"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pymol/__init__.py" between
pymol-v1.8.6.0.tar.bz2 and pymol-v2.1.0.tar.bz2

About: PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.

__init__.py  (pymol-v1.8.6.0.tar.bz2)	:	__init__.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 70		skipping to change at line 70
# from a terminal where the user could set pymol_argv		# from a terminal where the user could set pymol_argv
args = getattr(__main__, "pymol_argv", None)		args = getattr(__main__, "pymol_argv", None)
# standard launch (consume main thread)		# standard launch (consume main thread)
import pymol		import pymol
pymol.launch(args)		pymol.launch(args)
# this should never be reached because PyMOL will exit the process		# this should never be reached because PyMOL will exit the process
raise SystemExit		raise SystemExit
if sys.version_info[0] > 2:		IS_PY2 = sys.version_info[0] == 2
		IS_PY3 = sys.version_info[0] == 3
		IS_WINDOWS = sys.platform.startswith('win')
		IS_MACOS = sys.platform.startswith('darwin')
		IS_LINUX = sys.platform.startswith('linux')
		if IS_PY3:
# legacy string API, still used by Pmw for example		# legacy string API, still used by Pmw for example
import string		import string
for attr in ['capitalize', 'count', 'find', 'index', 'lower',		for attr in ['capitalize', 'count', 'find', 'index', 'lower',
'replace', 'rstrip', 'split', 'strip', 'upper', 'zfill']:		'replace', 'rstrip', 'split', 'strip', 'upper', 'zfill']:
setattr(string, attr, getattr(str, attr))		setattr(string, attr, getattr(str, attr))
string.letters = string.ascii_letters		string.letters = string.ascii_letters
string.lowercase = string.ascii_lowercase		string.lowercase = string.ascii_lowercase
string.join = lambda words, sep=' ': sep.join(words)		string.join = lambda words, sep=' ': sep.join(words)
string.atoi = int		string.atoi = int
skipping to change at line 191		skipping to change at line 197
Guess PYMOL_PATH from typical locations and return it as string.		Guess PYMOL_PATH from typical locations and return it as string.
'''		'''
init_file = os.path.abspath(__file__)		init_file = os.path.abspath(__file__)
pymol_path_candidates = [		pymol_path_candidates = [
# $PYMOL_PATH == <site-packages>/pymol/pymol_path		# $PYMOL_PATH == <site-packages>/pymol/pymol_path
os.path.join(os.path.dirname(init_file), 'pymol_path'),		os.path.join(os.path.dirname(init_file), 'pymol_path'),
# $PYMOL_PATH/modules/pymol/__init__.py		# $PYMOL_PATH/modules/pymol/__init__.py
re.sub(r"[\/\\]modules[\/\\]pymol[\/\\]__init__\.py[c]*$", "", init_file ),		re.sub(r"[\/\\]modules[\/\\]pymol[\/\\]__init__\.py[c]*$", "", init_file ),
		# /usr/share/pymol
		os.path.join(sys.prefix, 'share', 'pymol'),
]		]
for pymol_path in pymol_path_candidates:		for pymol_path in pymol_path_candidates:
if os.path.isdir(pymol_path):		if os.path.isdir(pymol_path):
return pymol_path		return pymol_path
return '.'		return '.'
def setup_environ():		def setup_environ():
# guess PYMOL_PATH if unset		# guess PYMOL_PATH if unset
skipping to change at line 254		skipping to change at line 263
def exec_deferred(self):		def exec_deferred(self):
'''		'''
Execute the stuff from invocations.options.deferred		Execute the stuff from invocations.options.deferred
'''		'''
try:		try:
from socket import error as socket_error		from socket import error as socket_error
except ImportError:		except ImportError:
socket_error = None		socket_error = None
print('import socket failed')		print('import socket failed')
import pymol as _pymol
cmd = self.cmd		cmd = self.cmd
		_pymol = cmd._pymol
# read from stdin (-p)		# read from stdin (-p)
if self.invocation.options.read_stdin and not _pymol._stdin_reader_thread:		if self.invocation.options.read_stdin and not _pymol._stdin_reader_thread:
try:		try:
t = _pymol._stdin_reader_thread = \		t = _pymol._stdin_reader_thread = \
threading.Thread(target=cmd._parser.stdin_reader)		threading.Thread(target=cmd._parser.stdin_reader)
t.setDaemon(1)		t.setDaemon(1)
t.start()		t.start()
except:		except:
traceback.print_exc()		traceback.print_exc()
skipping to change at line 315		skipping to change at line 323
elif vendor.startswith('Mesa'):		elif vendor.startswith('Mesa'):
if renderer[0:18]=='Mesa GLX Indirect':		if renderer[0:18]=='Mesa GLX Indirect':
pass		pass
elif vendor.startswith('ATI'):		elif vendor.startswith('ATI'):
if renderer[0:17] == 'FireGL2 / FireGL3': # obsolete ?		if renderer[0:17] == 'FireGL2 / FireGL3': # obsolete ?
