

      boolean_dict = {
         'yes'           : 1,
         'no'            : 0,
         '1'             : 1,
         '0'             : 0,
         'on'            : 1,
         'off'           : 0
         }

      boolean_sc = Shortcut(boolean_dict.keys())

      palette_dict = {
         'rainbow_cycle'           : ('o',3,0  ,999), # perceptive rainbow
         'rainbow_cycle_rev'       : ('o',3,999,  0),      
         'rainbow'                 : ('o',3,107,893),
         'rainbow_rev'             : ('o',3,893,107),
         'rainbow2'                : ('s',3,167, 833), # cartesian rainbow 
         'rainbow2_rev'            : ('s',3,833,167),

         'gcbmry' : ('r',3,166,999),
         'yrmbcg' : ('r',3,999,166),

         'cbmr'   : ('r',3,166,833),
         'rmbc'   : ('r',3,833,166),      

         'green_yellow_red'        : ('s',3,500,833),
         'red_yellow_green'        : ('s',3,833,500),      

         'yellow_white_blue'       : ('w',3,  0, 83),
         'blue_white_yellow'       : ('w',3, 83,  0),      

         'blue_white_red'          : ('w',3, 83,167),
         'red_white_blue'          : ('w',3,167, 83),

         'red_white_green'         : ('w',3,167,250),
         'green_white_red'         : ('w',3,250,167),

         'green_white_magenta'     : ('w',3,250,333),
         'magenta_white_green'     : ('w',3,333,250),      

         'magenta_white_cyan'      : ('w',3,333,417),
         'cyan_white_magenta'      : ('w',3,417,333),

         'cyan_white_yellow'       : ('w',3,417,500),
         'yellow_cyan_white'       : ('w',3,500,417),

         'yellow_white_green'      : ('w',3,500,583),
         'green_white_yellow'      : ('w',3,583,500),

         'green_white_blue'        : ('w',3,583,667),
         'blue_white_green'        : ('w',3,667,583),      

         'blue_white_magenta'      : ('w',3,667,750),
         'magenta_white_blue'      : ('w',3,750,667),

         'magenta_white_yellow'    : ('w',3,750,833),
         'yellow_white_magenta'    : ('w',3,833,750),

         'yellow_white_red'        : ('w',3,833,917),
         'red_white_yellow'        : ('w',3,817,833),

         'red_white_cyan'          : ('w',3,916,999),
         'cyan_white_red'          : ('w',3,999,916),      

         'yellow_blue'       : ('c',3,  0, 83),
         'blue_yellow'       : ('c',3, 83,  0),      

         'blue_red'          : ('c',3, 83,167),
         'red_blue'          : ('c',3,167, 83),

         'red_green'         : ('c',3,167,250),
         'green_red'         : ('c',3,250,167),

         'green_magenta'     : ('c',3,250,333),
         'magenta_green'     : ('c',3,333,250),      

         'magenta_cyan'      : ('c',3,333,417),
         'cyan_magenta'      : ('c',3,417,333),

         'cyan_yellow'       : ('c',3,417,500),
         'yellow_cyan'       : ('c',3,500,417),

         'yellow_green'      : ('c',3,500,583),
         'green_yellow'      : ('c',3,583,500),

         'green_blue'        : ('c',3,583,667),
         'blue_green'        : ('c',3,667,583),      

         'blue_magenta'      : ('c',3,667,750),
         'magenta_blue'      : ('c',3,750,667),

         'magenta_yellow'    : ('c',3,750,833),
         'yellow_magenta'    : ('c',3,833,750),

         'yellow_red'        : ('c',3,833,917),
         'red_yellow'        : ('c',3,817,833),

         'red_cyan'          : ('c',3,916,999),
         'cyan_red'          : ('c',3,999,916),      
         }

      palette_sc = Shortcut(palette_dict.keys())

      def null_function():
         pass

      #--------------------------------------------------------------------
      # convenient type-checking

      def is_string(obj):
         return isinstance(obj,types.StringType)

      def is_list(obj):
         return isinstance(obj,types.ListType)

      def is_tuple(obj):
         return isinstance(obj,types.TupleType)

      #--------------------------------------------------------------------
      # locks and threading

      # the following lock is used by both C and Python to insure that no more than
      # one active thread enters PyMOL at a given time. 

      lock_api = pymol.lock_api
      lock_api_c = pymol.lock_api_c
      lock_api_status = pymol.lock_api_status
      lock_api_glut = pymol.lock_api_glut
      
      # WARNING: internal routines, subject to change      
      def lock_c(): 
         lock_api_c.acquire(1)

      def unlock_c():
         lock_api_c.release()

      def lock_status(): 
         lock_api_status.acquire(1)

      def unlock_status():
         lock_api_status.release()

      def lock_glut(): 
         lock_api_glut.acquire(1)

      def unlock_glut():
         lock_api_glut.release()

      def lock_without_glut():
         try:
            lock_glut()
            lock()
         finally:
            unlock_glut()

      def lock(): # INTERNAL -- API lock
   #      print " lock: acquiring as 0x%x"%thread.get_ident(),(thread.get_ident() == pymol.glutThread)
         if not lock_api.acquire(0):
            w = 0.001
            while 1:
   #            print " lock: ... as 0x%x"%thread.get_ident(),(thread.get_ident() == pymol.glutThread)
               e = threading.Event() 
               e.wait(w)  
               del e
               if lock_api.acquire(0):
                  break
               if w<0.1:
                  w = w * 2 # wait twice as long each time until flushed
   #      print "lock: acquired by 0x%x"%thread.get_ident()

      def lock_attempt(): # INTERNAL
         result = lock_api.acquire(blocking=0)
         return result

      def unlock(): # INTERNAL
         if (thread.get_ident() == pymol.glutThread):
            global reaper
            if reaper:
               try:
                  if not reaper.isAlive():
                     if pymol.invocation.options.no_gui:
                        _cmd.quit()
                     else:
                        reaper = None
               except:
                  pass
            lock_api.release()
   #         print "lock: released by 0x%x (glut)"%thread.get_ident()
            _cmd.flush_now()
         else:
   #         print "lock: released by 0x%x (not glut), waiting queue"%thread.get_ident()
            lock_api.release()
            if _cmd.wait_queue(): # commands waiting to be executed?
               e = threading.Event() # abdicate control for a 100 usec for quick tasks
               e.wait(0.0001)
               del e
               # then give PyMOL increasingly longer intervals to get its work done...
               w = 0.0005  # NOTE: affects API perf. for "do" and delayed-exec
               while _cmd.wait_queue(): 
                  e = threading.Event() # abdicate control for a 100 usec for quick tasks
                  e.wait(w)
                  del e
                  if w > 0.1: # wait up 0.2 sec max for PyMOL to flush queue
                     if _feedback(fb_module.cmd,fb_mask.debugging):
                        fb_debug.write("Debug: avoiding possible dead-lock?\n")
   #                  print "dead locked as 0x%x"%thread.get_ident()
                     break
                  w = w * 2 # wait twice as long each time until flushed

      def is_glut_thread(): # internal
         if thread.get_ident() == pymol.glutThread:
            return 1
         else:
            return 0

      def get_progress(reset=0):
         r = -1.0
         try:
            lock_status()
            r = _cmd.get_progress(int(reset))
         finally:
            unlock_status()
         return r

      def check_redundant_open(file):
         found = 0
         for a in pymol.invocation.options.deferred:
            if a == file:
               found = 1
               break
         for a in sys.argv:
            if a == file:
               found = 1
               break;
         return found

      #--------------------------------------------------------------------
      # Feedback

      class fb_action:
         set = 0
         enable = 1
         disable = 2
         push = 3
         pop = 4

      fb_action_sc = Shortcut(fb_action.__dict__.keys())

      class fb_module:

      # This first set represents internal C systems

         all                       =0
         isomesh                   =1
         map                       =2
         matrix                    =3
         mypng                     =4
         triangle                  =5
         match                     =6
         raw                       =7
         isosurface                =8
         opengl                    =9

         color                     =10
         cgo                       =11
         feedback                  =12
         scene                     =13
         threads                   =14  
         symmetry                  =15
         ray                       =16
         setting                   =17
         object                    =18
         ortho                     =19
         movie                     =20
         python                    =21
         extrude                   =22
         rep                       =23
         shaker                    =24

         coordset                  =25
         distset                   =26
         gadgetset                 =27

         objectmolecule            =30
         objectmap                 =31
         objectmesh                =32
         objectdist                =33 
         objectcgo                 =34
         objectcallback            =35
         objectsurface             =36
         objectgadget              =37
         objectslice               =38

         repangle                  =43
         repdihederal              =44
         repwirebond               =45
         repcylbond                =46
         replabel                  =47
         repsphere                 =49
         repsurface                =50
         repmesh                   =51
         repdot                    =52
         repnonbonded              =53
         repnonbondedsphere        =54
         repdistdash               =55
         repdistlabel              =56
         repribbon                 =57
         repcartoon                =58
         sculpt                    =59
         vfont                     =60

         executive                 =70
         selector                  =71
         editor                    =72

         export                    =75
         ccmd                      =76
         api                       =77   

         main                      =80  

      # This second set, with negative indices
      # represent "python-only" subsystems

         parser                    =-1
         cmd                       =-2

      fb_module_sc = Shortcut(fb_module.__dict__.keys())

      class fb_mask:
         output =              0x01 # Python/text output
         results =             0x02
         errors =              0x04
         actions =             0x08
         warnings =            0x10
         details =             0x20
         blather =             0x40
         debugging =           0x80
         everything =          0xFF

      fb_mask_sc = Shortcut(fb_mask.__dict__.keys())

      fb_dict ={}

      for a in fb_module.__dict__.keys():
         vl = getattr(fb_module,a)
         if vl<0:
            fb_dict[vl] = 0x1F # default mask

      fb_debug = sys.stderr # can redirect python debugging output elsewhere if desred...

      def feedback(action="?",module="?",mask="?"):
         '''
DESCRIPTION

   "feedback" allows you to change the amount of information output by pymol.

