"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "modules/pymol/querying.py" between
pymol-v2.1.0.tar.bz2 and pymol-open-source-2.2.0.tar.gz

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.

querying.py  (pymol-v2.1.0.tar.bz2)	:	querying.py  (pymol-open-source-2.2.0)
skipping to change at line 242		skipping to change at line 242
if not quiet:		if not quiet:
if r!=None:		if r!=None:
print(" get_title: %s"%r)		print(" get_title: %s"%r)
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException		if _raising(r,_self): raise pymol.CmdException
return r		return r
def angle(name=None, selection1="(pk1)", selection2="(pk2)",		def angle(name=None, selection1="(pk1)", selection2="(pk2)",
selection3="(pk3)", mode=None, label=1, reset=0,		selection3="(pk3)", mode=None, label=1, reset=0,
zoom=0, state=0, quiet=1, _self=cmd):		zoom=0, state=0, quiet=1, _self=cmd,
		state1=-3, state2=-3, state3=-3):
'''		'''
DESCRIPTION		DESCRIPTION
"angle" shows the angle formed between any three atoms.		"angle" shows the angle formed between any three atoms.
USAGE		USAGE
angle [ name [, selection1 [, selection2 [, selection3 ]]]]		angle [ name [, selection1 [, selection2 [, selection3 ]]]]
skipping to change at line 319		skipping to change at line 320
try:		try:
_self.lock(_self)		_self.lock(_self)
if selection2!="same":		if selection2!="same":
selection2 = "("+selection2+")"		selection2 = "("+selection2+")"
if selection3!="same":		if selection3!="same":
selection3 = "("+selection3+")"		selection3 = "("+selection3+")"
r = _cmd.angle(_self._COb,str(nam),"("+str(selection1)+")",		r = _cmd.angle(_self._COb,str(nam),"("+str(selection1)+")",
str(selection2),		str(selection2),
str(selection3),		str(selection3),
int(mode),int(label),int(reset),		int(mode),int(label),int(reset),
int(zoom),int(quiet),int(state)-1)		int(zoom),int(quiet),int(state)-1,
		int(state1)-1, int(state2)-1, int(state3)-1)
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException		if _raising(r,_self): raise pymol.CmdException
return r		return r
def dihedral(name=None, selection1="(pk1)", selection2="(pk2)",		def dihedral(name=None, selection1="(pk1)", selection2="(pk2)",
selection3="(pk3)", selection4="(pk4)", mode=None,		selection3="(pk3)", selection4="(pk4)", mode=None,
label=1, reset=0, zoom=0, state=0, quiet=1, _self=cmd):		label=1, reset=0, zoom=0, state=0, quiet=1, _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
skipping to change at line 419		skipping to change at line 421
int(mode),int(label),		int(mode),int(label),
int(reset),int(zoom),		int(reset),int(zoom),
int(quiet),int(state)-1)		int(quiet),int(state)-1)
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if _raising(r,_self): raise pymol.CmdException		if _raising(r,_self): raise pymol.CmdException
return r		return r
def distance(name=None, selection1="(pk1)", selection2="(pk2)",		def distance(name=None, selection1="(pk1)", selection2="(pk2)",
cutoff=None, mode=None, zoom=0, width=None, length=None,		cutoff=None, mode=None, zoom=0, width=None, length=None,
gap=None, label=1, quiet=1, reset=0, state=0, _self=cmd):		gap=None, label=1, quiet=1, reset=0, state=0,
		state1=-3, state2=-3, _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
"distance" creates a new distance object between two selections.		"distance" creates a new distance object between two selections.
USAGE		USAGE
distance [name [, selection1 [, selection2 [, cutoff [, mode ]]]]]		distance [name [, selection1 [, selection2 [, cutoff [, mode ]]]]]
skipping to change at line 451		skipping to change at line 454
mode = 1: only bond distances		mode = 1: only bond distances
mode = 2: only show polar contact distances		mode = 2: only show polar contact distances
mode = 3: like mode=0, but use distance_exclusion setting		mode = 3: like mode=0, but use distance_exclusion setting
mode = 4: distance between centroids (does not support		mode = 4: distance between centroids (does not support
dynamic_measures; new in PyMOL 1.8.2)		dynamic_measures; new in PyMOL 1.8.2)
		state = int: object state to create the measurement object in
