"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "examples/cookbook/symsph.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.

symsph.py  (pymol-v1.8.6.0.tar.bz2)	:	symsph.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 14		skipping to change at line 14
#		#
# symexp name [,selection [,cutoff ]]		# symexp name [,selection [,cutoff ]]
from pymol import cmd as global_cmd		from pymol import cmd as global_cmd
def symsph(name, selection="sele", cutoff=20.0, self_cmd=global_cmd):		def symsph(name, selection="sele", cutoff=20.0, self_cmd=global_cmd):
cutoff = float(cutoff)		cutoff = float(cutoff)
prefix = selection+"_symarea_"		prefix = selection+"_symarea_"
tmp_obj = selection+"_tmp"		tmp_obj = selection+"_tmp"
if selection not in self_cmd.get_names("selections"):		if selection not in self_cmd.get_names("selections"):
print " error: '"+selection+"' is not defined."		print(" error: '"+selection+"' is not defined.")
return self_cmd.DEFAULT_FAILURE		return self_cmd.DEFAULT_ERROR
if not self_cmd.count_atoms(selection):		if not self_cmd.count_atoms(selection):
print " error: '"+selection+"' contains no atoms."		print(" error: '"+selection+"' contains no atoms.")
return self_cmd.DEFAULT_FAILURE		return self_cmd.DEFAULT_ERROR
obj_list = self_cmd.get_object_list(selection)		obj_list = self_cmd.get_object_list(selection)
if len(obj_list)!=1:		if len(obj_list)!=1:
print script_name+" error: '"+selection+"' must only span one object.'"		print(script_name+" error: '"+selection+"' must only span one object.'")
return self_cmd.DEFAULT_FAILURE		return self_cmd.DEFAULT_ERROR
obj = obj_list[0]		obj = obj_list[0]
cmd.center(selection)		cmd.center(selection)
cmd.pseudoatom(tmp_obj)		cmd.pseudoatom(tmp_obj)
cmd.delete(prefix+"*")		cmd.delete(prefix+"*")
cmd.symexp(prefix,obj,tmp_obj,cutoff,segi=1)		cmd.symexp(prefix,obj,tmp_obj,cutoff,segi=1)
cmd.create(name,"("+obj+" or "+prefix+"*) within %1.9f of %s"%(cutoff,tmp_ob j))		cmd.create(name,"("+obj+" or "+prefix+"*) within %1.9f of %s"%(cutoff,tmp_ob j))
cmd.delete(tmp_obj)		cmd.delete(tmp_obj)
cmd.delete(prefix+"*")		cmd.delete(prefix+"*")
#symsph("sele",20)		#symsph("sele",20)
End of changes. 3 change blocks.
6 lines changed or deleted		6 lines changed or added

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