"Fossies" - the Fresh Open Source Software Archive  

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

viewing.py  (pymol-v1.8.6.0.tar.bz2)	:	viewing.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 38		skipping to change at line 38
import pymol		import pymol
from . import selector		from . import selector
import copy		import copy
from . import parsing		from . import parsing
import re		import re
cmd = sys.modules["pymol.cmd"]		cmd = sys.modules["pymol.cmd"]
from .cmd import _cmd,lock,unlock,Shortcut,QuietException,_raising, \		from .cmd import _cmd,lock,unlock,Shortcut,QuietException,_raising, \
_feedback,fb_module,fb_mask, \		_feedback,fb_module,fb_mask, \
repres,repres_sc, is_string, is_list, is_ok, is_error, \		repres,repres_sc, is_string, is_list, is_ok, is_error, \
		repmasks,repmasks_sc, \
toggle_dict,toggle_sc,stereo_dict,stereo_sc, \		toggle_dict,toggle_sc,stereo_dict,stereo_sc, \
palette_dict, palette_sc, window_dict, window_sc, \		palette_dict, palette_sc, window_dict, window_sc, \
safe_list_eval, safe_alpha_list_eval, \		safe_list_eval, safe_alpha_list_eval, \
location_code, location_sc, boolean_dict, boolean_sc, \		location_code, location_sc, boolean_dict, boolean_sc, \
DEFAULT_ERROR, DEFAULT_SUCCESS		DEFAULT_ERROR, DEFAULT_SUCCESS
palette_colors_dict = {		palette_colors_dict = {
'rainbow_cycle' : 'magenta blue cyan green yellow orange red magenta ',		'rainbow_cycle' : 'magenta blue cyan green yellow orange red magenta ',
'rainbow_cycle_rev' : 'magenta red orange yellow green cyan blue magenta ',		'rainbow_cycle_rev' : 'magenta red orange yellow green cyan blue magenta ',
'rainbow' : 'blue cyan green yellow orange red',		'rainbow' : 'blue cyan green yellow orange red',
skipping to change at line 485		skipping to change at line 486
_self.unlock(r,_self)		_self.unlock(r,_self)
else:		else:
try:		try:
_self.lock(_self)		_self.lock(_self)
r = _cmd.onoff(_self._COb,str(name),0,0);		r = _cmd.onoff(_self._COb,str(name),0,0);
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException		if _self._raising(r,_self): raise QuietException
return r		return r
		def _rep_to_repmask(rep):
		repn = 0
		for rep in rep.split():
		rep = repmasks_sc.auto_err(rep, 'representation')
		repn |= repmasks[rep]
		return repn
def toggle(representation="lines", selection="all", _self=cmd):		def toggle(representation="lines", selection="all", _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"toggle" toggles the visibility of a representation within a		"toggle" toggles the visibility of a representation within a
selection.		selection.
USAGE		USAGE
toggle [ representation [, selection ]]		toggle [ representation [, selection ]]
skipping to change at line 521		skipping to change at line 529
SEE ALSO		SEE ALSO
show, hide		show, hide
'''		'''
r = DEFAULT_ERROR		r = DEFAULT_ERROR
try:		try:
_self.lock(_self)		_self.lock(_self)
if representation == 'object':		if representation == 'object':
repn = -2		repn = -2
else:		else:
rep = representation		repn = _rep_to_repmask(representation)
rep = repres_sc.auto_err(rep,'representation')
repn = repres[rep];
# preprocess selection		# preprocess selection
selection = selector.process(selection)		selection = selector.process(selection)
r = _cmd.toggle(_self._COb,str(selection),int(repn));		r = _cmd.toggle(_self._COb,str(selection),int(repn));
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException		if _self._raising(r,_self): raise QuietException
return r		return r
def show(representation="", selection="", _self=cmd):		def _showhide(rep, selection, value, _self):
		if not selection and (rep in ("", "all") or '(' in rep or '/' in rep):
		# rep looks like a selection
		selection = rep
		rep = "wire" if value else "everything"
		selection = selector.process(selection) or "all"
		repn = _rep_to_repmask(rep)
		r = DEFAULT_ERROR
		with _self.lockcm:
		r = _cmd.showhide(_self._COb, str(selection), int(repn), value)
		if _self._raising(r,_self): raise QuietException
		return r
		def show(representation="wire", selection="", _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"show" turns on representations for objects and selections.		"show" turns on representations for objects and selections.