if invocation.options.show_splash:		if invocation.options.show_splash:
print(" Adapting to FireGL hardware.")		print(" Adapting to FireGL hardware.")
cmd.set('line_width', 2, quiet=1)		cmd.set('line_width', 2, quiet=1)
if sys.platform.startswith('win'):		if IS_WINDOWS:
if sys.getwindowsversion()[0] > 5:		if sys.getwindowsversion()[0] > 5:
# prevent color corruption by calling glFlush etc.		# prevent color corruption by calling glFlush etc.
cmd.set('ati_bugs', 1)		cmd.set('ati_bugs', 1)
if 'Radeon HD' in renderer:		if 'Radeon HD' in renderer:
if invocation.options.show_splash:		if invocation.options.show_splash:
print(" Adjusting settings to improve performance for ATI cards. ")		print(" Adjusting settings to improve performance for ATI cards. ")
if cmd.get_setting_int("use_shaders")==0:		if cmd.get_setting_int("use_shaders")==0:
# limit frame rate to 30 fps to avoid ATI "jello"		# limit frame rate to 30 fps to avoid ATI "jello"
skipping to change at line 368		skipping to change at line 376
except:		except:
pass		pass
# store our adapted state as default		# store our adapted state as default
cmd.reinitialize("store")		cmd.reinitialize("store")
def launch_gui(self):		def launch_gui(self):
'''		'''
Launch if requested:		Launch if requested:
- external GUI		- external GUI
- RPC server
'''		'''
pymol_path = os.getenv('PYMOL_PATH', '')		pymol_path = os.getenv('PYMOL_PATH', '')
try:		try:
poll = (sys.platform == 'darwin')		poll = IS_MACOS
if self.invocation.options.external_gui == 3:		if self.invocation.options.external_gui == 3:
if 'DISPLAY' not in os.environ:		if 'DISPLAY' not in os.environ:
os.environ['DISPLAY'] = ':0.0'		os.environ['DISPLAY'] = ':0.0'
if self.invocation.options.external_gui in (1, 3):		if self.invocation.options.external_gui in (1, 3):
__import__(self.invocation.options.gui)		__import__(self.invocation.options.gui)
sys.modules[self.invocation.options.gui].__init__(self, poll,		sys.modules[self.invocation.options.gui].__init__(self, poll,
skin = self.invocation.options.skin)		skin = self.invocation.options.skin)
# import plugin system		# import plugin system
import pymol.plugins		import pymol.plugins
# -- Greg Landrum's RPC stuff
if self.invocation.options.rpcServer:
from pymol import rpc
rpc.launch_XMLRPC()
# --
except:		except:
traceback.print_exc()		traceback.print_exc()
def prime_pymol():		def prime_pymol():
'''		'''
Set the current thread as the glutThread		Set the current thread as the glutThread
Launch X11 on OSX (legacy)
'''		'''
global glutThread		global glutThread
if not glutThread:		if not glutThread:
glutThread = thread.get_ident()		glutThread = thread.get_ident()
# legacy X11 launching on OSX		def _launch_no_gui():
if sys.platform == 'darwin' and invocation.options.external_gui == 1:		import pymol2
xdpyinfo = "/opt/X11/bin/xdpyinfo"
if not os.path.exists(xdpyinfo) or \		p = pymol2.SingletonPyMOL()
os.system(xdpyinfo + " >/dev/null 2>&1"):		p.start()
# launch X11 (if needed)
os.system("/usr/bin/open -a X11")		# TODO sufficient?
		while (p.idle() or p.getRedisplay() or
		invocation.options.keep_thread_alive or
		cmd.get_modal_draw() or
		cmd.get_setting_int('keep_alive') or
		cmd._pymol._stdin_reader_thread is not None):
		p.draw()
		# TODO needed?
		cmd.sync()
		p.stop()
def launch(args=None, block_input_hook=0):		def launch(args=None, block_input_hook=0):
'''		'''
Run PyMOL with args		Run PyMOL with args
Only returns if we are running pretend GLUT.		Only returns if we are running pretend GLUT.
