How to use test_compound method in avocado

Best Python code snippet using avocado_python

kegg_compound_test.py

Source:kegg_compound_test.py

1#!/usr/bin/python2import unittest3import json4from pygibbs import kegg_compound5from pygibbs import pseudoisomer6class TestKeggCompound(unittest.TestCase):7    8    def setUp(self):9        self.cid = 132310        self.str_cid = str(self.cid)11        self.name = 'Glyxolaterium-monohysterianase'12        self.names = ['Glyxolaterium-monohysterianase',13                      'GMH']14        self.mass = '60.99'15        self.formula = 'H2CO3'16        self.inchi = 'InChI=1S/C2H2O2/c3-1-2-4/h1-2H' # inchi for glyoxal17        18        self.test_compound = kegg_compound.Compound(19            cid=self.cid, name=self.name, all_names=self.names,20            mass=self.mass, formula=self.formula, inchi=self.inchi)21        22    def testProperties(self):23        self.assertEqual(self.cid, self.test_compound.cid)24        self.assertEqual(self.name, self.test_compound.name)25        self.assertEqual(self.names, self.test_compound.all_names)26        self.assertEqual(self.mass, self.test_compound.mass)27        self.assertEqual(self.formula, self.test_compound.formula)28        self.assertEqual(self.inchi, self.test_compound.inchi)29        self.assertTrue(self.test_compound.from_kegg)30        31        kegg_link = self.test_compound.kegg_link32        self.assertNotEqual(-1, kegg_link.find(self.str_cid))33        34    def testSimpleGetters(self):35        molecule = self.test_compound.GetMolecule()36        self.assertTrue(molecule is not None)37        38        smiles = self.test_compound.get_smiles()39        self.assertTrue(smiles is not None)40        41        self.assertEqual(self.inchi, self.test_compound.get_inchi())42        self.assertNotEqual(-1, self.test_compound.get_string_cid().find(self.str_cid))43        44        # We call these methods to make sure they don't error.45        self.test_compound.get_atom_bag()46        self.test_compound.get_nH_and_charge()47        self.test_compound.get_num_electrons()48        49    def testAddThermodynamicData(self):50        pmap = pseudoisomer.PseudoisomerMap(nH=8, z=0, nMg=0, dG0=18.8)51        source_string = 'Noor, Bar-Even 2011'52        self.test_compound.AddThermodynamicData(pmap,53                                                source_string=source_string,54                                                priority=2)55        pmap = self.test_compound.pmaps[-1]56        self.assertEqual(source_string, pmap['source'])57        self.assertEqual(2, pmap['priority'])        58    59    def testSetThermodynamicError(self):60        error = 'Group contribution failed to solve your problems.'61        self.test_compound.SetThermodynamicError(error)62        self.assertEqual(error, self.test_compound.pmap_error)63    64    def testJSONDict(self):65        json_dict = self.test_compound.ToJSONDict()66        67        key_set = set(json_dict.keys())68        expected_keys = set(['CID', 'mass', 'formula', 'name',69                             'names', 'InChI', 'num_electrons', 'from_kegg'])70        self.assertEqual(expected_keys, key_set)71        72        self.assertEqual(self.test_compound.get_string_cid(), json_dict['CID'])73        self.assertEqual(self.mass, json_dict['mass'])74        self.assertEqual(self.formula, json_dict['formula'])75        self.assertEqual(self.names[0], json_dict['name'])76        self.assertEqual(sorted(self.names), json_dict['names'])77        self.assertEqual(self.inchi, json_dict['InChI'])78        self.assertTrue(json_dict['num_electrons'] is not None)79    80    def testToDBRow(self):81        expected_row = [self.cid, self.name, json.dumps(self.names),82                        self.mass, self.formula, self.inchi,83                        self.test_compound.get_num_electrons(),84                        self.test_compound.from_kegg,85                        self.test_compound.pubchem_id,86                        self.test_compound.cas]87        db_row = self.test_compound.ToDBRow()88        self.assertEqual(expected_row, db_row)89        90def Suite():91    return unittest.makeSuite(TestKeggCompound,'test')92    93if __name__ == '__main__':...

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