/usr/lib/python2.7/dist-packages/pymol/computing.py is in pymol 1.8.4.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------------------------------------------------------------------
#G* Please see the accompanying LICENSE file for further information.
#H* -------------------------------------------------------------------
#I* Additional authors of this source file include:
#-*
#-*
#-*
#Z* -------------------------------------------------------------------
from __future__ import print_function, absolute_import
cmd_module = __import__("sys").modules["pymol.cmd"]
from .cmd import _cmd, lock, unlock, Shortcut, \
_feedback, fb_module, fb_mask, \
DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, is_ok, is_error, \
is_list, safe_list_eval, is_string
import traceback
import threading
import os
def model_to_sdf_list(self_cmd,model):
from chempy import io
sdf_list = io.mol.toList(model)
fixed = []
restrained = []
at_id = 1
for atom in model.atom:
if atom.flags & 4:
if hasattr(atom,'ref_coord'):
restrained.append( [at_id,atom.ref_coord])
if atom.flags & 8:
fixed.append(at_id)
at_id = at_id + 1
fit_flag = 1
if len(fixed):
fit_flag = 0
sdf_list.append("> <FIXED_ATOMS>\n")
sdf_list.append("+ ATOM\n");
for ID in fixed:
sdf_list.append("| %4d\n"%ID)
sdf_list.append("\n")
if len(restrained):
fit_flag = 0
sdf_list.append("> <RESTRAINED_ATOMS>\n")
sdf_list.append("+ ATOM MIN MAX F_CONST X Y Z\n")
for entry in restrained:
xrd = entry[1]
sdf_list.append("| %4d %6.3f %6.3f %6.3f %10.4f %10.4f %10.4f\n"%
(entry[0],0,0,3,xrd[0],xrd[1],xrd[2]))
sdf_list.append("\n")
electro_mode = int(self_cmd.get('clean_electro_mode'))
if electro_mode == 0:
fit_flag = 0
sdf_list.append("> <ELECTROSTATICS>\n")
sdf_list.append("+ TREATMENT\n")
sdf_list.append("| NONE\n")
sdf_list.append("\n")
sdf_list.append("$$$$\n")
# for line in sdf_list:
# print line,
return (fit_flag, sdf_list)
def get_energy_from_rec(rec):
# we really need to replace this with a proper SD parser...
result = 9999.00
try:
rec_list = rec.splitlines()
read_energy = 0
for line in rec_list:
if read_energy == 1:
result = float(line.strip())
break
if line.strip() == '> <MMFF94 energy>':
read_energy = 1
except:
traceback.print_exc()
return result
class CleanJob:
def __init__(self,self_cmd,sele,state=-1,message=None):
self.cmd = self_cmd
if message == '':
message = None
if state<1:
state = self_cmd.get_state()
# this code will moved elsewhere
self.ok = 1
try:
from freemol import mengine
except:
self.ok = 0
print("Error: unable to import freemol.mengine module.")
print("This PyMOL build appears not to include full modeling capabilities.")
return
if self.ok:
if not mengine.validate():
self.ok = 0
print("Error: Unable to validate freemol.mengine")
return
if self.ok:
if self_cmd.count_atoms(sele) > 999:
self.ok = 0
print("Error: Sorry, clean is currently limited to 999 atoms")
return
if not self.ok:
pass
# we can't call warn because this is the not the tcl-tk gui thread
# warn("Please be sure that FreeMOL is correctly installed.")
else:
if message != None:
self.cmd.do("_ cmd.wizard('message','''%s''')"%message)
obj_list = self_cmd.get_object_list("bymol ("+sele+")")
self.ok = 0
result = None
if is_list(obj_list) and (len(obj_list)==1):
obj_name = obj_list[0]
self_cmd.sculpt_deactivate(obj_name)
# eliminate all sculpting information for object
self.cmd.sculpt_purge()
self.cmd.set("sculpting",0)
state = self_cmd.get_state()
if self_cmd.count_atoms(obj_name+" and flag 2"): # any atoms restrained?