USAGE

   feedback action,module,mask

   action is one of ['set','enable','disable']
   module is a space-separated list of strings or simply "all"
   mask is a space-separated list of strings or simply "everything"

NOTES:

   "feedback" alone will print a list of the available module choices

PYMOL API

   cmd.feedback(string action,string module,string mask)

EXAMPLES

   feedback enable, all , debugging
   feedback disable, selector, warnings actions
   feedback enable, main, blather

DEVELOPMENT TO DO

   Add a way of querying the current feedback settings.
   Check C source code to make source correct modules are being used.
   Check C source code to insure that all output is properly
   Update Python API and C source code to use "quiet" parameter as well.
      '''
         r = None

         # validate action

         if action=="?":
            print " feedback: possible actions: \nset, enable, disable"
            act_int = 0
         else:
            act_kee = fb_action_sc.interpret(action)
            if act_kee == None:
               print "Error: invalid feedback action '%s'."%action
               if _raising():
                  raise QuietException
               else:
                  return None
            elif not is_string(act_kee):
               print "Error: ambiguous feedback action '%s'."%action
               print action_amb
               if _raising():
                  raise QuietException
               else:
                  return None
            act_int = int(getattr(fb_action,act_kee))

         if (act_int<3) and ("?" in [action,module,mask]):
            if module=="?":
               print " feedback: Please specify module names:"
               lst = fb_module.__dict__.keys()
               lst.sort()
               for a in lst:
                  if a[0]!='_':
                     print "   ",a
            if mask=="?":
               print " feedback: Please specify masks:"
               lst = fb_mask.__dict__.keys()
               lst.sort()
               for a in lst:
                  if a[0]!='_':
                     print "   ",a
         else:
            if (act_int>=3):
               module='all'
               mask='everything'

            # validate and combine masks

            mask_int = 0
            mask_lst = string.split(mask)
            for mask in mask_lst:
               mask_kee = fb_mask_sc.interpret(mask)
               if mask_kee == None:
                  print "Error: invalid feedback mask '%s'."%mask
                  if _raising(): raise QuietException
                  else: return None
               elif not is_string(mask_kee):
                  print "Error: ambiguous feedback mask '%s'."%mask
                  if _raising(): raise QuietException
                  else: return None
               mask_int = int(getattr(fb_mask,mask_kee))

            # validate and iterate modules

            mod_lst = string.split(module)
            for module in mod_lst:
               mod_kee = fb_module_sc.interpret(module)
               if mod_kee == None:
                  print "Error: invalid feedback module '%s'."%module
                  if _raising(): raise QuietException
                  else: return None
               elif not is_string(mod_kee):
                  print "Error: ambiguous feedback module '%s'."%module
                  if _raising(): raise QuietException
                  else: return None
               mod_int = int(getattr(fb_module,mod_kee))
               if mod_int>=0:
                  try:
                     lock()
                     r = _cmd.set_feedback(act_int,mod_int,mask_int)
                  finally:
                     unlock()
               if mod_int<=0:
                  if mod_int:
                     if act_int==0:
                        fb_dict[mod_int] = mask_int
                     elif act_int==1:
                        fb_dict[mod_int] = fb_dict[mod_int] | mask_int
                     elif act_int==2:
                        fb_dict[mod_int] = fb_dict[mod_int] & ( 0xFF - mask_int )
                  else:
                     for mod_int in fb_dict.keys():
                        if act_int==0:
                           fb_dict[mod_int] = mask_int
                        elif act_int==1:
                           fb_dict[mod_int] = fb_dict[mod_int] | mask_int
                        elif act_int==2:
                           fb_dict[mod_int] = fb_dict[mod_int] & ( 0xFF - mask_int )
                  if _feedback(fb_module.feedback,fb_mask.debugging):
                      sys.stderr.write(" feedback: mode %d on %d mask %d\n"%(
                         act_int,mod_int,mask_int))
         return r

      #--------------------------------------------------------------------
      # internal API routines

      def _ray_anti_spawn(thread_info):
         # WARNING: internal routine, subject to change      
         # internal routine to support multithreaded raytracing
         thread_list = []
         for a in thread_info[1:]:
            t = threading.Thread(target=_cmd.ray_anti_thread,
                                 args=(a,))
            t.setDaemon(1)
            thread_list.append(t)
         for t in thread_list:
            t.start()
         _cmd.ray_anti_thread(thread_info[0])
         for t in thread_list:
            t.join()

      def _ray_hash_spawn(thread_info):
         # WARNING: internal routine, subject to change      
         # internal routine to support multithreaded raytracing
         thread_list = []
         for a in thread_info[1:2]:
            t = threading.Thread(target=_cmd.ray_hash_thread,
                                 args=(a,))
            t.setDaemon(1)
            t.start()
            thread_list.append(t)
         _cmd.ray_hash_thread(thread_info[0])
         for t in thread_list:
            t.join()

      def _ray_spawn(thread_info):
         # WARNING: internal routine, subject to change      
         # internal routine to support multithreaded raytracing
         thread_list = []
         for a in thread_info[1:]:
            t = threading.Thread(target=_cmd.ray_trace_thread,
                                 args=(a,))
            t.setDaemon(1)
            thread_list.append(t)
         for t in thread_list:
            t.start()
         _cmd.ray_trace_thread(thread_info[0])
         for t in thread_list:
            t.join()

      # status reporting

      def _feedback(module,mask): # feedback query routine
         # WARNING: internal routine, subject to change      
         r = 0
         module = int(module)
         mask = int(mask)
         if module>0:
            try:
               lock()
               r = _cmd.feedback(module,mask)
            finally:
               unlock()
         else:
            if fb_dict.has_key(module):
               r = fb_dict[module]&mask
         return r

      # do command (while API already locked)

      def _do(cmmd,log=0,echo=1):
         return _cmd.do(cmmd,log,echo)

      # movie rendering

      def _mpng(*arg): # INTERNAL
         # WARNING: internal routine, subject to change
         try:
            lock()   
            fname = arg[0]
            if re.search("\.png$",fname):
               fname = re.sub("\.png$","",fname)
            fname = os.path.expanduser(fname)
            fname = os.path.expandvars(fname)
            r = _cmd.mpng_(str(fname),int(arg[1]),int(arg[2]))
         finally:
            unlock()
         return r

      # loading

      
      def _load(oname,finfo,state,ftype,finish,discrete,
                quiet=1,multiplex=0,zoom=-1):
         # WARNING: internal routine, subject to change
         # caller must already hold API lock
         # NOTE: state index assumes 1-based state
         r = 1
         size = 0
         if ftype not in (loadable.model,loadable.brick):
            if ftype == loadable.r3d:
               import cgo
               obj = cgo.from_r3d(finfo)
               if obj:
                  _cmd.load_object(str(oname),obj,int(state)-1,loadable.cgo,
                                   int(finish),int(discrete),int(quiet),
                                   int(zoom))
               else:
                  print " load: couldn't load raster3d file."
            elif ftype == loadable.cc1: # ChemDraw 3D
               obj = io.cc1.fromFile(finfo)
               if obj:
                  _cmd.load_object(str(oname),obj,int(state)-1,loadable.model,
                                   int(finish),int(discrete),
                                   int(quiet),int(zoom))            
            else:
               if ftype in _load2str.keys() and (string.find(finfo,":")>1):
                  tmp_file = urllib.urlopen(finfo)
                  finfo = tmp_file.read(tmp_file) # WARNING: will block and hang -- thread instead?
                  tmp_file.close()
                  ftype = _load2str[ftype]
               r = _cmd.load(str(oname),finfo,int(state)-1,int(ftype),
                             int(finish),int(discrete),int(quiet),
                             int(multiplex),int(zoom))
         else:
            try:
               x = io.pkl.fromFile(finfo)
               if isinstance(x,types.ListType) or isinstance(x,types.TupleType):
                  for a in x:
                     r = _cmd.load_object(str(oname),a,int(state)-1,
                                          int(ftype),0,int(discrete),int(quiet),
                                          int(zoom))
                     if(state>0):
                        state = state + 1
                  _cmd.finish_object(str(oname))
               else:
                  r = _cmd.load_object(str(oname),x,
                                       int(state)-1,int(ftype),
                                       int(finish),int(discrete),
                                       int(quiet),int(zoom))
            except:
               print 'Error: can not load file "%s"' % finfo
         return r

      # function keys and other specials

      def _special(k,x,y,m=0): # INTERNAL (invoked when special key is pressed)
         # WARNING: internal routine, subject to change
         k=int(k)
         m=int(m)
         my_special = special
         if(m>0) and (m<5):
            my_special = (special, shft_special, ctrl_special, ctsh_special, alt_special)[m]
         if my_special.has_key(k):
            if my_special[k][1]:
               apply(my_special[k][1],my_special[k][2],my_special[k][3])
            else:
               key = my_special[k][0]
               if(m>0) and (m<5):
                  key = ('','SHFT-','CTRL-','CTSH-','ALT-')[m] + key
               if viewing.scene_dict.has_key(key):
                  scene(key)
               elif viewing.view_dict.has_key(key):
                  view(key)
         return None

      # control keys

      def _ctrl(k):
         # WARNING: internal routine, subject to change
         if ctrl.has_key(k):
            ck = ctrl[k]
            if ck[0]!=None:
               apply(ck[0],ck[1],ck[2])
         return None

      # alt keys

      def _alt(k):
         # WARNING: internal routine, subject to change
         if alt.has_key(k):
            ak=alt[k]
            if ak[0]!=None:
               apply(ak[0],ak[1],ak[2])
         return None

