/usr/lib/python2.7/dist-packages/pymol/invocation.py is in pymol 1.7.0.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#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* -------------------------------------------------------------------
# invocation.py
#
# This module unifies argument handling for embedded and modular PyMOL
#
if __name__=='pymol.invocation':
import copy
import re
import os
import glob
import string
import sys
import traceback
pymolrc_pat1 = '.pymolrc*'
pymolrc_pat2 = 'pymolrc*'
ros_pat = 'run_on_startup*'
class generic:
pass
global_options = generic();
options = global_options
options.deferred = []
options.no_gui = 0
options.internal_gui = 1
options.internal_feedback = 1
options.external_gui = 1
options.force_stereo = 0
options.game_mode = 0
options.gui = 'pmg_tk'
options.skin = 'normal'
options.show_splash = 1
options.read_stdin = 0
options.win_x = 640
options.win_y = 480
options.win_px = 4
options.sigint_handler = 1 # terminate on Ctrl-C?
options.reuse_helper = 0
options.auto_reinitialize = 0
options.keep_thread_alive = 0
options.after_load_script = ""
options.quiet = 0
options.multisample = 0
options.incentive_product = 0
options.window_visible = 1
options.presentation = 0
options.defer_builds_mode = 0
options.full_screen = 0
options.sphere_mode = -1
options.stereo_capable = 0
options.stereo_mode = 0
options.zoom_mode = -1
options.no_quit = 0
options.plugins = 2
options.exit_on_error = 0
options.win_py = { 'irix':240,
'darwin': 214, # hmm...need to set to 192 for Leopard?...
'linux2': 220,
'win32' : 230}.get(sys.platform,200)
options.ext_y = 168 # external gui height (eg. for Tcl/Tk top bar)
options.blue_line = 0
# Greg Landrum
options.rpcServer = 0
# end
options.security = 1
script_re = re.compile(r"pymolrc$|\.pml$|\.PML$|\.p1m$|\.P1M$")
py_re = re.compile(r"\.py$|\.pym$|\.PY$|\.PYM$")
def get_user_config():
for d in [os.getcwd(), '$HOME', '$HOMEPATH$HOMEDRIVE', '$PYMOL_PATH']:
d = os.path.expandvars(d)
for pat in [pymolrc_pat1, pymolrc_pat2]:
lst = glob.glob(d + os.sep + pat)
if lst:
break
if lst:
break
# global run_on_startup script (not overridden by pymolrc files, but is disabled by "-k")
if os.environ.has_key("PYMOL_PATH"):
first = glob.glob(os.environ['PYMOL_PATH']+"/"+ros_pat)
else:
first = []
second = []
for a in lst:
if py_re.search(a):
first.append("_do__ run "+a) # preceeding "_ " cloaks
elif script_re.search(a):
second.append("_do__ @"+a) # preceeding "_ " cloaks
first.sort()
second.sort()
return first+second
def parse_args(argv, _pymol=None, options=None, restricted=0):
if not restricted:
global _argv
_argv = copy.deepcopy(argv) # pymol.invocation._argv
global global_options
if options == None:
if _pymol==None:
options = global_options
else:
options = _pymol.invocation.options
av = copy.deepcopy(argv)
av = av[1:] # throw out the executable path
av.reverse()
once_dict = {}
options.deferred = []
final_actions = []
loaded_something = 0
python_script = None
# append user settings file as an option
pymolrc = get_user_config()
while 1:
if not len(av):
break
a = av.pop()
a = re.sub(r'''^"|"$|^'|'$''','',a) # strip extra quotes
if a[0:1]=='-':
if (a[1:2]=='-'):
# double hypen signals end of PyMOL arguments
if python_script == None:
python_script = argv[0]
rev_av = copy.deepcopy(av)
rev_av.reverse()
if len(a)>2:
sys.argv = [python_script] + [a] + rev_av
else:
sys.argv = [python_script] + rev_av
break
if ("A" in a) or ("a" in a): # application configuration
new_args = []