'''		'''
if args is None:		if args is None:
args = sys.argv		args = sys.argv
invocation.parse_args(args)		invocation.parse_args(args)
		if invocation.options.gui == 'pmg_qt':
		if invocation.options.no_gui:
		return _launch_no_gui()
		try:
		from pmg_qt import pymol_qt_gui
		sys.exit(pymol_qt_gui.execapp())
		except ImportError:
		print('Qt not available, using GLUT/Tk interface')
		invocation.options.gui = 'pmg_tk'
prime_pymol()		prime_pymol()
_cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)		_cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
def finish_launching(args=None):		def finish_launching(args=None):
'''		'''
Start the PyMOL process in a thread		Start the PyMOL process in a thread
'''		'''
global glutThreadObject		global glutThreadObject
if cmd._COb is not None:		if cmd._COb is not None:
skipping to change at line 480		skipping to change at line 502
if label:		if label:
self.label = label		self.label = label
def __str__(self):		def __str__(self):
return " %s: %s" % (self.label, self.message)		return " %s: %s" % (self.label, self.message)
class IncentiveOnlyException(CmdException):		class IncentiveOnlyException(CmdException):
'''		'''
Exception type for features that are not available in Open-Source PyMOL		Exception type for features that are not available in Open-Source PyMOL
'''		'''
label = "Incentive-Only-Error"		label = "Incentive-Only-Error"
def __init__(self, *args, **kwargs):		def __init__(self, message=''):
super(IncentiveOnlyException, self).__init__(*args, **kwargs)		if not message:
if not self.message:
try:		try:
funcname = sys._getframe(1).f_code.co_name		funcname = sys._getframe(1).f_code.co_name
self.message = '"%s" is not available in Open-Source PyMOL' % (f uncname,)		message = '"%s" is not available in Open-Source PyMOL' % (funcna me,)
except:		except:
self.message = 'Not available in Open-Source PyMOL'		message = 'Not available in Open-Source PyMOL'
self.message += '\n\n' \		message += '\n\n' \
' Please visit http://pymol.org if you are interested in the\n' \		' Please visit http://pymol.org if you are interested in the\n' \
' full featured "Incentive PyMOL" version.\n'		' full featured "Incentive PyMOL" version.\n'
		super(IncentiveOnlyException, self).__init__(message)
class Scratch_Storage:		class Scratch_Storage:
'''		'''
Generic namespace		Generic namespace
'''		'''
		def __reduce__(self):
		# for loading Python 3 (new-style class) pickle with Python 2
		return (self.__class__, (), self.__dict__)
def get_unused_name(self, prefix='tmp'):		def get_unused_name(self, prefix='tmp'):
'''		'''
Get an unused name from this namespace		Get an unused name from this namespace
'''		'''
i = 1		i = 1
while True:		while True:
name = prefix + str(i)		name = prefix + str(i)
if not hasattr(self, name):		if not hasattr(self, name):
setattr(self, name, None)		setattr(self, name, None)
return name		return name
i += 1		i += 1
class Session_Storage:		class Session_Storage:
'''		'''
Generic namespace		Generic namespace
'''		'''
pass		def __reduce__(self):
		# for loading Python 3 (new-style class) pickle with Python 2
		return (self.__class__, (), self.__dict__)
		def _colortype(cmd):
		# backwards compatible color index type for iterate, which used
		# to expose colors as RGB tuples
		get_color_tuple = cmd.get_color_tuple
		class Color(int):
		def __getitem__(self, i):
		return get_color_tuple(self)[i]
		def __len__(self):
		return 3
		return Color
######### VARIABLES ############################		######### VARIABLES ############################
glutThread = 0		glutThread = 0
######### ENVIRONMENT ##########################		######### ENVIRONMENT ##########################
setup_environ()		setup_environ()
# initialize instance-specific module/object internals		# initialize instance-specific module/object internals
skipping to change at line 562		skipping to change at line 602
# The following causes an import error for "import cmd":		# The following causes an import error for "import cmd":
class _NoCmdFinder:		class _NoCmdFinder:
def find_spec(self, fullname, path=None, target=None):		def find_spec(self, fullname, path=None, target=None):
if path is None and fullname == 'cmd':		if path is None and fullname == 'cmd':
msg = 'use "from pymol import cmd" instead of "import cmd"'		msg = 'use "from pymol import cmd" instead of "import cmd"'
raise CmdException(msg)		raise CmdException(msg)
return None		return None
find_module = find_spec		find_module = find_spec
		sys.meta_path.insert(0, _NoCmdFinder())
########## LEGACY PRINT STATEMENT FOR PYMOL COMMAND LINE ###################		########## LEGACY PRINT STATEMENT FOR PYMOL COMMAND LINE ###################
if sys.version_info[0] > 2:		if IS_PY3:
def _print_statement(*args, **_):		def _print_statement(*args, **_):
'''Legacy Python-2-like print statement for the PyMOL command line'''		'''Legacy Python-2-like print statement for the PyMOL command line'''
kw = {}		kw = {}
if args and args[0].startswith('>>'):		if args and args[0].startswith('>>'):
kw['file'] = eval(args[0][2:])		kw['file'] = eval(args[0][2:])
args = args[1:]		args = args[1:]
if args and not args[-1]:		if args and not args[-1]:
kw['end'] = ' '		kw['end'] = ' '
args = args[:-1]		args = args[:-1]
args = [eval(a) for a in args]		args = [eval(a) for a in args]
End of changes. 19 change blocks.
28 lines changed or deleted		70 lines changed or added

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