def amber99(selection="(all)",quiet=0,_self=cmd):
cmd=_self
result = 1
# first, set all parameters to zero
cmd.alter(selection,"partial_charge=0")
cmd.alter(selection,"elec_radius=0.0")
cmd.alter(selection,"text_type=''")
# next, flag all atoms so that we'll be able to detect what we miss
cmd.flag(23,selection,'set')
# get the amber99 dictionary
if not hasattr(champ,'amber99_dict'):
from chempy.champ.amber99 import amber99_dict
champ.amber99_dict = amber99_dict
# iterate through the residue dictionary matching each residue based on chemistry
# and generating the expressions for reassigning formal charges
alter_list = []
for resn in champ.amber99_dict.keys():
if cmd.select(tmp_sele1,"(%s) and resn %s"%(selection,resn))>0:
entry = champ.amber99_dict[resn]
for rule in entry:
model = cmd.get_model(tmp_sele1)
ch = Champ()
model_pat = ch.insert_model(model)
ch.pattern_detect_chirality(model_pat)
assn_pat = ch.insert_pattern_string(rule[0])
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1])==1: # one and only one match
tag = atom_tag[1][0]
prop_list = rule[1][tag]
# the following expression both changes the formal charge and resets flag 23
alter_list.append([atom_tag[0],
"name='''%s''';text_type='''%s''';partial_charge=%f;elec_radius=%f;flags=flags&-8388609"%prop_list])
# now evaluate all of these expressions efficiently en-masse
cmd.alter_list(selection,alter_list)
# see if we missed any atoms
missed_count = cmd.count_atoms("("+selection+") and flag 23")
if missed_count>0:
if not quiet:
# looks like we did, so alter the user
print " WARNING: %d atoms did not have properties assigned"%missed_count
result = 0
# remove the temporary selection we used to select appropriate residues
cmd.delete(tmp_sele1)
return result
def formal_charges(selection="(all)", quiet=0, _self=cmd):
cmd = _self
result = 1
# assumes that hydogens are not present!
# first, set all formal charges to zero
cmd.alter(selection, "formal_charge=0")
# next, flag all atoms so that we'll be able to detect what we miss
cmd.flag(23, selection, 'set')
# get the residue dictionary for formal charges
if not hasattr(champ, 'formal_charge_dict'):
from chempy.champ.formal_charges import formal_charge_dict
champ.formal_charge_dict = formal_charge_dict
# iterate through the residue dictionary matching each residue based on chemistry
# and generating the expressions for reassigning formal charges
alter_list = []
for resn in champ.formal_charge_dict.keys():
if cmd.select(tmp_sele1, "(%s) and resn %s" % (selection, resn)) > 0:
entry = champ.formal_charge_dict[resn]
for rule in entry:
model = cmd.get_model(tmp_sele1)
ch = Champ()
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string(rule[0])
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat, model_pat, 10000, 2) > 0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1]) == 1: # one and only one match
tag = atom_tag[1][0]
formal_charge = rule[1][tag]
# the following expression both changes the formal charge and resets flag 23
alter_list.append([
atom_tag[0],
"formal_charge=%d;flags=flags&-8388609" %
formal_charge
])
if 1: # n-terminal amine
# non-proline
ch = Champ()
model = cmd.get_model(selection)
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("[N;D1]<0>CC(=O)")
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat, model_pat, 10000, 2) > 0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1]) == 1: # one and only one match
if atom_tag[1][0] == 0:
# the following expression both changes the formal charge and resets flag 23
alter_list.append([
atom_tag[0], "formal_charge=1;flags=flags&-8388609"
])
# proline residues
ch = Champ()
model = cmd.get_model(selection)
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("C1CC[N;D2]<0>C1C(=O)")
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat, model_pat, 10000, 2) > 0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1]) == 1: # one and only one match
if atom_tag[1][0] == 0:
# the following expression both changes the formal charge and resets flag 23
alter_list.append([
atom_tag[0], "formal_charge=1;flags=flags&-8388609"
])
if 1: # c-terminal acid
ch = Champ()
model = cmd.get_model(selection)
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("NCC(=O<0>)[O;D1]<1>")
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat, model_pat, 10000, 2) > 0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1]) == 1: # one and only one match
if atom_tag[1][0] == 1:
# the following expression both changes the formal charge and resets flag 23
alter_list.append([
atom_tag[0],
"formal_charge=-1;flags=flags&-8388609"
])
# now evaluate all of these expressions efficiently en-masse
cmd.alter_list(selection, alter_list)
# see if we missed any atoms
missed_count = cmd.count_atoms("(" + selection + ") and flag 23")
if missed_count > 0:
if not quiet:
# looks like we did, so alter the user
print(" WARNING: %d atoms did not have formal charges assigned" %
missed_count)
result = 0
# remove the temporary selection we used to select appropriate residues
cmd.delete(tmp_sele1)
return result
def formal_charges(selection="(all)",quiet=0,_self=cmd):
