diff options
Diffstat (limited to 'plip/test/test_xml_parser.py')
| -rw-r--r-- | plip/test/test_xml_parser.py | 56 |
1 files changed, 28 insertions, 28 deletions
diff --git a/plip/test/test_xml_parser.py b/plip/test/test_xml_parser.py index 1f45daa..da99e50 100644 --- a/plip/test/test_xml_parser.py +++ b/plip/test/test_xml_parser.py @@ -13,27 +13,27 @@ class XMLParserTest(unittest.TestCase): """Checks if the XML parser is working correctly""" def setUp(self): - self.px = PlipXML('./xml/1vsn.report.xml') - self.bsite = self.px.bsites['NFT:A:283'] - self.smiles = 'CC(C)CC(NC(c1ccc(cc1)c1ccc(cc1)S(N)(=O)=O)C(F)(F)F)C(=O)NCC=N' + self.px = PlipXML("./xml/1vsn.report.xml") + self.bsite = self.px.bsites["NFT:A:283"] + self.smiles = "CC(C)CC(NC(c1ccc(cc1)c1ccc(cc1)S(N)(=O)=O)C(F)(F)F)C(=O)NCC=N" def test_general_information(self): """Test if general information is correctly parsed.""" - self.assertEqual(self.px.version, '1.4.2') - self.assertEqual(self.px.pdbid, '1VSN') + self.assertEqual(self.px.version, "1.4.2") + self.assertEqual(self.px.pdbid, "1VSN") self.assertFalse(self.px.fixed) - self.assertEqual(self.px.filename, '1vsn.pdb') + self.assertEqual(self.px.filename, "1vsn.pdb") self.assertEqual(self.px.excluded, []) def test_bsite_information(self): """Test if the binding site information is correctly parsed.""" - self.assertEqual(self.bsite.pdbid, '1VSN') - self.assertEqual(self.bsite.uniqueid, '1VSN:NFT:A:283') - self.assertEqual(self.bsite.hetid, 'NFT') - self.assertEqual(self.bsite.longname, 'NFT') - self.assertEqual(self.bsite.ligtype, 'SMALLMOLECULE') + self.assertEqual(self.bsite.pdbid, "1VSN") + self.assertEqual(self.bsite.uniqueid, "1VSN:NFT:A:283") + self.assertEqual(self.bsite.hetid, "NFT") + self.assertEqual(self.bsite.longname, "NFT") + self.assertEqual(self.bsite.ligtype, "SMALLMOLECULE") self.assertEqual(self.bsite.smiles, self.smiles) - self.assertEqual(self.bsite.members, ['NFT:A:283']) + self.assertEqual(self.bsite.members, ["NFT:A:283"]) self.assertFalse(self.bsite.composite) # ligand properties @@ -50,7 +50,7 @@ class XMLParserTest(unittest.TestCase): self.assertAlmostEqual(self.bsite.logp, 6, 0) # Atom mappings (non-exhaustive test) - lmap = self.bsite.mappings['pdb_to_smiles'] + lmap = self.bsite.mappings["pdb_to_smiles"] self.assertEqual(lmap[1625], 24) self.assertEqual(lmap[1649], 33) self.assertEqual(lmap[1617], 14) @@ -59,7 +59,7 @@ class XMLParserTest(unittest.TestCase): self.assertEqual(len(self.bsite.bs_res), 35) # Interacting chains - self.assertEqual(self.bsite.interacting_chains, ['A']) + self.assertEqual(self.bsite.interacting_chains, ["A"]) # Has Interactions? self.assertTrue(self.bsite.has_interactions, True) @@ -72,8 +72,8 @@ class XMLParserTest(unittest.TestCase): hydrophobic1 = self.bsite.hydrophobics[0] self.assertEqual(hydrophobic1.dist, 3.67) self.assertEqual(hydrophobic1.resnr, 61) - self.assertEqual(hydrophobic1.restype, 'ASP') - self.assertEqual(hydrophobic1.reschain, 