self_cmd.reference("validate",obj_name,state) # then we have reference coordinates
input_model = self_cmd.get_model(obj_name,state=state)
(fit_flag, sdf_list) = model_to_sdf_list(self_cmd,input_model)
input_sdf = ''.join(sdf_list)
# print input_sdf
result = mengine.run(input_sdf)
if result != None:
if len(result):
clean_sdf = result[0]
clean_rec = clean_sdf.split("$$$$")[0]
clean_name = ""
self.energy = get_energy_from_rec(clean_rec)
try:
if len(clean_rec) and int(self.energy) != 9999:
clean_name = "builder_clean_tmp"
self_cmd.set("suspend_updates")
self.ok = 1
else:
self.ok = 0
if self.ok:
self_cmd.read_molstr(clean_rec, clean_name, zoom=0)
# need to insert some error checking here
if clean_name in self_cmd.get_names("objects"):
self_cmd.set("retain_order","1",clean_name)
if fit_flag:
self_cmd.fit(clean_name, obj_name, matchmaker=4,
mobile_state=1, target_state=state)
self_cmd.push_undo(obj_name)
self_cmd.update(obj_name, clean_name, matchmaker=0,
source_state=1, target_state=state)
self_cmd.sculpt_activate(obj_name)
self_cmd.sculpt_deactivate(obj_name)
self.ok = 1
message = "Clean: Finished. Energy = %3.2f" % self.energy
if message != None:
self.cmd.do("_ cmd.wizard('message','''%s''')"%message)
self.cmd.do("_ wizard")
except ValueError:
self.ok = 0
finally:
self_cmd.delete(clean_name)
self_cmd.unset("suspend_updates")
if not self.ok:
# we can't call warn because this is the not the tcl-tk gui thread
if result != None:
if len(result)>1:
print("\n=== mengine errors below === ")
print(result[1].replace("\n\n","\n"), end=' ')
print("=== mengine errors above ===\n")
failed_file = "cleanup_failed.sdf"
print("Clean-Error: Structure cleanup failed. Invalid input or software malfuction?")
aromatic = 0
for bond in input_model.bond:
if bond.order == 4:
aromatic = 1
try:
open(failed_file,'wb').write(input_sdf)
print("Clean-Error: Wrote SD file '%s' into the directory:"%failed_file)
print("Clean-Error: '%s'."%os.getcwd())
print("Clean-Error: If you believe PyMOL should be able to handle this structure")
print("Clean-Error: then please email that SD file to help@schrodinger.com. Thank you!")
except IOError:
print("Unabled to write '%s"%failed_file)
if aromatic:
print("Clean-Warning: Please eliminate aromatic bonds and then try again.")
if message!=None:
self_cmd.do("_ wizard")
def _clean(selection, present='', state=-1, fix='', restrain='',
method='mmff', async=0, save_undo=1, message=None,
_self=cmd_module):
self_cmd = _self
clean1_sele = "_clean1_tmp"
clean2_sele = "_clean2_tmp"
clean_obj = "_clean_obj"
r = DEFAULT_SUCCESS
c = None
if self_cmd.select(clean1_sele,selection,enable=0)>0:
try:
if present=='':
self_cmd.select(clean2_sele," byres (byres ("+selection+") extend 1)",enable=0) # go out 2 residues
else:
self_cmd.select(clean2_sele, clean1_sele+" or ("+present+")",enable=0)
suspend_undo = self_cmd.get("suspend_undo")
self_cmd.set("suspend_undo", updates=0)
self_cmd.set("suspend_updates")
self_cmd.rename(clean2_sele) # ensure identifiers are unique
self_cmd.create(clean_obj, clean2_sele, zoom=0, source_state=state,target_state=1)
self_cmd.disable(clean_obj)
self_cmd.unset("suspend_updates")
self_cmd.flag(3,clean_obj+" in ("+clean2_sele+" and not "+clean1_sele+")","set")
# fix nearby atoms
self_cmd.h_add(clean_obj) # fill any open valences
if message == None:
at_cnt = self_cmd.count_atoms(clean_obj)
message = 'Clean: Cleaning %d atoms. Please wait...'%at_cnt
c = CleanJob(self_cmd, clean_obj, state, message=message)
if c.ok:
self_cmd.set("suspend_undo", suspend_undo, updates=0)
self_cmd.push_undo(selection)
self_cmd.update(clean1_sele, clean_obj,
source_state=1, target_state=state)
self_cmd.set("suspend_undo", True, updates=0)
self_cmd.delete(clean_obj)
self_cmd.delete(clean1_sele)
self_cmd.delete(clean2_sele)
self_cmd.set("suspend_undo", suspend_undo, updates=0)
except:
traceback.print_exc()
if hasattr(c,"energy"):
return c.energy
else:
return None
def clean(selection, present='', state=-1, fix='', restrain='',
method='mmff', async=0, save_undo=1, message=None,
_self=cmd_module):
if not int(async):
return _clean(selection,present,state,fix,restrain,method,async,save_undo,message,_self)
else:
try:
t = threading.Thread(target=_clean,
args=(selection,present,state,fix,restrain,
method,async,save_undo,message,_self))
t.setDaemon(1)
t.start()
except:
traceback.print_exc()
return 0
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