      # writing PNG files (thread-unsafe)

      def _png(a,quiet=1): # INTERNAL - can only be safely called by GLUT thread 
         # WARNING: internal routine, subject to change
         try:
            lock()   
            fname = a
            if not re.search("\.png$",fname):
               fname = fname +".png"
            fname = os.path.expanduser(fname)
            fname = os.path.expandvars(fname)         
            r = _cmd.png(str(fname),int(quiet))
         finally:
            unlock()
         return r

      # quitting (thread-specific)

      def _quit():
         # WARNING: internal routine, subject to change
         try:
            lock()
            try: # flush and close log if possible to avoid threading exception
               if pymol._log_file!=None:
                  try:
                     pymol._log_file.flush()
                  except:
                     pass
                  pymol._log_file.close()
                  del pymol._log_file
            except:
               pass
            if reaper!=None:
               try:
                  reaper.join()
               except:
                  pass
            r = _cmd.quit()
         finally:
            unlock()
         return r

      # screen redraws (thread-specific)

      def _refresh(swap_buffers=1):  # Only call with GLUT thread!
         # WARNING: internal routine, subject to change
         try:
            lock()
            if thread.get_ident() == pymol.glutThread:
               if swap_buffers:
                  r = _cmd.refresh_now()
               else:
                  r = _cmd.refresh()
            else:
               print "Error: Ignoring an unsafe call to cmd._refresh"
         finally:
            unlock()
         return r

      # stereo (platform dependent )

      def _sgi_stereo(flag): # SGI-SPECIFIC - bad bad bad
         # WARNING: internal routine, subject to change
         if sys.platform[0:4]=='irix':
            if os.path.exists("/usr/gfx/setmon"):
               if flag:
                  mode = os.environ.get('PYMOL_SGI_STEREO','1024x768_96s')
                  os.system("/usr/gfx/setmon -n "+mode)
               else:
                  mode = os.environ.get('PYMOL_SGI_MONO','72hz')
                  os.system("/usr/gfx/setmon -n "+mode)

      # color alias interpretation

      def _interpret_color(color):
         # WARNING: internal routine, subject to change
         _validate_color_sc()
         new_color = color_sc.interpret(color)
         if new_color:
            if is_string(new_color):
               return new_color
            else:
               color_sc.auto_err(color,'color')
         else:
            return color

      def _validate_color_sc():
         # WARNING: internal routine, subject to change
         global color_sc
         if color_sc == None: # update color shortcuts if needed
            lst = get_color_indices()
            lst.extend([('default',-1),('auto',-2),('current',-3),('atomic',-4)])
            color_sc = Shortcut(map(lambda x:x[0],lst))
            color_dict = {}
            for a in lst: color_dict[a[0]]=a[1]

      def _invalidate_color_sc():
         # WARNING: internal routine, subject to change
         global color_sc
         color_sc = None

      def _get_color_sc():
         # WARNING: internal routine, subject to change
         _validate_color_sc()
         return color_sc

      def _get_feedback(): # INTERNAL
         # WARNING: internal routine, subject to change
         l = []
         if lock_attempt():
            try:
               r = _cmd.get_feedback()
               while r:
                  l.append(r)
                  r = _cmd.get_feedback()
            finally:
               unlock()
         return l
      get_feedback = _get_feedback # for legacy compatibility

      def _fake_drag(): # internal
         lock()
         try:
            _cmd.fake_drag()
         finally:
            unlock()
         return 1
      # testing tools

      # for comparing floating point numbers calculated using
      # different FPUs

      def _dump_floats(lst,format="%7.3f",cnt=9):
         # WARNING: internal routine, subject to change
         c = cnt
         for a in lst:
            print format%a,
            c = c -1
            if c<=0:
               print
               c=cnt
         if c!=cnt:
            print

      def _dump_ufloats(lst,format="%7.3f",cnt=9):
         # WARNING: internal routine, subject to change
         c = cnt
         for a in lst:
            print format%abs(a),
            c = c -1
            if c<=0:
               print
               c=cnt
         if c!=cnt:
            print

      # HUH?
      def _adjust_coord(a,i,x):
         a.coord[i]=a.coord[i]+x
         return None

      def _raising():
         # WARNING: internal routine, subject to change
         return get_setting_legacy("raise_exceptions")

      #######################################################################
      # now import modules which depend on the above
      #######################################################################

      import editor

      #######################################################################
      # cmd module functions...
      #######################################################################

      def ready(): # INTERNAL
         # WARNING: internal routine, subject to change
         return _cmd.ready()

      def setup_global_locks(): # INTERNAL, OBSOLETE?
         # WARNING: internal routine, subject to change
         pass

      def null():
         pass

      # for extending the language

      def extend(name,function):
         '''
DESCRIPTION

   "extend" is an API-only function which binds a new external
   function as a command into the PyMOL scripting language.

PYMOL API

   cmd.extend(string name,function function)

PYTHON EXAMPLE

   def foo(moo=2): print moo
   cmd.extend('foo',foo)

   The following would now work within PyMOL:

   PyMOL>foo
   2
   PyMOL>foo 3
   3
   PyMOL>foo moo=5
   5
   PyMOL>foo ?
   Usage: foo [ moo ]

NOTES

   For security reasons, new PyMOL commands created using "extend" are
   not saved or restored in sessions.

SEE ALSO

   alias, api
         '''
         keyword[name] = [function, 0,0,',',parsing.STRICT]
         kwhash.append(name)
         help_sc.append(name)

      # for aliasing compound commands to a single keyword

      def alias(name,command):
         '''
DESCRIPTION

   "alias" allows you to bind a commonly used command to a single PyMOL keyword.

USAGE

   alias name, command-sequence

PYMOL API

   cmd.alias(string name,string command)

EXAMPLES

   alias go,load $TUT/1hpv.pdb; zoom 200/; show sticks, 200/ around 8
   go

NOTES

   For security reasons, new PyMOL commands created using "extend" are
   not saved or restored in sessions.

SEE ALSO

   extend, api
         '''
         keyword[name] = [eval("lambda :do('''%s ''')"%command), 0,0,',',parsing.STRICT]
         kwhash.append(name)

      def write_html_ref(file):
         lst = globals()
         f=open(file,'w')
         head = 'H2'
         f.write("<HTML><BODY><H1>Reference</H1>")
         kees = lst.keys()
         kees.sort()
         for a in kees:
            if hasattr(lst[a],'__doc__'):
               if a[0:1]!='_' and (a not in ['string','thread',
                                             'setup_global_locks',
                                             'real_system','sys','imp','glob','vl','time',
                                             'threading','repres','re','python_help','os',
                                             'fb_debug','fb_dict','ctrl','auto_arg','alt','a',
                                             'help_only','special','stereo_dict','toggle_dict',
                                             'palette_dict','types'
                                             ]):
                  doc = lst[a].__doc__
                  if is_string(doc):
                     if len(doc):
                        doc = string.strip(doc)
                        doc = string.replace(doc,"<","&lt;")
                        f.write("<HR SIZE=1><%s>"%head+a+"</%s>\n"%head)
                        f.write("<PRE>"+string.strip(doc)+"\n\n</PRE>")
         f.write("</BODY></HTML>")
         f.close()

      def dummy(*arg):
         '''
DESCRIPTION

   This is a dummy function which returns None.
         '''
         #'
         return None

      def python_help(*arg):
         r'''
DESCRIPTION

   You've asked for help on a Python keyword which is available from
   within the PyMOL command language.  Please consult the official
   Python documentation at http://www.python.org for detailed
   information on Python keywords.

   You may include Python blocks in your PyMOL command scripts, but do
   note that multi-line blocks of Python in PyMOL command files will
   require explicit continuation syntax in order to execute properly
   (see below).

   Generally, if you want to write Python block which span multiple
   lines, you will want to use ".py" file, and then use "extend" in
   order to expose your new code to the PyMOL command language.  This
   will give you better error checking and more predictable results.

EXAMPLES

   a=1
   while a<10: \
      print a \
      a=a+1

SEE ALSO

   extend, run, @
         '''
         return None

      #####################################################################
      # Here is where the PyMOL Command Language and API are built.
      #####################################################################


      # first we need to import a set of symbols into this module's local
      # namespace

      #--------------------------------------------------------------------
      from importing import \
           finish_object,      \
           load,               \
           load_brick,         \
           load_callback,      \
           load_cgo,           \
           load_embedded,      \
           load_map,           \
           load_model,         \
           load_object,        \
           load_traj,          \
           loadable,           \
           read_mmodstr,       \
           read_molstr,        \
           read_pdbstr,        \
           read_xplorstr,      \
           set_session,        \
           space              

      #--------------------------------------------------------------------
      import creating
      from creating import \
           copy,               \
           create,             \
           fragment,           \
           isodot,             \
           isolevel,           \
           isomesh,            \
           isosurface,         \
           slice_new,          \
           symexp,             \
           map_new,            \
           ramp_new

      #--------------------------------------------------------------------
      from commanding import \
           cls,                \
           delete,             \
           do,                 \
           log,                \
           log_close,          \
           log_open,           \
           quit,               \
           resume,             \
           splash,             \
           reinitialize,       \
           sync

      #--------------------------------------------------------------------
      import controlling
      from controlling import \
           button,             \
           config_mouse,       \
           mouse,              \
           mask,               \
           order,              \
           set_key,            \
           unmask,             \
           edit_mode

      #--------------------------------------------------------------------
      from querying import \
           angle,              \
           count_atoms,        \
           count_frames,       \
           count_states,       \
           dist,               \
           dihedral,           \
           distance,           \
           export_dots,        \
           find_pairs,         \
           get_angle,          \
           get_area,           \
           get_chains,         \
           get_color_index,    \
           get_color_indices,  \
           get_object_color_index, \
           get_object_list,    \
           get_color_tuple,    \
           get_atom_coords,    \
           get_dihedral,       \
           get_distance,       \
           get_extent,         \
           get_model,          \
           get_movie_locked,   \
           get_names,          \
           get_names_of_type,  \
           get_object_matrix, \
           get_phipsi,         \
           get_position,       \
           get_povray,         \
           get_renderer,       \
           get_symmetry,       \
           get_title,          \
           get_type,           \
           id_atom,            \
           identify,           \
           index,              \
           overlap,            \
           phi_psi