'A') + self.assertEqual(hydrophobic1.restype, "ASP") + self.assertEqual(hydrophobic1.reschain, "A") self.assertEqual(hydrophobic1.ligcarbonidx, 1639) self.assertEqual(hydrophobic1.protcarbonidx, 448) self.assertEqual(hydrophobic1.ligcoo, (-7.395, 24.225, 6.614)) @@ -83,17 +83,17 @@ class XMLParserTest(unittest.TestCase): self.assertEqual(len(self.bsite.hbonds), 6) hbond1 = self.bsite.hbonds[0] self.assertEqual(hbond1.resnr, 19) - self.assertEqual(hbond1.restype, 'GLN') - self.assertEqual(hbond1.reschain, 'A') + self.assertEqual(hbond1.restype, "GLN") + self.assertEqual(hbond1.reschain, "A") self.assertTrue(hbond1.sidechain) self.assertEqual(hbond1.dist_h_a, 2.16) self.assertEqual(hbond1.dist_d_a, 3.11) self.assertEqual(hbond1.don_angle, 160.05) self.assertTrue(hbond1.protisdon) self.assertEqual(hbond1.donoridx, 153) - self.assertEqual(hbond1.donortype, 'Nam') + self.assertEqual(hbond1.donortype, "Nam") self.assertEqual(hbond1.acceptoridx, 1649) - self.assertEqual(hbond1.acceptortype, 'N2') + self.assertEqual(hbond1.acceptortype, "N2") self.assertEqual(hbond1.ligcoo, (2.820, 18.145, 6.806)) self.assertEqual(hbond1.protcoo, (3.976, 15.409, 7.712)) @@ -101,17 +101,17 @@ class XMLParserTest(unittest.TestCase): self.assertEqual(len(self.bsite.wbridges), 1) wbridge1 = self.bsite.wbridges[0] self.assertEqual(wbridge1.resnr, 159) - self.assertEqual(wbridge1.restype, 'HIS') - self.assertEqual(wbridge1.reschain, 'A') + self.assertEqual(wbridge1.restype, "HIS") + self.assertEqual(wbridge1.reschain, "A") self.assertEqual(wbridge1.dist_a_w, 3.67) self.assertEqual(wbridge1.dist_d_w, 3.13) self.assertEqual(wbridge1.don_angle, 126.73) self.assertEqual(wbridge1.water_angle, 116.36) self.assertTrue(wbridge1.protisdon) self.assertEqual(wbridge1.donor_idx, 1210) - self.assertEqual(wbridge1.donortype, 'Nar') + self.assertEqual(wbridge1.donortype, "Nar") self.assertEqual(wbridge1.acceptor_idx, 1649) - self.assertEqual(wbridge1.acceptortype, 'N2') + self.assertEqual(wbridge1.acceptortype, "N2") self.assertEqual(wbridge1.ligcoo, (2.820, 18.145, 6.806)) self.assertEqual(wbridge1.protcoo, (6.401, 19.307, 4.971)) self.assertEqual(wbridge1.watercoo, (3.860, 18.563, 3.309)) @@ -129,16 +129,16 @@ class XMLParserTest(unittest.TestCase): self.assertEqual(len(self.bsite.halogens), 2) hal1 = self.bsite.halogens[0] self.assertEqual(hal1.resnr, 67) - self.assertEqual(hal1.restype, 'TYR') - self.assertEqual(hal1.reschain, 'A') + self.assertEqual(hal1.restype, "TYR") + self.assertEqual(hal1.reschain, "A") self.assertTrue(hal1.sidechain) self.assertEqual(hal1.dist, 3.37) self.assertEqual(hal1.don_angle, 156.70) self.assertEqual(hal1.acc_angle, 100.53) self.assertEqual(hal1.don_idx, 1627) - self.assertEqual(hal1.donortype, 'F') + self.assertEqual(hal1.donortype, "F") self.assertEqual(hal1.acc_idx, 485) - self.assertEqual(hal1.acceptortype, 'O3') + self.assertEqual(hal1.acceptortype, "O3") self.assertEqual(hal1.ligcoo, (-1.862, 29.303, 4.507)) self.assertEqual(hal1.protcoo, (-1.005, 26.276, 3.287)) |