# ====== mode 1 - simple viewer window ======
if a[2:3] == "1":
if not once_dict.has_key('A1'):
once_dict['A1'] = 1
new_args = ["-qxiF",
"-X","68",
"-Y","100",
]
# ====== mode 2 - not available -- clashes with -2 =======
# ====== mode 3 - internal GUI only no splash ======
if a[2:3] == "3":
if not once_dict.has_key('A3'):
once_dict['A3'] = 1
new_args = ["-qx",
"-X","68",
"-Y","100",
]
# ====== mode 4 - internal GUI only with splash ======
if a[2:3] == "4": # used by PYMOLVIEWER
if not once_dict.has_key('A4'):
once_dict['A4'] = 1
new_args = [
"-X","68",
"-Y","100",
]
# ====== mode 5 - mode 5 helper application ======
if a[2:3] == "5":
if not once_dict.has_key('A5'):
once_dict['A5'] = 1
new_args = ["-QxiICUF",
"-X","68",
"-Y","100",
]
# ====== mode 6 - mode 6 presentation (no GUI) ======
if a[2:3] == "6":
if not once_dict.has_key('A6'):
once_dict['A6'] = 1
new_args = ["-qxieICUPF",
]
# ===============================================
new_args.reverse()
av = av + new_args
if "1" in a[1:2]:
options.deferred.append("_do__ config_mouse one_button")
if "2" in a[1:2]:
options.deferred.append("_do__ config_mouse two_button")
if "q" in a:
options.show_splash = 0
if "i" in a:
options.internal_gui = 0
if "f" in a:
options.internal_feedback = int(av.pop())
if "F" in a:
options.internal_feedback = 0
if "B" in a:
options.blue_line = 1
if "E" in a:
options.multisample = int(av.pop())
if "P" in a:
options.presentation = 1
if "W" in a:
options.win_x = int(av.pop())
if "H" in a:
options.win_y = int(av.pop())
if "X" in a:
options.win_px = int(av.pop())
if "y" in a:
options.exit_on_error = 1
if "Y" in a:
options.win_py = int(av.pop())
if "D" in a:
options.defer_builds_mode = int(av.pop())
if "V" in a:
options.ext_y = int(av.pop())
if "N" in a: # external gui name...
options.gui = av.pop()
if "x" in a:
options.external_gui = 0
if "n" in a:
options.incentive_product = 1
if "t" in a: # type of stereo to use
options.stereo_mode = int(av.pop())
if "T" in a: # what skin to use?
options.skin = str(av.pop())
if "w" in a: # what gui to use
options.gui = str(av.pop())
if "O" in a:
options.sphere_mode = int(av.pop())
if "z" in a:
options.window_visible = 0
if "Z" in a:
options.zoom_mode = int(av.pop())
if options.zoom_mode==5:
final_actions.append("_do__ zoom")
if not restricted:
if "c" in a:
options.no_gui=1
options.external_gui=0
if "m" in a: # mac external GUI
if options.external_gui == 2:
options.external_gui = 3
if options.win_py == 184: # mac external GUI default
options.win_py = 216
else:
options.external_gui = 2
options.win_py = 184
if "e" in a:
options.full_screen = 1
if "G" in a: # Game mode (reqd for Mac stereo)
options.game_mode = 1
options.win_x = 1024
options.win_y = 768
if "S" in a: # Force stereo context on stereo-capable hardware
options.force_stereo = 1
if sys.platform=='darwin':
options.deferred.append(
"_do__ set stereo_double_pump_mono,1,quiet=1")
if "M" in a: # Force mono on stereo hardware (all)
options.force_stereo = -1
if "j" in a: # Geowall: two side-by-side images
options.stereo_mode = 4
options.deferred.append("_do__ stereo on")
if ("d" in a):
options.deferred.append(
"_do_%s"%string.replace(av.pop(),'%',' '))
if ("J" in a): # cd to user's home directory on startup (if possible)
if sys.platform == 'win32':
if os.environ.has_key("HOMEDRIVE") and os.environ.has_key("HOMEPATH"):
path = os.environ["HOMEDRIVE"] + os.environ["HOMEPATH"]
if os.path.isdir(path) and os.path.exists(path):
my_docs = os.path.join(path,"Documents") # for VISTA compatibility