      #--------------------------------------------------------------------
      from selecting import \
           deselect,           \
           indicate,           \
           select,             \
           select_list,        \
           pop

      #--------------------------------------------------------------------
      from exporting import \
           png,                \
           export_coords,      \
           get_pdbstr,         \
           get_session,        \
           multisave,          \
           save               

      #--------------------------------------------------------------------
      import editing
      from editing import \
           alter,              \
           alter_list,         \
           alter_state,        \
           attach,             \
           bond,               \
           cycle_valence,      \
           deprotect,          \
           dss,                \
           edit,               \
           fix_chemistry,      \
           flag,               \
           fuse,               \
           h_add,              \
           h_fill,             \
           invert,             \
           iterate,            \
           iterate_state,      \
           map_set_border,     \
           map_double,         \
           matrix_transfer,    \
           matrix_reset,       \
           protect,            \
           push_undo,          \
           redo,               \
           remove,             \
           remove_picked,      \
           rename,             \
           replace,            \
           rotate,             \
           sculpt_purge,       \
           sculpt_deactivate,  \
           sculpt_activate,    \
           sculpt_iterate,     \
           set_dihedral,       \
           set_name,           \
           set_geometry,       \
           set_object_ttt,     \
           set_symmetry,       \
           set_title,          \
           smooth,             \
           sort,               \
           split_states,       \
           torsion,            \
           transform_object,   \
           transform_selection,\
           translate,          \
           translate_atom,     \
           unbond,             \
           undo,               \
           unpick,             \
           update

      #--------------------------------------------------------------------

      from externing import \
           cd,                 \
           ls,                 \
           paste,              \
           pwd,                \
           system

      #--------------------------------------------------------------------
      from wizarding import \
           get_wizard,         \
           get_wizard_stack,   \
           refresh_wizard,     \
           replace_wizard,     \
           set_wizard,         \
           set_wizard_stack,   \
           dirty_wizard,       \
           wizard

      #--------------------------------------------------------------------
      from fitting import \
           align,             \
           fit,               \
           rms,               \
           rms_cur,           \
           intra_fit,         \
           intra_rms,         \
           intra_rms_cur,     \
           pair_fit          

      #--------------------------------------------------------------------
      from preset import \
           simple,            \
           technical,         \
           pretty,         \
           publication

      #--------------------------------------------------------------------
      import moving
      from moving import \
           madd,              \
           mset,              \
           mclear,            \
           mdo,               \
           mappend,           \
           mmatrix,           \
           mdump,             \
           accept,            \
           decline,           \
           mpng,              \
           mview,             \
           forward,           \
           backward,          \
           rewind,            \
           middle,            \
           ending,            \
           mplay,             \
           mtoggle,           \
           mstop,             \
           mpng,              \
           mray,              \
           frame,             \
           get_movie_playing, \
           get_state,         \
           get_frame         

      #--------------------------------------------------------------------
      import viewing
      from viewing import \
           as,                 \
           bg_color,           \
           bg_colour,          \
           cartoon,            \
           clip,               \
           color,              \
           colour,             \
           del_colorection,    \
           dirty,              \
           disable,            \
           enable,             \
           full_screen,        \
           get_colorection,    \
           get_view,           \
           get_vis,            \
           get_scene_dict,     \
           hide,               \
           label,              \
           load_png,           \
           meter_reset,        \
           move,               \
           orient,             \
           origin,             \
           center,             \
           ray,                \
           rebuild,            \
           recolor,            \
           recolour,           \
           refresh,            \
           reset,              \
           rock,               \
           scene,              \
           set_color,          \
           set_colour,         \
           set_colorection,    \
           set_colorection_name,\
           set_vis,            \
           set_view,           \
           show,               \
           spectrum,           \
           stereo,             \
           toggle,             \
           turn,               \
           view,               \
           viewport,           \
           window,             \
           zoom
   #        rgbfunction,        \
   #        slice_lock,         \
   #        slice_unlock,       \
   #        slice_heightmap,    \

      #--------------------------------------------------------------------
      import setting
      from setting import \
           set,                 \
           get,                 \
           unset,               \
           get_setting_legacy,  \
           get_setting_tuple,   \
           get_setting_updates, \
           get_setting_text

      #--------------------------------------------------------------------
      import helping
      from helping import \
           show_help,           \
           help,                \
           commands

      #--------------------------------------------------------------------
      from experimenting import \
           check,              \
           dump,               \
           expfit,             \
           get_bond_print,     \
           fast_minimize,      \
           import_coords,      \
           load_coords,        \
           mem,                \
           minimize,           \
           spheroid,           \
           test

      #--------------------------------------------------------------------
      #from m4x import \
      #     metaphorics

      #--------------------------------------------------------------------
      # Modules which contain programs used explicity as "module.xxx"