USAGE		USAGE
show [ representation [, selection ]]		show [ representation [, selection ]]
ARGUMENTS		ARGUMENTS
skipping to change at line 567		skipping to change at line 589
show		show
show ribbon		show ribbon
show lines, (name CA+C+N)		show lines, (name CA+C+N)
SEE ALSO		SEE ALSO
hide, enable, disable		hide, enable, disable
'''		'''
r = DEFAULT_ERROR		return _showhide(representation, selection, 1, _self)
try:
_self.lock(_self)
if (representation=="") and (selection==""):
if is_ok(_cmd.showhide(_self._COb,"(all)",repres['lines'],1)): #
show lines by default
r = _cmd.showhide(_self._COb,"(all)",repres['nonbonded'],2)
elif (representation!="") and (selection!=""):
rep = representation
rep = repres_sc.auto_err(rep,'representation')
repn = repres[rep];
# preprocess selection
selection = selector.process(selection)
#
r = _cmd.showhide(_self._COb,str(selection),int(repn),1);
elif representation=='all':
if is_ok(_cmd.showhide(_self._COb,"all",repres['lines'],1)): # s
how lines by default
r = _cmd.showhide(_self._COb,"all",repres['nonbonded'], 1) #
nonbonded
elif (representation[0:1]=='(') or '/' in representation:
# preprocess selection
selection = selector.process(representation)
#
if is_ok(_cmd.showhide(_self._COb,str(selection),repres['lines']
,1)):
r = _cmd.showhide(_self._COb,str(selection),repres['nonbonde
d'],2);
else: # selection==""
rep = representation
rep = repres_sc.auto_err(rep,'representation')
repn = repres[rep]
r = _cmd.showhide(_self._COb,"all",int(repn),1);
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def show_as(representation="", selection="", _self=cmd):		def show_as(representation="wire", selection="", _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"as" turns on and off atom and bond representations.		"as" turns on and off atom and bond representations.
USAGE		USAGE
as representation [, selection ]		as representation [, selection ]
ARGUMENTS		ARGUMENTS
skipping to change at line 638		skipping to change at line 629
NOTES		NOTES
"selection" can be an object name		"selection" can be an object name
"as" alone will turn on lines and nonbonded and hide everything else.		"as" alone will turn on lines and nonbonded and hide everything else.
SEE ALSO		SEE ALSO
show, hide, enable, disable		show, hide, enable, disable
'''		'''
r = DEFAULT_ERROR		return _showhide(representation, selection, 2, _self)
try:
_self.lock(_self)
vis_sel = None
if (representation=="") and (selection==""):
if is_ok(_cmd.showhide(_self._COb,str(selection),-1,0)):
if is_ok(_cmd.showhide(_self._COb,"(all)",repres['lines'],1)
):
r = _cmd.showhide(_self._COb,"(all)",repres['nonbonded']
,1)
elif (representation!="") and (selection!=""):
rep = representation
rep = repres_sc.auto_err(rep,'representation')
repn = repres[rep]
# preprocess selection
selection = selector.process(selection)
# user specified 'visible' -- this has always been problematic
if "visible".startswith(selection.lower()) and len(selection.spl		def hide(representation="everything", selection="",_self=cmd):
it())==1:
vis_sel = _self.get_unused_name("_vis")
_self.select(vis_sel, selection)
selection = vis_sel
if is_ok(_cmd.showhide(_self._COb,str(selection),-1,0)):
r = _cmd.showhide(_self._COb,str(selection),int(repn),1)
elif representation=='all':
if is_ok(_cmd.showhide(_self._COb,str(selection),-1,0)):
if if_ok(_cmd.showhide(_self._COb,"all",repres['lines'],1)):
# show lines by default
r = _cmd.showhide(_self._COb,"all",repres['nonbonded'],1
) # show nonbonded by default
elif (representation[0:1]=='(') or '/' in representation:
# preprocess selection
selection = selector.process(representation)
if is_ok(_cmd.showhide(_self._COb,str(selection),-1,0)):
r = _cmd.showhide(_self._COb,str(selection),repres['lines'],
1)
else: # selection==""
rep = representation
rep = repres_sc.auto_err(rep,'representation')
repn = repres[rep];
if is_ok(_cmd.showhide(_self._COb,"all",-1,0)):
r = _cmd.showhide(_self._COb,"all",int(repn),1);
finally:
if vis_sel is not None:
_self.delete(vis_sel)
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def hide(representation="", selection="",_self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"hide" turns off atom and bond representations.		"hide" turns off atom and bond representations.
