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from rdkit import Chem
from rdkit.Chem import rdConformerParser
from rdkit import RDConfig
import unittest
import os
from rdkit.RDLogger import logger
logger = logger()
class TestCase(unittest.TestCase):
def setUp(self):
pass
def testReadAmberTraj(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Contrib', 'ConformerParser', 'test_data',
'water_coords.trx')
mol = Chem.MolFromSmiles('O')
mol = Chem.AddHs(mol)
ids = rdConformerParser.AddConformersFromAmberTrajectory(mol, fileN)
self.failUnless(mol.GetNumConformers() == 1)
self.failUnless(len(ids) == 1)
self.failUnless(ids[0] == 0)
fileN = os.path.join(RDConfig.RDBaseDir, 'Contrib', 'ConformerParser', 'test_data',
'water_coords2.trx')
ids = rdConformerParser.AddConformersFromAmberTrajectory(mol, fileN, clearConfs=True)
self.failUnless(mol.GetNumConformers() == 2)
ids = rdConformerParser.AddConformersFromAmberTrajectory(mol, fileN, clearConfs=False)
self.failUnless(mol.GetNumConformers() == 4)
ids = rdConformerParser.AddConformersFromAmberTrajectory(mol, fileN, numConfs=1,
clearConfs=True)
self.failUnless(mol.GetNumConformers() == 1)
if __name__ == '__main__':
unittest.main()
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