def test_incomplete_termini(self):
monomer1 = protein.ProteinForm().from_str('{AA0062}')
monomer2 = protein.ProteinForm().from_str('{AA0318}')
dimer = protein.ProteinForm().from_str('{AA0062}{AA0318}')
self.assertEqual(dimer.validate(), [])
self.assertEqual(dimer.get_formula(),
monomer1.get_formula() + monomer2.get_formula() - EmpiricalFormula('OH3'))
self.assertEqual(dimer.get_charge(),
monomer1.get_charge() + monomer2.get_charge() - 1)
dimer = protein.ProteinForm().from_str('{AA0318}{AA0062}')
self.assertNotEqual(dimer.validate(), [])
def test_c_terminus_only(self):
# AA0062
form = protein.ProteinForm().from_str('{AA0062}')
self.assertEqual(form.validate(), [])
self.assertEqual(form.export('smiles'), form.seq[0].export('smiles'))
self.assertEqual(form.get_formula(), form.seq[0].get_formula())
self.assertEqual(form.get_charge(), form.seq[0].get_charge())
form = protein.ProteinForm().from_str('A{AA0062}')
self.assertNotEqual(form.validate(), [])
form = protein.ProteinForm().from_str('{AA0062}A')
self.assertEqual(form.validate(), [])
def test_no_termini(self):
# AA0344
monomer = Monomer(structure='OC[C@H](N1SC[C@@H](C1=O)[NH3+])C=O')
form = protein.ProteinForm()
form.seq.append(monomer)
self.assertEqual(form.validate(), [])
self.assertEqual(form.export('smiles'), form.seq[0].export('smiles'))
self.assertEqual(form.get_formula(), form.seq[0].get_formula())
self.assertEqual(form.get_charge(), form.seq[0].get_charge())
form = protein.ProteinForm()
form.seq.append(monomer)
form.seq.append(protein.protein_alphabet.monomers.A)
self.assertNotEqual(form.validate(), [])
form = protein.ProteinForm()
form.seq.append(protein.protein_alphabet.monomers.A)
form.seq.append(monomer)
self.assertNotEqual(form.validate(), [])
def test_ProteinForm_properties(self):
monomers = protein.canonical_protein_alphabet.monomers
form = protein.CanonicalProteinForm().from_str('A')
self.assertEqual(form.get_formula(), EmpiricalFormula('C3H7NO2') + EmpiricalFormula('H'))
self.assertEqual(form.get_charge(), 1)
self.assertEqual(form.export('smiles'), ALA_smiles)
form = protein.CanonicalProteinForm().from_str('AA')
self.assertEqual(form.get_formula(), EmpiricalFormula('C6H12N2O3') + EmpiricalFormula('H'))
self.assertEqual(form.get_charge(), 1)
self.assertEqual(form.export('smiles'), di_ALA_smiles)
form = protein.CanonicalProteinForm().from_str('AAA')
self.assertEqual(form.get_formula(), EmpiricalFormula('C9H17N3O4') + EmpiricalFormula('H'))
self.assertEqual(form.get_charge(), 1)
self.assertEqual(form.export('smiles'), tri_ALA_smiles)
form = protein.ProteinForm().from_str('AAA')
self.assertEqual(form.get_formula(), EmpiricalFormula('C9H17N3O4') + EmpiricalFormula('H'))
self.assertEqual(form.get_charge(), 1)
self.assertEqual(form.export('smiles'), tri_ALA_smiles)
def test_gen_genomic_viz(self):
form = protein.ProteinForm().from_str(('ACR:GCRGAARGCH:ILCA{SEL}RC' *
30) +
(' | x-link: ['
' l-bond-atom: 2S11'
' | r-bond-atom: 5S11'
' | l-displaced-atom: 2H11'
' | r-displaced-atom: 5H11'
']'
' | x-link: ['
' l-bond-atom: 40S11'
' | r-bond-atom: 80S11'
' | l-displaced-atom: 40H11'
' | r-displaced-atom: 80H11'
']'
' | x-link: ['
' l-bond-atom: 60S11'
' | r-bond-atom: 100S11'
' | l-displaced-atom: 60H11'
' | r-displaced-atom: 100H11'
']'
' | x-link: ['
' l-bond-atom: 20S11'
' | r-bond-atom: 160S11'
' | l-displaced-atom: 20H11'
' | r-displaced-atom: 160H11'
']'
' | x-link: ['
' l-bond-atom: 140S11'
' | r-bond-atom: 220S11'
' | l-displaced-atom: 140H11'
' | r-displaced-atom: 220H11'
']'))
seq_features = [{
'label': 'Processed',
'color': '#cccccc',
'positions': {
0: [[1, 30], [50, 85]]
},
}]
svg = util.gen_genomic_viz(
[form, form, form, form],
inter_crosslinks=[
mock.Mock(
get_l_bond_atoms=lambda:
[mock.Mock(subunit='0', monomer=100)],
get_r_bond_atoms=lambda:
[mock.Mock(subunit='3', monomer=150)],
),
mock.Mock(
get_l_bond_atoms=lambda:
[mock.Mock(subunit='2', monomer=150)],
get_r_bond_atoms=lambda:
[mock.Mock(subunit='1', monomer=50)],
comments='Disulfide',
),
],
polymer_labels={
0: 'Title 1',
1: 'Title 2',
2: 'Title 3',
3: 'Title 4',
},
seq_features=seq_features,
width=1200,
nt_per_track=80,
cols=2)
self.assertIsInstance(svg, str)
def test_ProteinForm_init(self):
protein.ProteinForm()
protein.CanonicalProteinForm()
def test_validate_form(self):
form = protein.ProteinForm()
form.from_str('ARG')
self.assertEqual(form.validate(), [])
def test_validate_bonds(self):
validate_bpform_bonds(protein.CanonicalProteinForm)
validate_bpform_bonds(protein.ProteinForm)
self.validate_alphabet(protein.CanonicalProteinForm().alphabet)
self.validate_alphabet(protein.ProteinForm().alphabet)
def test_get_structure(self):
form = protein.ProteinForm().from_str('ARCGY' * 100)
structure, _ = form.get_structure()
self.assertIsInstance(structure, openbabel.OBMol)
cml = OpenBabelUtils.export(structure, 'cml')
self.assertTrue(cml.startswith('<molecule'))