"Fossies" - the Fresh Open Source Software Archive  

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

editor.py  (pymol-v1.8.6.0.tar.bz2)	:	editor.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 27		skipping to change at line 27
tmp_editor = _prefix + "0"		tmp_editor = _prefix + "0"
tmp_connect = _prefix + "_con"		tmp_connect = _prefix + "_con"
tmp_domain = _prefix + "_dom"		tmp_domain = _prefix + "_dom"
tmp1 = _prefix + "1"		tmp1 = _prefix + "1"
tmp2 = _prefix + "2"		tmp2 = _prefix + "2"
tmp3 = _prefix + "3"		tmp3 = _prefix + "3"
tmp4 = _prefix + "4"		tmp4 = _prefix + "4"
# routines to assist in molecular editing		# routines to assist in molecular editing
		class undocontext:
		def __init__(self, cmd, sele):
		# not implemented in open-source
		pass
		def __enter__(self):
		# not implemented in open-source
		pass
		def __exit__(self, exc_type, exc_value, traceback):
		# not implemented in open-source
		pass
def attach_fragment(selection,fragment,hydrogen,anchor,_self=cmd):		def attach_fragment(selection,fragment,hydrogen,anchor,_self=cmd):
'''		'''
ARGUMENTS		ARGUMENTS
selection = str: must be "pk1"		selection = str: must be "pk1"
fragment = str: fragment name to load from fragment library		fragment = str: fragment name to load from fragment library
hydrogen = int: hydrogen atom ID in fragment to fuse		hydrogen = int: hydrogen atom ID in fragment to fuse
skipping to change at line 48		skipping to change at line 61
'''		'''
if not selection in _self.get_names("selections"):		if not selection in _self.get_names("selections"):
if fragment in _self.get_names("objects"):		if fragment in _self.get_names("objects"):
print(" Error: an object with than name already exists")		print(" Error: an object with than name already exists")
raise QuietException		raise QuietException
else:		else:
_self.fragment(fragment)		_self.fragment(fragment)
if _self.get_setting_boolean("auto_remove_hydrogens"):		if _self.get_setting_boolean("auto_remove_hydrogens"):
_self.remove("(hydro and %s)"%fragment)		_self.remove("(hydro and %s)"%fragment)
else:		else:
_self.fragment(fragment,tmp_editor)		_self.fragment(fragment,tmp_editor, origin=0)
if _self.count_atoms("((%s) and elem H)"%selection,quiet=1):		if _self.count_atoms("((%s) and elem H)"%selection,quiet=1):
_self.fuse("(%s and id %d)"%(tmp_editor,hydrogen),"(pk1)",1)		_self.fuse("(%s and id %d)"%(tmp_editor,hydrogen),"(pk1)",1)
if _self.get_setting_boolean("auto_remove_hydrogens"):		if _self.get_setting_boolean("auto_remove_hydrogens"):
_self.remove("(hydro and pkmol)")		_self.remove("(hydro and pkmol)")
else:		else:
_self.remove("(%s and id %d)"%(tmp_editor,hydrogen))		_self.remove("(%s and id %d)"%(tmp_editor,hydrogen))
_self.fuse("(%s and id %d)"%(tmp_editor,anchor),"(pk1)",1)		_self.fuse("(%s and id %d)"%(tmp_editor,anchor),"(pk1)",1)
if _self.get_setting_boolean("auto_remove_hydrogens"):		if _self.get_setting_boolean("auto_remove_hydrogens"):
_self.remove("(hydro and pkmol)")		_self.remove("(hydro and pkmol)")
		elif _self.count_atoms('hydro and (neighbor pk2)'):
		_self.h_fill()
_self.delete(tmp_editor)		_self.delete(tmp_editor)
def combine_fragment(selection,fragment,hydrogen,anchor,_self=cmd):		def combine_fragment(selection,fragment,hydrogen,anchor,_self=cmd):
if selection in _self.get_names("selections"):		with undocontext(_self, selection):
_self.fragment(fragment,tmp_editor)		_self.fragment(fragment,tmp_editor)
if _self.count_atoms("((%s) and elem H)"%selection,quiet=1):		try:
_self.fuse("(%s and id %d)"%(tmp_editor,hydrogen),"(pk1)",3)
if _self.get_setting_boolean("auto_remove_hydrogens"):
_self.remove("(hydro and pkmol)")
else:
_self.fuse("(%s and id %d)"%(tmp_editor,anchor),"(pk1)",3)
if _self.get_setting_boolean("auto_remove_hydrogens"):		if _self.get_setting_boolean("auto_remove_hydrogens"):
