"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pymol/cmd.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.

cmd.py  (pymol-v1.8.6.0.tar.bz2)	:	cmd.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 98		skipping to change at line 98
_pymol._view_dict_sc = Shortcut({})		_pymol._view_dict_sc = Shortcut({})
_pymol._scene_dict_sc = Shortcut({})		_pymol._scene_dict_sc = Shortcut({})
#		#
if __name__=='pymol.cmd':		if __name__=='pymol.cmd':
import traceback		import traceback
import sys		import sys
		# pymol2.cmd2 exposes a weak reference, this is not possible (and not
		# necessary) on the module level, so we simply make a self reference.
		_weakrefproxy = sys.modules[__name__]
try:		try:
import re		import re
from pymol import _cmd		from pymol import _cmd
import string		import string
import threading		import threading
import pymol		import pymol
import os		import os
from . import parsing		from . import parsing
import time		import time
skipping to change at line 143		skipping to change at line 147
def _nt_expandvars(path): # allow for //share/folder$/file		def _nt_expandvars(path): # allow for //share/folder$/file
path = nt_hidden_path_re.sub(r"$$\\",path)		path = nt_hidden_path_re.sub(r"$$\\",path)
return os.path.expandvars(path)		return os.path.expandvars(path)
if "nt" in sys.builtin_module_names:		if "nt" in sys.builtin_module_names:
_expandvars = _nt_expandvars		_expandvars = _nt_expandvars
else:		else:
_expandvars = os.path.expandvars		_expandvars = os.path.expandvars
def exp_path(path):		def exp_path(path):
		path = as_pathstr(path)
return _expandvars(os.path.expanduser(path))		return _expandvars(os.path.expanduser(path))
		def as_pathstr(path):
		# On Windows, always work with unicode file names. On Unix,
		# UTF-8 byte strings seem to be fine, so keep them for now.
		if isinstance(path, bytes) and sys.platform == 'win32':
		for encoding in ('utf-8', 'mbcs'):
		try:
		return path.decode(encoding)
		except UnicodeError:
		pass
		return path
#--------------------------------------------------------------------		#--------------------------------------------------------------------
# locks and threading		# locks and threading
reaper = None		reaper = None
# the following locks are used by both C and Python to insure that no mo re than		# the following locks are used by both C and Python to insure that no mo re than
# one active thread enters PyMOL at a given time.		# one active thread enters PyMOL at a given time.
lock_api = pymol.lock_api		lock_api = pymol.lock_api
lock_api_c = pymol.lock_api_c		lock_api_c = pymol.lock_api_c
skipping to change at line 179		skipping to change at line 195
# Feedback		# Feedback
from .feedingback import *		from .feedingback import *
from .feedingback import _feedback		from .feedingback import _feedback
#--------------------------------------------------------------------		#--------------------------------------------------------------------
# internal API routines		# internal API routines
from . import internal		from . import internal
_adjust_coord = internal._adjust_coord
_alt = internal._alt		_alt = internal._alt
_coordset_update_spawn = internal._coordset_update_spawn		_coordset_update_spawn = internal._coordset_update_spawn
_coordset_update_thread = internal._coordset_update_thread		_coordset_update_thread = internal._coordset_update_thread
_copy_image = internal._copy_image		_copy_image = internal._copy_image
_ctrl = internal._ctrl		_ctrl = internal._ctrl
_ctsh = internal._ctsh		_ctsh = internal._ctsh
_do = internal._do		_do = internal._do
_dump_floats = internal._dump_floats		_dump_floats = internal._dump_floats
_dump_ufloats = internal._dump_ufloats		_dump_ufloats = internal._dump_ufloats
_fake_drag = internal._fake_drag		_fake_drag = internal._fake_drag
skipping to change at line 390		skipping to change at line 405
'model ', 'chain ', 'segi ', 'resn ', 'resi ', 'name ', 'alt ', 'ind ex ',		'model ', 'chain ', 'segi ', 'resn ', 'resi ', 'name ', 'alt ', 'ind ex ',
'id ', 'rank ',		'id ', 'rank ',
'partial_charge ', 'formal_charge ', 'b ', 'q ', 'ss ', 'elem ',		'partial_charge ', 'formal_charge ', 'b ', 'q ', 'ss ', 'elem ',
'rep ', 'color ', 'pepseq ',		'rep ', 'color ', 'pepseq ',
'all', 'enabled', 'visible', 'bonded', 'protected', 'masked',		'all', 'enabled', 'visible', 'bonded', 'protected', 'masked',
'organic', 'inorganic', 'solvent', 'polymer', 'guide', 'hetatm',		'organic', 'inorganic', 'solvent', 'polymer', 'guide', 'hetatm',
'hydrogens', 'backbone', 'sidechain', 'metals', 'donors',		'hydrogens', 'backbone', 'sidechain', 'metals', 'donors',
'acceptors',		'acceptors',
		'polymer.protein', 'polymer.nucleic',
'center', 'origin',		'center', 'origin',
])		])
object_sc = lambda sc=Shortcut,gn=get_names:sc(gn('objects'))		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') )		map_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:map') )
contour_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object: mesh')+gnot('object:surface'))		contour_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object: mesh')+gnot('object:surface'))
group_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:gro up'))		group_sc = lambda sc=Shortcut,gnot=get_names_of_type:sc(gnot('object:gro up'))
# Table for argument autocompletion		# Table for argument autocompletion
End of changes. 5 change blocks.
1 lines changed or deleted		17 lines changed or added

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