def protein_assign_charges_and_radii(obj_name, _self=cmd):
cmd = _self
from chempy.champ import assign
# apply a few kludges
# convent Seleno-methionine to methionine
cmd.alter(obj_name + "///MSE/SE", "elem='S';name='SD'", quiet=1)
cmd.alter(obj_name + "///MSE/", "resn='MET'", quiet=1)
cmd.flag("ignore", obj_name, "clear")
# remove alternate conformers
cmd.remove(obj_name + " and not alt ''+A")
cmd.alter(obj_name, "alt=''")
cmd.sort(obj_name)
cmd.fix_chemistry(obj_name, obj_name, 1)
# make sure all atoms are included...
cmd.alter(obj_name, "q=1.0", quiet=1)
print(" Util: Fixing termini and assigning formal charges...")
assign.missing_c_termini(obj_name, quiet=1, _self=_self)
while not assign.formal_charges(obj_name, quiet=1, _self=_self):
print(
" WARNING: unrecognized or incomplete residues are being deleted:")
cmd.iterate(
"(byres (" + obj_name + " and flag 23)) and flag 31",
'print(" "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/")',
quiet=1)
cmd.remove(
"byres (" + obj_name +
" and flag 23)") # get rid of residues that weren't assigned
assign.missing_c_termini(obj_name, quiet=1, _self=_self)
print(" Util: Assigning Amber 99 charges and radii...")
cmd.h_add(obj_name)
if not assign.amber99(obj_name, quiet=1, _self=_self):
print(" WARNING: some unassigned atoms are being deleted:")
cmd.iterate(
"byres (" + obj_name + " and flag 23)",
'print(" "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"+name+"? ["+elem+"]")',
quiet=1)
cmd.remove(
obj_name +
" and flag 23") # get rid of any atoms that weren't assigned
# show the user what the net charges are...
formal = sum_formal_charges(obj_name, quiet=0, _self=_self)
partial = sum_partial_charges(obj_name, quiet=0, _self=_self)
if round(formal) != round(partial):
print(
" WARNING: formal and partial charge sums don't match -- there is a problem!"
)
def test_random():
'''
This is a simple test function which drops most coordinates from a
polypeptide and tries to reposition them with simple_unknowns().
Works fine to position hydrogens, fails to position other atoms.
'''
import random
from pymol import cmd
from chempy.champ import assign
cmd.fab('ACDEFGHIKLMNPQRSTVWY', 'm0')
assign.amber99()
for i in xrange(100):
m = cmd.get_model('m0').convert_to_connected()
for a in m.atom:
if random.random() < 0.8:
del a.coord
simple_unknowns(m)
cmd.load_model(m.convert_to_indexed(), 'm' + str(i + 1))
def protein_assign_charges_and_radii(obj_name,_self=cmd):
pymol=_self._pymol
cmd=_self
from chempy.champ import assign
# apply a few kludges
# convent Seleno-methionine to methionine
cmd.alter(obj_name+"///MSE/SE","elem='S';name='SD'",quiet=1)
cmd.alter(obj_name+"///MSE/","resn='MET'",quiet=1)
cmd.flag("ignore",obj_name,"clear")
# remove alternate conformers
cmd.remove(obj_name+" and not alt ''+A")
cmd.alter(obj_name,"alt=''")
cmd.sort(obj_name)
cmd.fix_chemistry(obj_name,obj_name,1)
# make sure all atoms are included...
cmd.alter(obj_name,"q=1.0",quiet=1)
print " Util: Fixing termini and assigning formal charges..."
assign.missing_c_termini(obj_name,quiet=1,_self=_self)
while not assign.formal_charges(obj_name,quiet=1,_self=_self):
print " WARNING: unrecognized or incomplete residues are being deleted:"
cmd.iterate("(byres ("+obj_name+" and flag 23)) and flag 31",
'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"',quiet=1)
cmd.remove("byres ("+obj_name+" and flag 23)") # get rid of residues that weren't assigned
assign.missing_c_termini(obj_name,quiet=1,_self=_self)
print " Util: Assigning Amber 99 charges and radii..."
cmd.h_add(obj_name)
if not assign.amber99(obj_name,quiet=1,_self=_self):
print " WARNING: some unassigned atoms are being deleted:"
cmd.iterate("byres ("+obj_name+" and flag 23)",
'print " "+model+"/"+segi+"/"+chain+"/"+resn+"`"+resi+"/"+name+"? ["+elem+"]"',quiet=1)
cmd.remove(obj_name+" and flag 23") # get rid of any atoms that weren't assigned
# show the user what the net charges are...
formal = sum_formal_charges(obj_name,quiet=0,_self=_self)
partial = sum_partial_charges(obj_name,quiet=0,_self=_self)
if round(formal)!=round(partial):
print " WARNING: formal and partial charge sums don't match -- there is a problem!"