USAGE		USAGE
hide [ representation [, selection ]]		hide [ representation [, selection ]]
ARGUMENTS		ARGUMENTS
skipping to change at line 717		skipping to change at line 664
PYMOL API		PYMOL API
cmd.hide(string representation, string selection)		cmd.hide(string representation, string selection)
SEE ALSO		SEE ALSO
show, enable, disable		show, enable, disable
'''		'''
r = DEFAULT_ERROR		return _showhide(representation, selection, 0, _self)
try:
_self.lock(_self)
if (representation=="") and (selection==""):
r = _cmd.showhide(_self._COb,"@",0,0);
elif (representation!="") and (selection!=""):
rep = representation
rep = repres_sc.auto_err(rep,'representation')
repn = repres[rep];
selection = selector.process(selection)
r = _cmd.showhide(_self._COb,str(selection),int(repn),0);
elif (representation=='all'):
r = _cmd.showhide(_self._COb,"@",0,0);
elif (representation[0:1]=='(') or '/' in representation:
selection = selector.process(representation)
r = _cmd.showhide(_self._COb,str(selection),-1,0);
else: # selection == ""
rep = representation
rep = repres_sc.auto_err(rep,'representation')
repn = repres[rep];
r = _cmd.showhide(_self._COb,"all",int(repn),0);
finally:
_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException
return r
def get_view(output=1, quiet=1, _self=cmd):		def get_view(output=1, quiet=1, _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"get_view" returns and optionally prints out the current view		"get_view" returns and optionally prints out the current view
information in a format which can be embedded into a command		information in a format which can be embedded into a command
script and can be used in subsequent calls to "set_view".		script and can be used in subsequent calls to "set_view".
If a log file is currently open, get_view will not write the view		If a log file is currently open, get_view will not write the view
skipping to change at line 1623		skipping to change at line 1546
def window(action='show', x=0, y=0, width=0, height=0, _self=cmd):		def window(action='show', x=0, y=0, width=0, height=0, _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"window" controls the visibility of PyMOL\'s output window		"window" controls the visibility of PyMOL\'s output window
USAGE		USAGE
window [ action [, x [, y [, width [, height ]]]]]		window [ action [, x [, y [, width [, height ]]]]]
NOTES
This command is not fully implemented in MacPyMOL.
PYMOL API		PYMOL API
cmd.window(string action, int x, int y, int width, int height)		cmd.window(string action, int x, int y, int width, int height)
'''		'''
action = window_sc.auto_err(action,'action')		action = window_sc.auto_err(action,'action')
action = window_dict[str(action)]		action = window_dict[str(action)]
r = DEFAULT_ERROR		r = DEFAULT_ERROR
try:		try:
_self.lock(_self)		_self.lock(_self)
r = _cmd.window(_self._COb,action,int(x),int(y),int(width),int(heigh		from pymol.gui import get_qtwindow as getPyMOLWindow
t))		qt_window = getPyMOLWindow()
		if qt_window:
		r = DEFAULT_SUCCESS
		qt_window.window_cmd(action, int(x),int(y),int(width),int(height
		))
		else:
		r = _cmd.window(_self._COb,action,int(x),int(y),int(width),int(h
		eight))
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException		if _self._raising(r,_self): raise QuietException
return r		return r
def viewport(width=-1,height=-1,_self=cmd):		def viewport(width=-1,height=-1,_self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"viewport" changes the size of the graphics display area.		"viewport" changes the size of the graphics display area.
