def test_collect_types_conditional_bond(self):
moldb = MolDatabase("test/data/mol-polyethene.json")
conv = PDB2LMP("test/data/polyethene.gro", moldb=moldb)
conv.collect_types(add_water=False)
self.assertListEqual(conv.moltypes, ["ETH", "ETE"])
self.assertListEqual(conv.atomtypes, ["TAIL"])
self.assertListEqual(conv.lentypes, ["test", "tail-tail"])
self.assertEqual(conv.natoms.total, 10)
self.assertEqual(conv.nlengths.total, 6)
conv.populate_pdb_data()
conv.write_forcefield("polyethene.ff")
conv.write_data("polyethene.data")
def test_template(self):
db = MolDatabase("data/mol-elba-sugar.json")
self.assertTrue("sugar" in db.molecules["1GA"].polymer_type)
self.assertEqual(db.molecules["1GA"].lengths[0].type, "sugar-glyc")
self.assertEqual(db.molecules["1GA"].lengths[0].atoms[0], "C1")
self.assertEqual(db.molecules["1GA"].lengths[0].atoms[1], "+C1")
self.assertEqual(db.molecules["1GA"].lengths[1].type, "sugar-ring")
self.assertEqual(db.molecules["1GA"].lengths[1].atoms[0], "C1")
self.assertEqual(db.molecules["1GA"].lengths[1].atoms[1], "C2")
self.assertEqual(6, len(db.molecules["0GA"].lengths))
self.assertEqual(7, len(db.molecules["1GA"].lengths))
self.assertEqual(6, len(db.molecules["0GA"].angles))
self.assertEqual(6, len(db.molecules["1GA"].angles))
def test_template_simple(self):
db = MolDatabase("test/data/template.json")
self.assertTrue("sugar" in db.molecules["3NA"].polymer_type)
self.assertEqual(db.molecules["3NA"].lengths[0].type, "sugar-glyc")
self.assertEqual(db.molecules["3NA"].lengths[0].atoms[0], "C3")
self.assertEqual(db.molecules["3NA"].lengths[0].atoms[1], "+C1")
self.assertEqual(db.molecules["3NA"].lengths[1].type, "sugar-ring")
self.assertEqual(db.molecules["3NA"].lengths[1].atoms[0], "C1")
self.assertEqual(db.molecules["3NA"].lengths[1].atoms[1], "C2")
self.assertEqual(6, len(db.molecules["0NA"].lengths))
self.assertEqual(7, len(db.molecules["3NA"].lengths))
self.assertEqual(6, len(db.molecules["0NA"].angles))
self.assertEqual(8, len(db.molecules["3NA"].angles))
self.assertEqual(6, len(db.molecules["0NA"].dihedrals))
self.assertEqual(9, len(db.molecules["3NA"].dihedrals))
def test_read_database(self):
db = MolDatabase()
self.assertTrue("MEO" in db.molecules)
self.assertTrue("ETO" in db.molecules)
self.assertEqual(db.molecules["MEO"].atoms["C"].name, "C")
self.assertEqual(db.molecules["MEO"].atoms["C"].type, "MEOH")
def test_polymer_type(self):
db = MolDatabase()
self.assertTrue("sugar" in db.molecules["0GA"].polymer_type)
self.assertTrue("sugar" not in db.molecules["MEO"].polymer_type)
def test_open_database(self):
db = MolDatabase()