		and to get coordinates from {default: 0 (all states)}
		state1, state2 = int: overrule 'state' argument to measure distances
		between different states {default: use state}
EXAMPLES		EXAMPLES
distance mydist, 14/CA, 29/CA		distance mydist, 14/CA, 29/CA
distance hbonds, all, all, 3.2, mode=2		distance hbonds, all, all, 3.2, mode=2
NOTES		NOTES
The distance wizard makes measuring distances easier than using		The distance wizard makes measuring distances easier than using
the "dist" command for real-time operations.		the "dist" command for real-time operations.
skipping to change at line 527		skipping to change at line 536
selection1 = selector.process(selection1)		selection1 = selector.process(selection1)
selection2 = selector.process(selection2)		selection2 = selector.process(selection2)
# now do the deed		# now do the deed
try:		try:
_self.lock(_self)		_self.lock(_self)
if selection2!="same":		if selection2!="same":
selection2 = "("+selection2+")"		selection2 = "("+selection2+")"
r = _cmd.dist(_self._COb,str(nam),"("+str(selection1)+")",		r = _cmd.dist(_self._COb,str(nam),"("+str(selection1)+")",
str(selection2),int(mode),float(cutoff),		str(selection2),int(mode),float(cutoff),
int(label),int(quiet),int(reset),		int(label),int(quiet),int(reset),
int(state)-1,int(zoom))		int(state)-1,int(zoom),
		int(state1)-1, int(state2)-1)
if width!=None:		if width!=None:
_self.set("dash_width",width,nam)		_self.set("dash_width",width,nam)
if length!=None:		if length!=None:
_self.set("dash_length",length,nam)		_self.set("dash_length",length,nam)
if gap!=None:		if gap!=None:
_self.set("dash_gap",gap,nam)		_self.set("dash_gap",gap,nam)
finally:		finally:
_self.unlock(r,_self)		_self.unlock(r,_self)
if (r<0.0) and (not quiet):		if (r<0.0) and (not quiet):
# a negative value is an warning signal from PyMOL...		# a negative value is an warning signal from PyMOL...
skipping to change at line 1644		skipping to change at line 1654
def get_object_state(name, _self=cmd):		def get_object_state(name, _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
Returns the effective object state.		Returns the effective object state.
'''		'''
states = _self.count_states('%' + name)		states = _self.count_states('%' + name)
if states < 2 and _self.get_setting_boolean('static_singletons'):		if states < 2 and _self.get_setting_boolean('static_singletons'):
return 1		return 1
		if _self.get_setting_int('all_states', name):
		return 0
state = _self.get_setting_int('state', name)		state = _self.get_setting_int('state', name)
if state > states:		if state > states:
raise pymol.CmdException('Invalid state %d for object %s' % (state, name))		raise pymol.CmdException('Invalid state %d for object %s' % (state, name))
return state		return state
def get_selection_state(selection, _self=cmd):		def get_selection_state(selection, _self=cmd):
'''		'''
DESCRIPTION		DESCRIPTION
Returns the effective object state for all objects in given selection.		Returns the effective object state for all objects in given selection.
skipping to change at line 1690		skipping to change at line 1702
(assume it was loaded from a file without occupancy information).		(assume it was loaded from a file without occupancy information).
SEE ALSO		SEE ALSO
get_extent		get_extent
'''		'''
from chempy import cpv		from chempy import cpv
state, quiet = int(state), int(quiet)		state, quiet = int(state), int(quiet)
if state < 0:		if state < 0:
states = [get_selection_state(selection)]		state = _self.get_selection_state(selection)
elif state == 0:		if state == 0:
states = list(range(1, _self.count_states(selection)+1))		states = list(range(1, _self.count_states(selection)+1))
else:		else:
states = [state]		states = [state]
com = cpv.get_null()		com = cpv.get_null()
totmass = 0.0		totmass = 0.0
for state in states:		for state in states:
model = _self.get_model(selection, state)		model = _self.get_model(selection, state)
for a in model.atom:		for a in model.atom:
End of changes. 7 change blocks.
6 lines changed or deleted		18 lines changed or added

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