cmd=_self
result = 1
# assumes that hydogens are not present!
# first, set all formal charges to zero
cmd.alter(selection,"formal_charge=0")
# next, flag all atoms so that we'll be able to detect what we miss
cmd.flag(23,selection,'set')
# get the residue dictionary for formal charges
if not hasattr(champ,'formal_charge_dict'):
from chempy.champ.formal_charges import formal_charge_dict
champ.formal_charge_dict = formal_charge_dict
# iterate through the residue dictionary matching each residue based on chemistry
# and generating the expressions for reassigning formal charges
alter_list = []
for resn in champ.formal_charge_dict.keys():
if cmd.select(tmp_sele1,"(%s) and resn %s"%(selection,resn))>0:
entry = champ.formal_charge_dict[resn]
for rule in entry:
model = cmd.get_model(tmp_sele1)
ch = Champ()
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string(rule[0])
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1])==1: # one and only one match
tag = atom_tag[1][0]
formal_charge = rule[1][tag]
# the following expression both changes the formal charge and resets flag 23
alter_list.append([atom_tag[0],
"formal_charge=%d;flags=flags&-8388609"%formal_charge])
if 1: # n-terminal amine
# non-proline
ch=Champ()
model = cmd.get_model(selection)
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("[N;D1]<0>CC(=O)")
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1])==1: # one and only one match
if atom_tag[1][0]==0:
# the following expression both changes the formal charge and resets flag 23
alter_list.append([atom_tag[0],
"formal_charge=1;flags=flags&-8388609"])
# proline residues
ch=Champ()
model = cmd.get_model(selection)
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("C1CC[N;D2]<0>C1C(=O)")
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1])==1: # one and only one match
if atom_tag[1][0]==0:
# the following expression both changes the formal charge and resets flag 23
alter_list.append([atom_tag[0],
"formal_charge=1;flags=flags&-8388609"])
if 1: # c-terminal acid
ch=Champ()
model = cmd.get_model(selection)
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("NCC(=O<0>)[O;D1]<1>")
ch.pattern_clear_tags(model_pat)
if ch.match_1v1_n(assn_pat,model_pat,10000,2)>0:
result = ch.pattern_get_ext_indices_with_tags(model_pat)
for atom_tag in result[0]: # just iterate over atom tags
if len(atom_tag[1])==1: # one and only one match
if atom_tag[1][0]==1:
# the following expression both changes the formal charge and resets flag 23
alter_list.append([atom_tag[0],
"formal_charge=-1;flags=flags&-8388609"])
# now evaluate all of these expressions efficiently en-masse
cmd.alter_list(selection,alter_list)
# see if we missed any atoms
missed_count = cmd.count_atoms("("+selection+") and flag 23")
if missed_count>0:
if not quiet:
# looks like we did, so alter the user
print " WARNING: %d atoms did not have formal charges assigned"%missed_count
result = 0
# remove the temporary selection we used to select appropriate residues
cmd.delete(tmp_sele1)
return result
def test_alter_list(self):
cmd.fragment('gly')
cmd.alter_list('gly', [[i+1, 'name = "X%d"' % i] for i in range(7)])
name_list = []
cmd.iterate('gly', 'name_list.append(name)', space=locals())
self.assertEqual(name_list, ['X%d' % i for i in range(7)])
def test_alter_list(self):
cmd.fragment('gly')
cmd.alter_list('gly', [[i + 1, 'name = "X%d"' % i] for i in range(7)])
name_list = []
cmd.iterate('gly', 'name_list.append(name)', space=locals())
self.assertEqual(name_list, ['X%d' % i for i in range(7)])
