def test_attach(self):
cmd.pseudoatom()
cmd.edit('first all')
cmd.attach('C', 1, 1)
self.assertEqual(2, cmd.count_atoms())
cmd.attach('C', 1, 1)
self.assertEqual(3, cmd.count_atoms())
self.assertEqual(['C01', 'C02', 'PS1'], sorted(get_atom_names()))
def test_attach(self):
cmd.pseudoatom()
cmd.edit('first all')
cmd.attach('C', 1, 1)
self.assertEqual(2, cmd.count_atoms())
cmd.attach('C', 1, 1)
self.assertEqual(3, cmd.count_atoms())
self.assertEqual(['C01', 'C02', 'PS1'], sorted(get_atom_names()))
def missing_c_termini(selection="(all)", quiet=0, _self=cmd):
cmd = _self
# assumes that hydogens are not present!
sele_list = []
ch = Champ()
model = cmd.get_model(selection)
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("[N+0+1]C[C;D2]<0>(=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:
sele_list.append(atom_tag[0])
cmd.select_list(tmp_sele1, selection, sele_list, mode='index')
while cmd.pop(tmp_sele2, tmp_sele1) > 0: # complete the carboxy terminus
cmd.edit(tmp_sele2)
cmd.attach("O", 1, 1, "OXT", quiet=1)
cmd.unpick()
cmd.delete(tmp_sele1)
def missing_c_termini(selection="(all)",quiet=0,_self=cmd):
cmd=_self
# assumes that hydogens are not present!
sele_list = []
ch=Champ()
model = cmd.get_model(selection)
model_pat = ch.insert_model(model)
assn_pat = ch.insert_pattern_string("[N+0+1]C[C;D2]<0>(=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:
sele_list.append(atom_tag[0])
cmd.select_list(tmp_sele1,selection,sele_list, mode='index')
while cmd.pop(tmp_sele2,tmp_sele1)>0: # complete the carboxy terminus
cmd.edit(tmp_sele2)
cmd.attach("O",1,1,"OXT",quiet=1)
cmd.unpick()
cmd.delete(tmp_sele1)
def test_attach(self):
cmd.pseudoatom()
cmd.edit('first all')
cmd.attach('C', 1, 1)
self.assertEqual(2, cmd.count_atoms())