Exemple #1
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 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()))
Exemple #2
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 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()))
Exemple #3
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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)
Exemple #4
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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)
Exemple #5
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 def test_attach(self):
     cmd.pseudoatom()
     cmd.edit('first all')
     cmd.attach('C', 1, 1)
     self.assertEqual(2, cmd.count_atoms())