"Fossies" - the Fresh Open Source Software Archive  

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

computing.py  (pymol-v1.8.6.0.tar.bz2)	:	computing.py  (pymol-v2.1.0.tar.bz2)
skipping to change at line 17		skipping to change at line 17
#G* Please see the accompanying LICENSE file for further information.		#G* Please see the accompanying LICENSE file for further information.
#H* -------------------------------------------------------------------		#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:		#I* Additional authors of this source file include:
#-*		#-*
#-*		#-*
#-*		#-*
#Z* -------------------------------------------------------------------		#Z* -------------------------------------------------------------------
from __future__ import print_function, absolute_import		from __future__ import print_function, absolute_import
		import sys
cmd_module = __import__("sys").modules["pymol.cmd"]		cmd_module = __import__("sys").modules["pymol.cmd"]
from .cmd import _cmd, lock, unlock, Shortcut, \		from .cmd import _cmd, lock, unlock, Shortcut, \
_feedback, fb_module, fb_mask, \		_feedback, fb_module, fb_mask, \
DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error, \		DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error, \
is_list, safe_list_eval, is_string		is_list, safe_list_eval, is_string
import traceback		import traceback
import threading		import threading
import os		import os
		import pymol
def model_to_sdf_list(self_cmd,model):		def model_to_sdf_list(self_cmd,model):
from chempy import io		from chempy import io
sdf_list = io.mol.toList(model)		sdf_list = io.mol.toList(model)
fixed = []		fixed = []
restrained = []		restrained = []
at_id = 1		at_id = 1
for atom in model.atom:		for atom in model.atom:
if atom.flags & 4:		if atom.flags & 4:
skipping to change at line 135		skipping to change at line 137
# eliminate all sculpting information for object		# eliminate all sculpting information for object
self.cmd.sculpt_purge()		self.cmd.sculpt_purge()
self.cmd.set("sculpting",0)		self.cmd.set("sculpting",0)
state = self_cmd.get_state()		state = self_cmd.get_state()
if self_cmd.count_atoms(obj_name+" and flag 2"): # any atoms res trained?		if self_cmd.count_atoms(obj_name+" and flag 2"): # any atoms res trained?
self_cmd.reference("validate",obj_name,state) # then we have reference coordinates		self_cmd.reference("validate",obj_name,state) # then we have reference coordinates
input_model = self_cmd.get_model(obj_name,state=state)		input_model = self_cmd.get_model(obj_name,state=state)
(fit_flag, sdf_list) = model_to_sdf_list(self_cmd,input_model)		(fit_flag, sdf_list) = model_to_sdf_list(self_cmd,input_model)
input_sdf = ''.join(sdf_list)		input_sdf = ''.join(sdf_list)
# print input_sdf		# print input_sdf
		if sys.version_info[0] > 2:
		input_sdf = input_sdf.encode()
result = mengine.run(input_sdf)		result = mengine.run(input_sdf)
if result != None:		if result != None:
if len(result):		if len(result):
clean_sdf = result[0]		clean_sdf = result[0]
		if sys.version_info[0] > 2:
		clean_sdf = clean_sdf.decode()
clean_rec = clean_sdf.split("$$$$")[0]		clean_rec = clean_sdf.split("$$$$")[0]
clean_name = ""		clean_name = ""
self.energy = get_energy_from_rec(clean_rec)		self.energy = get_energy_from_rec(clean_rec)
try:		try:
if len(clean_rec) and int(self.energy) != 9999:		if len(clean_rec) and int(self.energy) != 9999:
clean_name = "builder_clean_tmp"		clean_name = "builder_clean_tmp"
self_cmd.set("suspend_updates")		self_cmd.set("suspend_updates")
self.ok = 1		self.ok = 1
else:		else:
self.ok = 0		self.ok = 0
skipping to change at line 200		skipping to change at line 210
print("Clean-Error: If you believe PyMOL should be able to h andle this structure")		print("Clean-Error: If you believe PyMOL should be able to h andle this structure")
print("Clean-Error: then please email that SD file to help@s chrodinger.com. Thank you!")		print("Clean-Error: then please email that SD file to help@s chrodinger.com. Thank you!")
except IOError:		except IOError:
print("Unabled to write '%s"%failed_file)		print("Unabled to write '%s"%failed_file)
if aromatic:		if aromatic:
print("Clean-Warning: Please eliminate aromatic bonds and th en try again.")		print("Clean-Warning: Please eliminate aromatic bonds and th en try again.")
if message!=None:		if message!=None:
self_cmd.do("_ wizard")		self_cmd.do("_ wizard")
def _clean(selection, present='', state=-1, fix='', restrain='',		def _clean(selection, present='', state=-1, fix='', restrain='',
method='mmff', async=0, save_undo=1, message=None,		method='mmff', save_undo=1, message=None,
_self=cmd_module):		_self=cmd_module):
self_cmd = _self		self_cmd = _self
clean1_sele = "_clean1_tmp"		clean1_sele = "_clean1_tmp"
clean2_sele = "_clean2_tmp"		clean2_sele = "_clean2_tmp"
clean_obj = "_clean_obj"		clean_obj = "_clean_obj"
r = DEFAULT_SUCCESS		r = DEFAULT_SUCCESS
c = None		c = None
if self_cmd.select(clean1_sele,selection,enable=0)>0:		if self_cmd.select(clean1_sele,selection,enable=0)>0:
skipping to change at line 254		skipping to change at line 264
self_cmd.delete(clean2_sele)		self_cmd.delete(clean2_sele)
self_cmd.set("suspend_undo", suspend_undo, updates=0)		self_cmd.set("suspend_undo", suspend_undo, updates=0)
except:		except:
traceback.print_exc()		traceback.print_exc()
if hasattr(c,"energy"):		if hasattr(c,"energy"):
return c.energy		return c.energy
else:		else:
return None		return None
def clean(selection, present='', state=-1, fix='', restrain='',		def clean(selection, present='', state=-1, fix='', restrain='',
method='mmff', async=0, save_undo=1, message=None,		method='mmff', async_=0, save_undo=1, message=None,
_self=cmd_module):		_self=cmd_module, **kwargs):
if not int(async):		if int(state) == 0:
return _clean(selection,present,state,fix,restrain,method,async,save_und		raise pymol.CmdException('cleaning all states not supported')
o,message,_self)
		async_ = int(kwargs.pop('async', async_))
		if kwargs:
		raise pymol.CmdException('unknown argument: ' + ', '.join(kwargs))
		args = (selection, present, state, fix, restrain, method, save_undo, message
		, _self)
		if not async_:
		return _clean(*args)
else:		else:
try:		try:
t = threading.Thread(target=_clean,		t = threading.Thread(target=_clean,
args=(selection,present,state,fix,restrain,		args=args)
method,async,save_undo,message,_self))
t.setDaemon(1)		t.setDaemon(1)
t.start()		t.start()
except:		except:
traceback.print_exc()		traceback.print_exc()
return 0		return 0
End of changes. 7 change blocks.
8 lines changed or deleted		27 lines changed or added

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