      import util
      import movie

      # This is the main dictionary

      keyword = {

         # keyword : [ command, # min_arg, max_arg, separator, mode ]

         # NOTE: min_arg, max_arg, and separator, are hold-overs from the
         #       original PyMOL parser which will eventually be removed.
         #       all new commands should use NO_CHECK or STRICT modes
         #       which make much better use of built-in python features.
         'abort'         : [ dummy             , 0 , 0 , ''  , parsing.ABORT ],
         'accept'        : [ accept            , 0 , 0 , ''  , parsing.STRICT ],
         'alias'         : [ alias             , 0 , 0 , ''  , parsing.LITERAL1 ], # insecure
         'align'         : [ align             , 0 , 0 , ''  , parsing.STRICT ],
         'alter'         : [ alter             , 0 , 0 , ''  , parsing.LITERAL1 ], # insecure
         'alter_state'   : [ alter_state       , 0 , 0 , ''  , parsing.LITERAL2 ], # insecure
         'angle'         : [ angle             , 0 , 0 , ''  , parsing.STRICT ],          
         'as'            : [ as                , 0 , 0 , ''  , parsing.STRICT ],          
         'assert'        : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ], 
         'attach'        : [ attach            , 0 , 0 , ''  , parsing.STRICT ],
         'backward'      : [ backward          , 0 , 0 , ''  , parsing.STRICT ],
         'bg_color'      : [ bg_color          , 0 , 0 , ''  , parsing.STRICT ],
         'bond'          : [ bond              , 0 , 0 , ''  , parsing.STRICT ],
         'break'         : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],   
         'button'        : [ button            , 0 , 0 , ''  , parsing.STRICT ],
         'cartoon'       : [ cartoon           , 0 , 0 , ''  , parsing.STRICT ],
         'cd'            : [ cd                , 0 , 0 , ''  , parsing.STRICT ],
         'center'        : [ center            , 0 , 0 , ''  , parsing.STRICT ],     
         'check'         : [ check             , 0 , 0 , ''  , parsing.STRICT ],
         'class'         : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ], 
         'clip'          : [ clip              , 0 , 0 , ''  , parsing.STRICT ],
         'cls'           : [ cls               , 0 , 0 , ''  , parsing.STRICT ],
         'color'         : [ color             , 0 , 0 , ''  , parsing.STRICT ],
         'commands'      : [ helping.commands  , 0 , 0 , ''  , parsing.STRICT ],
         'config_mouse'  : [ config_mouse      , 0 , 0 , ''  , parsing.STRICT ],
         'continue'      : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'copy'          : [ copy              , 0 , 0 , ''  , parsing.LEGACY ],
         'count_atoms'   : [ count_atoms       , 0 , 0 , ''  , parsing.STRICT ],
         'count_frames'  : [ count_frames      , 0 , 0 , ''  , parsing.STRICT ],   
         'count_states'  : [ count_states      , 0 , 0 , ''  , parsing.STRICT ],
         'cycle_valence' : [ cycle_valence     , 0 , 0 , ''  , parsing.STRICT ],
         'create'        : [ create            , 0 , 0 , ''  , parsing.LEGACY ],
         'decline'       : [ decline           , 0 , 0 , ''  , parsing.STRICT ],      
         'delete'        : [ delete            , 0 , 0 , ''  , parsing.STRICT ],
         'def'           : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],   
         'del'           : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'deprotect'     : [ deprotect         , 0 , 0 , ''  , parsing.STRICT ],
         'deselect'      : [ deselect          , 0 , 0 , ''  , parsing.STRICT ],
         'dihedral'      : [ dihedral          , 0 , 0 , ''  , parsing.STRICT ],
         'dir'           : [ ls                , 0 , 0 , ''  , parsing.STRICT ],
         'disable'       : [ disable           , 0 , 0 , ''  , parsing.STRICT ],
         'distance'      : [ distance          , 0 , 0 , ''  , parsing.LEGACY ],   
         'dss'           : [ dss               , 0 , 0 , ''  , parsing.STRICT ],
         'dump'          : [ dump              , 0 , 0 , ''  , parsing.STRICT ],
         'dummy'         : [ dummy             , 0 , 0 , ''  , parsing.STRICT ],   
         'edit'          : [ edit              , 0 , 0 , ''  , parsing.STRICT ],
         'edit_mode'     : [ edit_mode         , 0 , 0 , ''  , parsing.STRICT ],
         'elif'          : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'else'          : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'embed'         : [ dummy             , 0 , 3 , ',' , parsing.EMBED  ],
         'enable'        : [ enable            , 0 , 0 , ''  , parsing.STRICT ],
         'ending'        : [ ending            , 0 , 0 , ''  , parsing.STRICT ],
         'except'        : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],      
         'exec'          : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],   
         'export_dots'   : [ export_dots       , 0 , 0 , ''  , parsing.STRICT ],
         'extend'        : [ extend            , 0 , 0 , ''  , parsing.STRICT ],
         'fast_minimize' : [ fast_minimize     , 1,  4 , ',' , parsing.SIMPLE ], # TO REMOVE
         'feedback'      : [ feedback          , 0,  0 , ''  , parsing.STRICT ],
         'fit'           : [ fit               , 0 , 0 , ''  , parsing.STRICT ],
         'finally'       : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'fix_chemistry' : [ fix_chemistry     , 0 , 0 , ''  , parsing.STRICT ],
         'flag'          : [ flag              , 0 , 0 , ''  , parsing.LEGACY ],
         'for'           : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'fork'          : [ helping.spawn     , 1 , 2 , ',' , parsing.SPAWN  ],
         'forward'       : [ forward           , 0 , 0 , ''  , parsing.STRICT ],
         'fragment'      : [ fragment          , 0 , 0 , ''  , parsing.STRICT ],
         'full_screen'   : [ full_screen       , 0 , 0 , ''  , parsing.STRICT ],
         'fuse'          : [ fuse              , 0 , 0 , ''  , parsing.STRICT ],
         'frame'         : [ frame             , 0 , 0 , ''  , parsing.STRICT ],
         'get'           : [ get               , 0 , 0 , ''  , parsing.STRICT ],
         'get_angle'     : [ get_angle         , 0 , 0 , ''  , parsing.STRICT ],      
         'get_area'      : [ get_area          , 0 , 0 , ''  , parsing.STRICT ],
         'get_chains'    : [ get_chains        , 0 , 0 , ''  , parsing.STRICT ],
         'get_dihedral'  : [ get_dihedral      , 0 , 0 , ''  , parsing.STRICT ],
         'get_distance'  : [ get_distance      , 0 , 0 , ''  , parsing.STRICT ],
         'get_extent'    : [ get_extent        , 0 , 0 , ''  , parsing.STRICT ],
         'get_position'  : [ get_position      , 0 , 0 , ''  , parsing.STRICT ],
         'get_symmetry'  : [ get_symmetry      , 0 , 0 , ''  , parsing.STRICT ],
         'get_title'     : [ get_title         , 0 , 0 , ''  , parsing.STRICT ],   
         'get_type'      : [ get_type          , 0 , 0 , ''  , parsing.STRICT ],
         'get_view'      : [ get_view          , 0 , 0 , ''  , parsing.STRICT ],
         'global'        : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],   
         'h_add'         : [ h_add             , 0 , 0 , ''  , parsing.STRICT ],
         'h_fill'        : [ h_fill            , 0 , 0 , ''  , parsing.STRICT ],
         'help'          : [ help              , 0 , 0 , ''  , parsing.STRICT ],
         'hide'          : [ hide              , 0 , 0 , ''  , parsing.STRICT ],
         'id_atom'       : [ id_atom           , 0 , 0 , ''  , parsing.STRICT ],
         'identify'      : [ identify          , 0 , 0 , ''  , parsing.STRICT ],
         'if'            : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'import'        : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],   
         'index'         : [ index             , 0 , 0 , ''  , parsing.STRICT ],
         'indicate'      : [ indicate          , 0 , 0 , ''  , parsing.STRICT ],   
         'intra_fit'     : [ intra_fit         , 0 , 0 , ''  , parsing.STRICT ],
         'intra_rms'     : [ intra_rms         , 0 , 0 , ''  , parsing.STRICT ],
         'intra_rms_cur' : [ intra_rms_cur     , 0 , 0 , ''  , parsing.STRICT ],
         'invert'        : [ invert            , 0 , 0 , ''  , parsing.STRICT ],
         'isodot'        : [ isodot            , 0 , 0 , ''  , parsing.LEGACY ],
         'isolevel'      : [ isolevel           , 0 , 0 , '' , parsing.STRICT ],      
         'isomesh'       : [ isomesh           , 0 , 0 , ''  , parsing.LEGACY ],
         'isosurface'    : [ isosurface        , 0 , 0 , ''  , parsing.LEGACY ],   
         'iterate'       : [ iterate           , 0 , 0 , ''  , parsing.LITERAL1 ], # insecure
         'iterate_state' : [ iterate_state     , 0 , 0 , ''  , parsing.LITERAL2 ], # insecure
         'label'         : [ label             , 0 , 0 , ''  , parsing.LITERAL1 ], # insecure
         'load'          : [ load              , 0 , 0 , ''  , parsing.STRICT ],
         'space'         : [ space             , 0 , 0 , ''  , parsing.STRICT ],
         'load_embedded' : [ load_embedded     , 0 , 0 , ''  , parsing.STRICT ],
         'load_png'      : [ load_png          , 0 , 0 , ''  , parsing.STRICT ],
         'load_traj'     : [ load_traj         , 0 , 0 , ''  , parsing.STRICT ],
         'log'           : [ log               , 0 , 0 , ''  , parsing.STRICT ],
         'log_close'     : [ log_close         , 0 , 0 , ''  , parsing.STRICT ],
         'log_open'      : [ log_open          , 0 , 0 , ''  , parsing.STRICT ],
         'ls'            : [ ls                , 0 , 0 , ''  , parsing.STRICT ],
         'madd'          : [ madd              , 0 , 0 , ''  , parsing.STRICT ],
         'mask'          : [ mask              , 0 , 0 , ''  , parsing.STRICT ],
         'map_set_border': [ map_set_border    , 0 , 0 , ''  , parsing.STRICT ],
         'map_double'    : [ map_double        , 0 , 0 , ''  , parsing.STRICT ],      
         'map_new'       : [ map_new           , 0 , 0 , ''  , parsing.STRICT ],    
         'mappend'       : [ mappend           , 2 , 2 , ':' , parsing.MOVIE  ],
         'matrix_reset'  : [ matrix_reset      , 0 , 0 , ''  , parsing.STRICT ],         
         'matrix_transfer': [ matrix_transfer  , 0 , 0 , ''  , parsing.STRICT ],
         'mem'           : [ mem               , 0 , 0 , ''  , parsing.STRICT ],
         'meter_reset'   : [ meter_reset       , 0 , 0 , ''  , parsing.STRICT ],
         'move'          : [ move              , 0 , 0 , ''  , parsing.STRICT ],
         'mset'          : [ mset              , 0 , 0 , ''  , parsing.STRICT ],
         'mdo'           : [ mdo               , 2 , 2 , ':' , parsing.MOVIE  ],