skipping to change at line 1863		skipping to change at line 1788
try:		try:
_self.lock(_self)		_self.lock(_self)
r = _cmd.draw(_self._COb,int(width),int(height),		r = _cmd.draw(_self._COb,int(width),int(height),
int(antialias),int(quiet))		int(antialias),int(quiet))
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException		if _self._raising(r,_self): raise QuietException
return r		return r
def ray(width=0, height=0, antialias=-1, angle=0.0, shift=0.0,		def ray(width=0, height=0, antialias=-1, angle=0.0, shift=0.0,
renderer=-1, quiet=1, async=0, _self=cmd):		renderer=-1, quiet=1, async_=0, _self=cmd, **kwargs):
'''		'''
DESCRIPTION		DESCRIPTION
"ray" creates a ray-traced image of the current frame. This		"ray" creates a ray-traced image of the current frame. This
can take some time (up to several minutes, depending on image		can take some time (up to several minutes, depending on image
complexity).		complexity).
USAGE		USAGE
ray [width [,height [,antialias [,angle [,shift [,renderer [,quiet		ray [width [,height [,antialias [,angle [,shift [,renderer [,quiet
skipping to change at line 1925		skipping to change at line 1850
built-in ray-tracing engine.		built-in ray-tracing engine.
PYMOL API		PYMOL API
cmd.ray(int width, int height, int antialias, float angle,		cmd.ray(int width, int height, int antialias, float angle,
float shift, int renderer, int quiet, int async)		float shift, int renderer, int quiet, int async)
SEE ALSO		SEE ALSO
draw, png, save		draw, png, save
'''		'''
		async_ = int(kwargs.pop('async', async_))
		if kwargs:
		raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs))
arg_tup = (int(width),int(height),		arg_tup = (int(width),int(height),
int(antialias),float(angle),		int(antialias),float(angle),
float(shift),int(renderer),int(quiet),_self)		float(shift),int(renderer),int(quiet),_self)
# stop movies, rocking, and sculpting if they're on...		# stop movies, rocking, and sculpting if they're on...
if _self.get_movie_playing():		if _self.get_movie_playing():
_self.mstop()		_self.mstop()
if _self.get_setting_boolean("sculpting"):		if _self.get_setting_boolean("sculpting"):
_self.set("sculpting","off",quiet=1)		_self.set("sculpting","off",quiet=1)
if _self.rock(-2)>0:		if _self.rock(-2)>0:
_self.rock(0)		_self.rock(0)
#		#
r = DEFAULT_ERROR		r = DEFAULT_ERROR
if not async:		if not async_:
r = _ray(*arg_tup)		r = _ray(*arg_tup)
else:		else:
render_thread = threading.Thread(target=_ray, args=arg_tup)		render_thread = threading.Thread(target=_ray, args=arg_tup)
render_thread.setDaemon(1)		render_thread.setDaemon(1)
render_thread.start()		render_thread.start()
r = DEFAULT_SUCCESS		r = DEFAULT_SUCCESS
if _self._raising(r,_self): raise QuietException		if _self._raising(r,_self): raise QuietException
return r		return r
def refresh(_self=cmd):		def refresh(_self=cmd):
skipping to change at line 1976		skipping to change at line 1906
r = None		r = None
if thread.get_ident() == pymol.glutThread:		if thread.get_ident() == pymol.glutThread:
try:		try:
_self.lock(_self)		_self.lock(_self)
r = _cmd.refresh_now(_self._COb)		r = _cmd.refresh_now(_self._COb)
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
else:		else:
try:		try:
_self.lock(_self)		_self.lock(_self)
r = _self._do("_ cmd._refresh(_self=cmd)",_self=_self)		r = _self._do("_ cmd._refresh()")
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if _self._raising(r,_self): raise QuietException		if _self._raising(r,_self): raise QuietException
return r		return r
def reset(object='',_self=cmd):		def reset(object='',_self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"reset" restores the rotation matrix to identity, sets the origin		"reset" restores the rotation matrix to identity, sets the origin
End of changes. 15 change blocks.
128 lines changed or deleted		48 lines changed or added

---