if os.path.isdir(my_docs): # start in Documents (if exists)
path = my_docs
else:
my_docs = os.path.join(path,"My Documents")
if os.path.isdir(my_docs): # start in My Documents (if exists)
path = my_docs
options.deferred.append("_do__ cmd.cd('''%s''',complain=0)"%string.replace(path,"\\","\\\\"))
elif os.environ.has_key("HOME"):
path = os.environ["HOME"]
if os.path.isdir(path):
options.deferred.append("_do__ cmd.cd('''%s''',complain=0)"%string.replace(path,"\\","\\\\"))
if ("l" in a):
options.deferred.append("_do_spawn %s"%av.pop())
if ("r" in a):
options.deferred.append("_do_run %s,main"%av.pop())
if ("u" in a):
options.deferred.append("_do_resume %s"%av.pop())
if ("s" in a):
options.deferred.append("_do_log_open %s"%av.pop())
if ("o" in a):
options.security = 0
if ("R" in a):
options.rpcServer = 1
if ("g" in a):
filename = av.pop()
if '.png' in filename:
options.deferred.append("_do__ cmd.png('''%s''')"%filename)
elif '.mpg' in filename:
options.deferred.append("_do__ movie.produce('''%s''')"%filename)
if ("C" in a):
options.sigint_handler = 0
if ("L" in a):
options.after_load_script = av.pop()
if ("b" in a): # CPU benchmark
options.deferred.append("_do__ feedback disable,all,everything")
options.deferred.append("_do__ feedback enable,python,output")
options.deferred.append("_do_wizard benchmark")
if a[2:]=='':
options.deferred.append("_do__ cmd.get_wizard().run_cpu()")
if a[2:]=='0':
options.deferred.append("_do__ cmd.get_wizard().ray_trace0()")
if a[2:]=='1':
options.deferred.append("_do__ cmd.get_wizard().ray_trace1()")
if a[2:]=='2':
options.deferred.append("_do__ cmd.get_wizard().ray_trace2()")
if "p" in a:
options.read_stdin = 1
if "K" in a:
options.keep_thread_alive = 1
if "k" in a: # suppress reading of .pymolrc and related files
pymolrc = None
options.plugins = 0
if "U" in a: #
options.reuse_helper = 1
if "Q" in a:
options.quiet = 1
options.show_splash = 0
if "I" in a:
options.auto_reinitialize = 1
if "h" in a: # generic helper application
options.internal_gui = 0
options.external_gui = 0
options.internal_feedback = 0
options.show_splash = 1
elif not restricted:
suffix = string.split(string.lower(a[-4:]),'.')[-1]
if suffix == "p5m":
# mode 5 helper application
av.append("-A5")
elif suffix == "psw":
# presentation mode
av.append("-A6")
elif suffix in [ 'pym' ,'py', 'pyc' ]:
python_script = a
elif suffix in [ 'pwg' ]:
try:
lines = open(a,'rb').readlines()
pseudo_argv = ["pymol"]
for line in lines:
line = line.strip()
if len(line) and line[0:1] != '#':
input = line.split(None,1)
if len(input) and input[0]!='#':
keyword = input[0].lower()
if keyword == 'options':
if len(input)>1:
pseudo_argv = ['pymol'] + input[1].split()
parse_args(pseudo_argv, _pymol=_pymol,
options=options, restricted=1)
except:
traceback.print_exc()
options.deferred.append(a)
loaded_something = 1
if pymolrc != None:
options.deferred = pymolrc + options.deferred
if options.plugins == 1:
# Load plugins independent of PMGApp (will not add menu items)
options.deferred.append('_do__ /import pymol.plugins;pymol.plugins.initialize(-1)')
if loaded_something and (options.after_load_script!=""):
options.deferred.append(options.after_load_script)
options.deferred.extend(final_actions)
if options.show_splash and not options.no_gui and not restricted:
options.deferred.insert(0,"_do__ cmd.splash(1)")
if options.full_screen:
options.deferred.append("_do__ full_screen on")
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