         'mdump'         : [ mdump             , 0 , 0 , ''  , parsing.STRICT ],      
         'mpng'          : [ mpng              , 0 , 0 , ''  , parsing.STRICT ],
         'mplay'         : [ mplay             , 0 , 0 , ''  , parsing.STRICT ],
         'mtoggle'       : [ mtoggle           , 0 , 0 , ''  , parsing.STRICT ],         
         'mray'          : [ mray              , 0 , 0 , ''  , parsing.STRICT ],
         'mstop'         : [ mstop             , 0 , 0 , ''  , parsing.STRICT ],
         'mclear'        : [ mclear            , 0 , 0 , ''  , parsing.STRICT ],
         'middle'        : [ middle            , 0 , 0 , ''  , parsing.STRICT ],
         'minimize'      : [ minimize          , 0 , 4 , ',' , parsing.SIMPLE ], # TO REMOVE
         'mmatrix'       : [ mmatrix           , 0 , 0 , ''  , parsing.STRICT ],
         'mouse'         : [ mouse             , 0 , 0 , ''  , parsing.STRICT ],
         'multisave'     : [ multisave         , 0 , 0 , ''  , parsing.STRICT ],
         'mview'         : [ mview             , 0 , 0 , ''  , parsing.STRICT ],
         'origin'        : [ origin            , 0 , 0 , ''  , parsing.STRICT ],
         'orient'        : [ orient            , 0 , 0 , ''  , parsing.STRICT ],
         'overlap'       : [ overlap           , 0 , 0 , ''  , parsing.STRICT ],
         'pair_fit'      : [ pair_fit          , 2 ,98 , ',' , parsing.SIMPLE ],
         'pass'          : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'phi_psi'       : [ phi_psi           , 0 , 0 , ''  , parsing.STRICT ],
         'pop'           : [ pop               , 0 , 0 , ''  , parsing.STRICT ],
         'protect'       : [ protect           , 0 , 0 , ''  , parsing.STRICT ],
         'push_undo'     : [ push_undo         , 0 , 0 , ''  , parsing.STRICT ],   
         'pwd'           : [ pwd               , 0 , 0 , ''  , parsing.STRICT ],
         'raise'         : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'ramp_new'      : [ ramp_new          , 0 , 0 , ''  , parsing.STRICT ],      
         'ray'           : [ ray               , 0 , 0 , ''  , parsing.STRICT ],
         'rebuild'       : [ rebuild           , 0 , 0 , ''  , parsing.STRICT ],
         'recolor'       : [ recolor           , 0 , 0 , ''  , parsing.STRICT ],   
         'redo'          : [ redo              , 0 , 0 , ''  , parsing.STRICT ],
         'reinitialize'  : [ reinitialize      , 0 , 0 , ''  , parsing.STRICT ],      
         'refresh'       : [ refresh           , 0 , 0 , ''  , parsing.STRICT ],
         'refresh_wizard' : [ refresh_wizard   , 0 , 0 , ''  , parsing.STRICT ],
         'remove'        : [ remove            , 0 , 0 , ''  , parsing.STRICT ],
         'remove_picked' : [ remove_picked     , 0 , 0 , ''  , parsing.STRICT ],
         'rename'        : [ rename            , 0 , 0 , ''  , parsing.STRICT ],
         'order'         : [ order             , 0 , 0 , ''  , parsing.STRICT ],
         'replace'       : [ replace           , 0 , 0 , ''  , parsing.STRICT ],
         'replace_wizard': [ replace_wizard    , 0 , 0 , ''  , parsing.STRICT ],
         'reset'         : [ reset             , 0 , 0 , ''  , parsing.STRICT ],
         'resume'        : [ resume            , 0 , 0 , ''  , parsing.STRICT ],
         'return'        : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],   
         'rewind'        : [ rewind            , 0 , 0 , ''  , parsing.STRICT ],
   #      'rgbfunction'   : [ rgbfunction       , 0 , 0 , ''  , parsing.LEGACY ],         
         'rock'          : [ rock              , 0 , 0 , ''  , parsing.STRICT ],
         'rotate'        : [ rotate            , 0 , 0 , ''  , parsing.STRICT ],
         'run'           : [ helping.run       , 1 , 2 , ',' , parsing.RUN    ], # insecure
         'rms'           : [ rms               , 0 , 0 , ''  , parsing.STRICT ],
         'rms_cur'       : [ rms_cur           , 0 , 0 , ''  , parsing.STRICT ],
         'save'          : [ save              , 0 , 0 , ''  , parsing.STRICT ],
         'scene'         : [ scene             , 0 , 0 , ''  , parsing.STRICT ],
         'sculpt_purge'  : [ sculpt_purge      , 0 , 0 , ''  , parsing.STRICT ],   
         'sculpt_deactivate': [ sculpt_deactivate,0, 0 , ''  , parsing.STRICT ],
         'sculpt_activate': [ sculpt_activate  , 0 , 0 , ''  , parsing.STRICT ],
         'sculpt_iterate': [ sculpt_iterate    , 0 , 0 , ''  , parsing.STRICT ],
         'spectrum'      : [ spectrum          , 0 , 0 , ''  , parsing.STRICT ],
         'select'        : [ select            , 0 , 0 , ''  , parsing.LEGACY ],
         'set'           : [ set               , 0 , 0 , ''  , parsing.LEGACY ],
         'set_color'     : [ set_color         , 0 , 0 , ''  , parsing.LEGACY ],
         'set_dihedral'  : [ set_dihedral      , 0 , 0 , ''  , parsing.STRICT ],
         'set_name'      : [ set_name          , 0 , 0 , ''  , parsing.STRICT ],
         'set_geometry'  : [ set_geometry      , 0 , 0 , ''  , parsing.STRICT ],
         'set_symmetry'  : [ set_symmetry      , 0 , 0 , ''  , parsing.STRICT ],         
         'set_title'     : [ set_title         , 0 , 0 , ''  , parsing.STRICT ],   
         'set_key'       : [ set_key           , 0 , 0 , ''  , parsing.STRICT ], # API only
         'set_view'      : [ set_view          , 0 , 0 , ''  , parsing.STRICT ],   
         'show'          : [ show              , 0 , 0 , ''  , parsing.STRICT ],
         'slice_new'     : [ slice_new         , 0 , 0 , ''  , parsing.STRICT ],
   #      'slice_lock'    : [ slice_lock        , 0 , 0 , ''  , parsing.LEGACY ],
   #      'slice_unlock'  : [ slice_unlock      , 0 , 0 , ''  , parsing.LEGACY ],
         'smooth'        : [ smooth            , 0 , 0 , ''  , parsing.STRICT ],
         'sort'          : [ sort              , 0 , 0 , ''  , parsing.STRICT ],
         'spawn'         : [ helping.spawn     , 1 , 2 , ',' , parsing.SPAWN  ], # insecure
         'spheroid'      : [ spheroid          , 0 , 0 , ''  , parsing.STRICT ],
         'splash'        : [ splash            , 0 , 0 , ''  , parsing.STRICT ],
         'split_states'  : [ split_states      , 0 , 0 , ''  , parsing.STRICT ],
         '_special'      : [ _special          , 0 , 0 , ''  , parsing.STRICT ],
         'stereo'        : [ stereo            , 0 , 0 , ''  , parsing.STRICT ],
         'symexp'        : [ symexp            , 0 , 0 , ''  , parsing.LEGACY ],
         'system'        : [ system            , 0 , 0 , ''  , parsing.LITERAL ],
         'test'          : [ test              , 0 , 0 , ''  , parsing.STRICT ],
         'toggle'        : [ toggle            , 0 , 0 , ''  , parsing.STRICT ],      
         'torsion'       : [ torsion           , 0 , 0 , ''  , parsing.STRICT ], # vs toggle_object
         'translate'     : [ translate         , 0 , 0 , ''  , parsing.STRICT ],
         'try'           : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],
         'turn'          : [ turn              , 0 , 0 , ''  , parsing.STRICT ],
         'quit'          : [ quit              , 0 , 0 , ''  , parsing.STRICT ],
         '_quit'         : [ _quit             , 0 , 0 , ''  , parsing.STRICT ],
         'png'           : [ png               , 0 , 0 , ''  , parsing.STRICT ],
         'unbond'        : [ unbond            , 0 , 0 , ''  , parsing.STRICT ],
         'unpick'        : [ unpick            , 0 , 0 , ''  , parsing.STRICT ],
         'undo'          : [ undo              , 0 , 0 , ''  , parsing.STRICT ],
         'unmask'        : [ unmask            , 0 , 0 , ''  , parsing.STRICT ],
         'unprotect'     : [ deprotect         , 0 , 0 , ''  , parsing.STRICT ],
         'unset'         : [ unset             , 0 , 0 , ''  , parsing.STRICT ],   
         'update'        : [ update            , 0 , 0 , ''  , parsing.STRICT ],
         'view'          : [ view              , 0 , 0 , ''  , parsing.STRICT ],   
         'viewport'      : [ viewport          , 0 , 0 , ''  , parsing.STRICT ],
         'window'        : [ window            , 0 , 0 , ''  , parsing.STRICT ],         
         'while'         : [ python_help       , 0 , 0 , ''  , parsing.PYTHON ],   
         'wizard'        : [ wizard            , 0 , 0 , ''  , parsing.STRICT ],
         'zoom'          : [ zoom              , 0 , 0 , ''  , parsing.STRICT ],
      # utility programs
         'util.cbag'     : [ util.cbag         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbac'     : [ util.cbac         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbay'     : [ util.cbay         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbas'     : [ util.cbas         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbap'     : [ util.cbap         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbak'     : [ util.cbak         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbaw'     : [ util.cbaw         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbab'     : [ util.cbab         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbao'     : [ util.cbao         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbam'     : [ util.cbam         , 0 , 0 , ''  , parsing.STRICT ],
         'util.cbc'      : [ util.cbc          , 0 , 0 , ''  , parsing.STRICT ],
         'util.chainbow' : [ util.chainbow     , 0 , 0 , ''  , parsing.STRICT ],
         'util.colors'   : [ util.colors       , 0 , 0 , ''  , parsing.STRICT ],
         'util.mrock'    : [ util.mrock        , 0 , 0 , ''  , parsing.STRICT ], # LEGACY
         'util.mroll'    : [ util.mroll        , 0 , 0 , ''  , parsing.STRICT ], # LEGACY
         'util.ss'       : [ util.ss           , 0 , 0 , ''  , parsing.STRICT ],# secondary structure
         'util.rainbow'  : [ util.rainbow      , 0 , 0 , ''  , parsing.STRICT ],
      # movie programs
         'movie.rock'    : [ movie.rock        , 0 , 0 , ''  , parsing.STRICT ],
         'movie.roll'    : [ movie.roll        , 0 , 0 , ''  , parsing.STRICT ],
         'movie.load'    : [ movie.load        , 0 , 0 , ''  , parsing.STRICT ],
         'movie.zoom'    : [ movie.zoom        , 0 , 0 , ''  , parsing.STRICT ],
         'movie.screw'   : [ movie.screw       , 0 , 0 , ''  , parsing.STRICT ],
         'movie.sweep'   : [ movie.sweep       , 0 , 0 , ''  , parsing.STRICT ],
         'movie.pause'   : [ movie.pause       , 0 , 0 , ''  , parsing.STRICT ],               
         'movie.nutate'  : [ movie.nutate      , 0 , 0 , ''  , parsing.STRICT ],
         'movie.tdroll'  : [ movie.tdroll      , 0 , 0 , ''  , parsing.STRICT ],
      # activate metaphorics extensions
      #   'metaphorics'   : [ metaphorics       , 0 , 0 , ''  , parsing.STRICT ],
         }