_self.remove("(hydro and pkmol)")		_self.remove("(hydro and ?%s)" % tmp_editor)
_self.delete(tmp_editor)		_self.fuse("?%s" % tmp_editor, "(%s)" % selection, 3)
		finally:
		_self.delete(tmp_editor)
#from time import time as ___time		#from time import time as ___time
#___total = 0.0		#___total = 0.0
#___seg1 = 0.0		#___seg1 = 0.0
#___seg2 = 0.0		#___seg2 = 0.0
#___seg3 = 0.0		#___seg3 = 0.0
#___pass = 0		#___pass = 0
#___last = ___time()		#___last = ___time()
def attach_amino_acid(selection,amino_acid,center=0,animate=-1,object="",hydro=- 1,ss=-1,_self=cmd):		def attach_amino_acid(selection,amino_acid,center=0,animate=-1,object="",hydro=- 1,ss=-1,_self=cmd):
skipping to change at line 154		skipping to change at line 166
psi=-47.0		psi=-47.0
elif ss==2: # antipara-beta		elif ss==2: # antipara-beta
phi=-139.0		phi=-139.0
psi=135.0		psi=135.0
elif ss==3: # para-beta		elif ss==3: # para-beta
phi=-119.0		phi=-119.0
psi=113.0		psi=113.0
else:		else:
phi=180.0		phi=180.0
psi=180.0		psi=180.0
_self.fragment(amino_acid,tmp_editor)		_self.fragment(amino_acid,tmp_editor, origin=0)
if _self.count_atoms("elem N",domain=tmp_connect):		if _self.count_atoms("elem N",domain=tmp_connect):
tmp = [ None ]		tmp = [ None ]
_self.iterate(tmp_connect,"tmp[0]=resv", space={ 'tmp' : tmp })		_self.iterate(tmp_connect,"tmp[0]=resv", space={ 'tmp' : tmp })
tmp[0] = str(tmp[0]-1) # counting down		tmp[0] = str(tmp[0]-1) # counting down
_self.alter(tmp_editor,"resi=tmp[0]",space={ 'tmp' : tmp})		_self.alter(tmp_editor,"resi=tmp[0]",space={ 'tmp' : tmp})
_self.set_geometry(tmp_connect, 3, 3) # make nitrogen planar		_self.set_geometry(tmp_connect, 3, 3) # make nitrogen planar
_self.fuse("(%s and name C)"%(tmp_editor),tmp_connect,2)		_self.fuse("(%s and name C)"%(tmp_editor),tmp_connect,2)
_self.select(tmp_domain, "byresi (pk1 | pk2)")		_self.select(tmp_domain, "byresi (pk1 | pk2)")
if not hydro:		if not hydro:
skipping to change at line 406		skipping to change at line 418
resi = resi - 1		resi = resi - 1
if not len(sequence):		if not len(sequence):
r = DEFAULT_SUCCESS		r = DEFAULT_SUCCESS
if _self.get_setting_int('auto_zoom'):		if _self.get_setting_int('auto_zoom'):
_self.zoom(name)		_self.zoom(name)
return r		return r
def fab(input,name=None,mode='peptide',resi=1,chain='',segi='',state=-1,		def fab(input,name=None,mode='peptide',resi=1,chain='',segi='',state=-1,
dir=1,hydro=-1,ss=0,async=-1,quiet=1,_self=cmd):		dir=1,hydro=-1,ss=0,async_=-1,quiet=1,_self=cmd, **kwargs):
'''		'''
DESCRIPTION		DESCRIPTION
Build a peptide		Build a peptide
ARGUMENTS		ARGUMENTS
input = str: sequence in one-letter code		input = str: sequence in one-letter code
name = str: name of object to create {default: }		name = str: name of object to create {default: }
ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat		ss = int: Secondary structure 1=alpha helix, 2=antiparallel beta, 3=parallel beta, 4=flat
EXAMPLE		EXAMPLE
fab ACDEFGH		fab ACDEFGH
fab ACDEFGH, helix, ss=1		fab ACDEFGH, helix, ss=1
'''		'''
if async<1:		async_ = int(kwargs.pop('async', async_))
		if kwargs:
		raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs))
		if async_ < 1:
r = _fab(input,name,mode,resi,chain,segi,		r = _fab(input,name,mode,resi,chain,segi,
state,dir,hydro,ss,quiet,_self)		state,dir,hydro,ss,quiet,_self)
else:		else:
fab_thread = threading.Thread(target=_fab, args=(input,name,mode,		fab_thread = threading.Thread(target=_fab, args=(input,name,mode,
resi,chain,		resi,chain,
segi,state,dir,		segi,state,dir,
hydro,ss,quiet,_self))		hydro,ss,quiet,_self))
fab_thread.setDaemon(1)		fab_thread.setDaemon(1)
fab_thread.start()		fab_thread.start()
r = DEFAULT_SUCCESS		r = DEFAULT_SUCCESS
End of changes. 9 change blocks.
13 lines changed or deleted		30 lines changed or added

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