      kwhash = Shortcut(keyword.keys())

      # Aliases for Mother England (NOTE: not hashed)

      keyword['colour'] = keyword['color']
      keyword['set_colour'] = keyword['set_color']
      keyword['recolour'] = keyword['recolor']
      keyword['bg_colour'] = keyword['bg_color']

      # informational, or API-only functions which don't exist in the
      # PyMOL command language namespace

      help_only = {  
         'api'           : [ helping.api          , 0 , 0 , '' , 0 ],
         'editing'       : [ helping.editing      , 0 , 0 , '' , 0 ],  
         'edit_keys'     : [ helping.edit_keys    , 0 , 0 , '' , 0 ],
         'examples'      : [ helping.examples     , 0 , 0 , '' , 0 ],
         'faster'        : [ helping.faster       , 0 , 0 , '' , 0 ],
         'get_pdbstr'    : [ get_pdbstr        , 0 , 0 , ''  , 0 ],
         'get_names'     : [ get_names             , 0 , 0 , '' , 0 ],
         'get_type'      : [ get_type              , 0 , 0 , '' , 0 ],
         'keyboard'      : [ helping.keyboard     , 0 , 0 , '' , 0 ],
         'launching'     : [ helping.launching    , 0 , 0 , '' , 0 ],
         'load_model'    : [ load_model            , 0 , 0 , '' , 0 ],
         'mouse'         : [ helping.mouse        , 0 , 0 , '' , 0 ],
         'movies'        : [ helping.movies       , 0 , 0 , '' , 0 ],
         'python_help'   : [ python_help          , 0 , 0 , '' , 0 ],        
         'povray'        : [ helping.povray       , 0 , 0 , '' , 0 ],
         'read_molstr'   : [ read_molstr           , 0 , 0 , '' , 0 ],
         'read_pdbstr'   : [ read_pdbstr           , 0 , 0 , '' , 0 ],      
         'release'       : [ helping.release      , 0 , 0 , '' , 0 ],   
         'selections'    : [ helping.selections   , 0 , 0 , '' , 0 ],
         'sync'          : [ sync                 , 0 , 0 , '' , 0],
         'transparency'  : [ helping.transparency , 0 , 0 , '' , 0 ],
         '@'             : [ helping.at_sign      , 0 , 0 , '' , 0 ],  
      }

      help_sc = Shortcut(keyword.keys()+help_only.keys())


      special = {
         1        : [ 'F1'        , None                   , () , {} ],
         2        : [ 'F2'        , None                   , () , {} ],
         3        : [ 'F3'        , None                   , () , {} ],
         4        : [ 'F4'        , None                   , () , {} ],
         5        : [ 'F5'        , None                   , () , {} ],
         6        : [ 'F6'        , None                   , () , {} ],
         7        : [ 'F7'        , None                   , () , {} ],
         8        : [ 'F8'        , None                   , () , {} ],
         9        : [ 'F9'        , None                   , () , {} ],
         10       : [ 'F10'       , None                   , () , {} ],
         11       : [ 'F11'       , None                   , () , {} ],
         12       : [ 'F12'       , None                   , () , {} ],
         100      : [ 'left'      , backward               , () , {} ],
         101      : [ 'up'        , None                   , () , {} ],
         102      : [ 'right'     , forward                , () , {} ],
         103      : [ 'down'      , None                   , () , {} ],
         104      : [ 'pgup'      , scene                  , ('','previous') , {} ],
         105      : [ 'pgdn'      , scene                  , ('','next') , {} ],
         106      : [ 'home'      , zoom                   , () ,  {'animate':-1} ],
         107      : [ 'end'       , mtoggle                , () , {} ],
         108      : [ 'insert'    , rock                   , () , {} ]   
      }

      shft_special = {
         1        : [ 'F1'        , None                   , () , {} ],
         2        : [ 'F2'        , None                   , () , {} ],
         3        : [ 'F3'        , None                   , () , {} ],
         4        : [ 'F4'        , None                   , () , {} ],
         5        : [ 'F5'        , None                   , () , {} ],
         6        : [ 'F6'        , None                   , () , {} ],
         7        : [ 'F7'        , None                   , () , {} ],
         8        : [ 'F8'        , None                   , () , {} ],
         9        : [ 'F9'        , None                   , () , {} ],
         10       : [ 'F10'       , None                   , () , {} ],
         11       : [ 'F11'       , None                   , () , {} ],
         12       : [ 'F12'       , None                   , () , {} ],
         100      : [ 'left'      , backward               , () , {} ],
         101      : [ 'up'        , None                   , () , {} ],
         102      : [ 'right'     , forward                , () , {} ],
         103      : [ 'down'      , None                   , () , {} ],
         104      : [ 'pgup'      , scene                  , ('','previous') , {} ],
         105      : [ 'pgdn'      , scene                  , ('','next') , {} ],
         106      : [ 'home'      , rewind                 , () ,  {'animate':-1} ],
         107      : [ 'end'       , ending                 , () , {} ],
         108      : [ 'insert'    , rock                   , () , {} ]   
      }

      alt_special = { # NOTE: some OSes/Windowing systems intercept ALT-Fn keys.
         1        : [ 'F1'        , None                   , () , {} ],
         2        : [ 'F2'        , None                   , () , {} ],
         3        : [ 'F3'        , None                   , () , {} ],
         4        : [ 'F4'        , None                   , () , {} ],
         5        : [ 'F5'        , None                   , () , {} ],
         6        : [ 'F6'        , None                   , () , {} ],
         7        : [ 'F7'        , None                   , () , {} ],
         8        : [ 'F8'        , None                   , () , {} ],
         9        : [ 'F9'        , None                   , () , {} ],
         10       : [ 'F10'       , None                   , () , {} ],
         11       : [ 'F11'       , None                   , () , {} ],
         12       : [ 'F12'       , None                   , () , {} ],
         100      : [ 'left'      , backward               , () , {} ],
         101      : [ 'up'        , None                   , () , {} ],
         102      : [ 'right'     , forward                , () , {} ],
         103      : [ 'down'      , None                   , () , {} ],
         104      : [ 'pgup'      , rewind                 , () , {} ],
         105      : [ 'pgdn'      , ending                 , () , {} ],
         106      : [ 'home'      , zoom                   , () ,  {'animate':-1} ],
         107      : [ 'end'       , ending                 , () , {} ],
         108      : [ 'insert'    , rock                   , () , {} ]   
      }

      ctrl_special = { # NOTE: some OSes/Windowing systems intercept CTRL-Fn keys.
         1        : [ 'F1'        , scene  , ('F1','store') , {} ],
         2        : [ 'F2'        , scene,('F2','store')    , {} ],
         3        : [ 'F3'        , scene,('F3','store')    , {} ],
         4        : [ 'F4'        , scene,('F4','store')    , {} ],
         5        : [ 'F5'        , scene,('F5','store')    , {} ],
         6        : [ 'F6'        , scene,('F6','store')    , {} ],
         7        : [ 'F7'        , scene,('F7','store')    , {} ],
         8        : [ 'F8'        , scene,('F8','store')    , {} ],
         9        : [ 'F9'        , scene,('F9','store')    , {} ],
         10       : [ 'F10'       , scene,('F10','store')   , {} ],
         11       : [ 'F11'       , scene,('F11','store')   , {} ],
         12       : [ 'F12'       , scene,('F12','store')   , {} ],
         100      : [ 'left'      , backward               , () , {} ],
         101      : [ 'up'        , None                   , () , {} ],
         102      : [ 'right'     , forward                , () , {} ],
         103      : [ 'down'      , None                   , () , {} ],
         104      : [ 'pgup'      , scene                  , ('','insert_before') , {} ],
         105      : [ 'pgdn'      , scene                  , ('','insert_after') , {} ],
         106      : [ 'home'      , zoom                   , () , {'animate':-1} ],
         107      : [ 'end'       , scene                  , ('new','store') , {} ],
         108      : [ 'insert'    , scene                  , ('auto','store') , {} ]   
      }

      ctsh_special = { # NOTE: some OSes/Windowing systems intercept CTRL-Fn keys.
         1        : [ 'F1'        , scene,('SHFT-F1','store') , {} ],
         2        : [ 'F2'        , scene,('SHFT-F2','store')    , {} ],
         3        : [ 'F3'        , scene,('SHFT-F3','store')    , {} ],
         4        : [ 'F4'        , scene,('SHFT-F4','store')    , {} ],
         5        : [ 'F5'        , scene,('SHFT-F5','store')    , {} ],
         6        : [ 'F6'        , scene,('SHFT-F6','store')    , {} ],
         7        : [ 'F7'        , scene,('SHFT-F7','store')    , {} ],
         8        : [ 'F8'        , scene,('SHFT-F8','store')    , {} ],
         9        : [ 'F9'        , scene,('SHFT-F9','store')    , {} ],
         10       : [ 'F10'       , scene,('SHFT-F10','store')   , {} ],
         11       : [ 'F11'       , scene,('SHFT-F11','store')   , {} ],
         12       : [ 'F12'       , scene,('SHFT-F12','store')   , {} ],
         100      : [ 'left'      , backward               , () , {} ],
         101      : [ 'up'        , None                   , () , {} ],
         102      : [ 'right'     , forward                , () , {} ],
         103      : [ 'down'      , None                   , () , {} ],
         104      : [ 'pgup'      , scene                  , ('','insert_before') , {} ],
         105      : [ 'pgdn'      , ending                 , ('','insert_after') , {} ],
         106      : [ 'home'      , zoom                 , () ,  {'animate':-1} ],
         107      : [ 'end'       , mtoggle                , () , {} ],
         108      : [ 'insert'    , rock                   , () , {} ]   
      }

      def auto_measure():
         lst = get_names("selections")
         if "pk1" in lst:
            if "pk2" in lst:
               if "pk3" in lst:
                  if "pk4" in lst:
                     dihedral()
                  else:
                     angle()
               else:
                  distance()
         unpick()   
         

      ctrl = {
         'A' : [ redo                   , () , {}],
         'B' : [ replace                , ('Br',1,1), {} ],
         'C' : [ replace                , ('C',4,4), {} ],
         'D' : [ remove_picked          , () , {'quiet':0} ],
         'E' : [ invert                 , () , {'quiet':0} ],      
         'F' : [ replace                , ('F',1,1), {} ],   
         'G' : [ replace                , ('H',1,1), {} ],
         'I' : [ replace                , ('I',1,1), {} ],
         'J' : [ alter                  , ('pk1','formal_charge=-1.0'), {} ],
         'K' : [ alter                  , ('pk1','formal_charge =1.0'), {} ],
         'L' : [ replace                , ('Cl',1,1) , {}],
         'N' : [ replace                , ('N',4,3) , {}],
         'O' : [ replace                , ('O',4,2) , {}],   
         'P' : [ replace                , ('P',4,1) , {}],
         'Q' : [ None                   , () , {}],   
         'R' : [ h_fill                 , () , {} ],   
         'S' : [ replace                , ('S',4,2) , {}],
         'T' : [ lambda a,b,c=bond,u=unpick: (c(a,b),u()) , ('pk1','pk2') , {} ],   
         'U' : [ alter                  , ('pk1','formal_charge =0.0') , {}],
         'W' : [ cycle_valence          , () , {}],
#         'X' : [ lambda a,b,c,d=dist,u=unpick:(d(a,b,c),u()), (None,'pk1','pk2') , {} ],
         'X' : [ auto_measure           , () , {} ],   
         'Y' : [ attach                 , ('H',1,1) , {} ],
         'Z' : [ undo                   , () , {} ],   
         }

      alt = {
         '1' : [ editor.attach_fragment  , ("pk1","formamide",5,0), {}],
         '2' : [ editor.attach_fragment  , ("pk1","formamide",4,0), {}],
         '3' : [ editor.attach_fragment  , ("pk1","sulfone",3,1), {}],
         '4' : [ editor.attach_fragment  , ("pk1","cyclobutane",4,0), {}],
         '5' : [ editor.attach_fragment  , ("pk1","cyclopentane",5,0), {}],
         '6' : [ editor.attach_fragment  , ("pk1","cyclohexane",7,0), {}],
         '7' : [ editor.attach_fragment  , ("pk1","cycloheptane",8,0), {}],
         '8' : [ editor.attach_fragment  , ("pk1","cyclopentadiene",5,0), {}],
         '9' : [ editor.attach_fragment  , ("pk1","benzene",6,0), {}],
         '0' : [ editor.attach_fragment  , ("pk1","formaldehyde",2,0), {}],
         'a' : [ editor.attach_amino_acid, ("pk1","ala"), {}],
         'b' : [ editor.attach_amino_acid, ("pk1","ace"), {}],                                 
         'c' : [ editor.attach_amino_acid, ("pk1","cys"), {}],
         'd' : [ editor.attach_amino_acid, ("pk1","asp"), {}],
         'e' : [ editor.attach_amino_acid, ("pk1","glu"), {}],
         'f' : [ editor.attach_amino_acid, ("pk1","phe"), {}],

         'g' : [ editor.attach_amino_acid, ("pk1","gly"), {}],
         'h' : [ editor.attach_amino_acid, ("pk1","his"), {}],
         'i' : [ editor.attach_amino_acid, ("pk1","ile"), {}],

         'j' : [ editor.attach_fragment,   ("pk1","acetylene",2,0), {}],
         'k' : [ editor.attach_amino_acid, ("pk1","lys"), {}],
         'l' : [ editor.attach_amino_acid, ("pk1","leu"), {}],

         'm' : [ editor.attach_amino_acid, ("pk1","met"), {}],
         'n' : [ editor.attach_amino_acid, ("pk1","asn"), {}],
         'p' : [ editor.attach_amino_acid, ("pk1","pro"), {}],
         'q' : [ editor.attach_amino_acid, ("pk1","gln"), {}],
         'r' : [ editor.attach_amino_acid, ("pk1","arg"), {}],

         's' : [ editor.attach_amino_acid, ("pk1","ser"), {}],
         't' : [ editor.attach_amino_acid, ("pk1","thr"), {}],
         'v' : [ editor.attach_amino_acid, ("pk1","val"), {}],
         'w' : [ editor.attach_amino_acid, ("pk1","trp"), {}],
         'y' : [ editor.attach_amino_acid, ("pk1","tyr"), {}],
         'z' : [ editor.attach_amino_acid, ("pk1","nme"), {}],         
         }


      selection_sc = lambda sc=Shortcut,gn=get_names:sc(gn('public')+['all'])
      object_sc = lambda sc=Shortcut,gn=get_names:sc(gn('objects'))
      map_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:map'))

      # Table for argument autocompletion

      auto_arg =[
   # 1st
         {
         'align'          : [ selection_sc           , 'selection'       , ','  ],
         'alter'          : [ selection_sc           , 'selection'       , ''   ],
         'as'             : [ repres_sc              , 'representation'  , ', ' ],
         'bg'             : [ _get_color_sc          , 'color'           , ''   ],      
         'button'         : [ controlling.button_sc  , 'button'          , ', ' ],
         'color'          : [ _get_color_sc          , 'color'           , ', ' ],
         'cartoon'        : [ viewing.cartoon_sc     , 'cartoon'         , ', ' ],
         'center'         : [ selection_sc           , 'selection'       , ''   ],   
         'clip'           : [ viewing.clip_action_sc , 'clipping action' , ', ' ],
         'count_atoms'    : [ selection_sc           , 'selection'       , ''   ],
         'delete'         : [ selection_sc           , 'selection'       , ''   ],
         'deprotect'      : [ selection_sc           , 'selection'       , ''   ],   
         'full_screen'    : [ toggle_sc              , 'option'          , ''   ],
         'feedback'       : [ fb_action_sc           , 'action'          , ', ' ],
         'flag'           : [ editing.flag_sc        , 'flag'            , ', ' ],
         'get'            : [ setting.setting_sc     , 'setting'         , ','  ],      
         'help'           : [ help_sc                , 'selection'       , ''   ],
         'hide'           : [ repres_sc              , 'representation'  , ', ' ],
         'iterate'        : [ selection_sc           , 'selection'       , ''   ],
         'iterate_state'  : [ selection_sc           , 'selection'       , ''   ],
         'indicate'       : [ selection_sc           , 'selection'       , ''   ],   
         'mask'           : [ selection_sc           , 'selection'       , ''   ],
         'mview'          : [ moving.mview_action_sc , 'action'          , ''   ],
         'map_double'     : [ map_sc                 , 'map object'      , ', ' ],
         'order'          : [ selection_sc           , 'name'            , ''   ],
         'origin'         : [ selection_sc           , 'selection'       , ''   ],
         'protect'        : [ selection_sc           , 'selection'       , ''   ],
         'ramp_new'       : [ object_sc              , 'ramp'            , ''   ],
         'scene'          : [ viewing.scene_dict_sc  , 'scene'           , ''   ],
         'set'            : [ setting.setting_sc     , 'setting'         , ','  ],
         'show'           : [ repres_sc              , 'representation'  , ', ' ],
         'smooth'         : [ selection_sc           , 'selection'       , ''   ],
         'space'          : [ space_sc               , 'space'           , ''   ],      
         'split_states'   : [ object_sc              , 'object'          , ','  ],
         'stereo'         : [ stereo_sc              , 'option'          , ''   ],      
         'view'           : [ viewing.view_dict_sc   , 'view'            , ''   ],                              
         'unmask'         : [ selection_sc           , 'selection'       , ''   ],
         'unset'          : [ setting.setting_sc     , 'setting'         , ','  ],
         'window'         : [ window_sc              , 'action'          , ''   ],      
         'zoom'           : [ selection_sc           , 'selection'       , ''   ],
         },
   # 2nd
         {
         'align'          : [ selection_sc           , 'selection'       , ''   ],
         'as'             : [ selection_sc           , 'selection'       , ''   ],
         'feedback'       : [ fb_module_sc           , 'module'          , ', ' ],
         'button'         : [ controlling.but_mod_sc , 'modifier'        , ', ' ],
         'show'           : [ selection_sc           , 'selection'       , ''   ],
         'hide'           : [ selection_sc           , 'selection'       , ''   ],
         'color'          : [ selection_sc           , 'selection'       , ''   ],
         'select'         : [ selection_sc           , 'selection'       , ''   ],
         'save'           : [ selection_sc           , 'selection'       , ', ' ],
         'flag'           : [ selection_sc           , 'selection'       , ', ' ],   
         'load'           : [ selection_sc           , 'selection'       , ', ' ],
         'load_traj'      : [ selection_sc           , 'selection'       , ', ' ],
         'create'         : [ selection_sc           , 'selection'       , ', ' ],
         'map_new'        : [ creating.map_type_sc   , 'map type'        , ', ' ],
         'spectrum'       : [ palette_sc             , 'palette'         , ''   ],      
         'order'          : [ boolean_sc             , 'sort'            , ','  ],
         'symexp'         : [ object_sc              , 'object'          , ', ' ],   
         'isomesh'        : [ map_sc                 , 'map object'      , ', ' ],
         'isosurface'     : [ map_sc                 , 'map object'      , ', ' ],
         'slice_new'      : [ map_sc                 , 'map object'      , ', ' ],
         'view'           : [ viewing.view_sc        , 'view action'     , ''   ],
         'scene'          : [ viewing.scene_action_sc, 'scene action'    , ','   ],                  
         'unset'          : [ selection_sc           , 'selection'        , ','  ],
         'ramp_new'       : [ map_sc                 , 'map object'       , ''   ],      
         },
   #3rd
         {
         'spectrum'       : [ selection_sc           , 'selection'       , ''   ],
         'feedback'       : [ fb_mask_sc             , 'mask'            , ''   ],
         'order'          : [ controlling.location_sc, 'location'        , ','  ],
         'button'         : [ controlling.but_act_sc , 'button action'   , ''   ],
         'flag'           : [ editing.flag_action_sc , 'flag action'     , ''   ],
         'set'            : [ selection_sc            , 'selection'         , ','  ],
         },
   #4th
         {
         'ramp_new'       : [ creating.ramp_spectrum_sc , 'ramp color spectrum'        , ', ' ],      
         'map_new'        : [ selection_sc           , 'selection'       , ', ' ],
         'isosurface'     : [ selection_sc           , 'selection'       , ', ' ],
         'isomesh'        : [ selection_sc           , 'selection'       , ', ' ],      
         }
         ]

      color_sc = None

      _load2str = { loadable.pdb : loadable.pdbstr,
                    loadable.mol : loadable.molstr,
                    loadable.xplor : loadable.xplorstr,
                    loadable.mol2 : loadable.mol2str,
                    loadable.mmod : loadable.mmodstr,
                    loadable.ccp4 : loadable.ccp4str,
                    loadable.sdf2 : loadable.sdf2str}

   except:
      print "Error: unable to initalize the pymol.cmd module"
      traceback.print_exc()
      sys.exit(0)
      
else:
   from pymol.cmd import *
   


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