def logs_extraction(ctx, stgn):
for record in ctx.obj['records']:
mdrecord = MDDataRecord(record)
info = mdrecord.get_stage_info(stg_name=stgn)
print(info)
class MDRecordTests(unittest.TestCase):
"""
Testing MD Record API
"""
def setUp(self):
fname = os.path.join(FILE_DIR, "mdrecord.oedb")
ifs = oechem.oeifstream(fname)
records = []
for record in read_records(ifs):
records.append(record)
self.assertEqual(len(records), 1)
self.record = OERecord(records[0])
self.mdrecord = MDDataRecord(records[0])
self.cwd = os.getcwd()
os.chdir(FILE_DIR)
@pytest.mark.travis
@pytest.mark.local
def test_get_primary(self):
mol = self.mdrecord.get_value(Fields.primary_molecule)
self.assertEqual(mol.NumAtoms(), self.mdrecord.get_primary.NumAtoms())
@pytest.mark.travis
@pytest.mark.local
def test_set_primary(self):
mol = self.mdrecord.get_value(Fields.primary_molecule)
self.assertTrue(self.mdrecord.set_primary(mol))
@pytest.mark.travis
@pytest.mark.local
def test_get_flask(self):
mol = self.mdrecord.get_value(Fields.flask)
self.assertEqual(mol.NumAtoms(), self.mdrecord.get_flask.NumAtoms())
@pytest.mark.travis
@pytest.mark.local
def test_set_flask(self):
mol = self.mdrecord.get_value(Fields.flask)
self.assertTrue(self.mdrecord.set_flask(mol))
@pytest.mark.travis
@pytest.mark.local
def test_get_flaskid(self):
id = self.mdrecord.get_value(Fields.flaskid)
self.assertEqual(id, 0)
@pytest.mark.travis
@pytest.mark.local
def test_has_flaskid(self):
self.assertTrue(self.mdrecord.has_flask_id)
@pytest.mark.travis
@pytest.mark.local
def test_set_flaskid(self):
self.mdrecord.set_flask_id(5)
self.assertEqual(self.mdrecord.get_flask_id, 5)
@pytest.mark.travis
@pytest.mark.local
def test_get_lig_id(self):
id = self.mdrecord.get_value(Fields.ligid)
self.assertEqual(id, 0)
@pytest.mark.travis
@pytest.mark.local
def test_has_lig_id(self):
self.assertTrue(self.mdrecord.has_lig_id)
@pytest.mark.travis
@pytest.mark.local
def test_set_lig_id(self):
self.mdrecord.set_lig_id(5)
self.assertEqual(self.mdrecord.get_lig_id, 5)
@pytest.mark.travis
@pytest.mark.local
def test_get_conf_id(self):
id = self.mdrecord.get_value(Fields.confid)
self.assertEqual(id, 0)
@pytest.mark.travis
@pytest.mark.local
def test_has_conf_id(self):
self.assertTrue(self.mdrecord.has_conf_id)
@pytest.mark.travis
@pytest.mark.local
def test_set_conf_id(self):
self.mdrecord.set_conf_id(5)
self.assertEqual(self.mdrecord.get_conf_id, 5)
@pytest.mark.travis
@pytest.mark.local
def test_get_title(self):
title = self.mdrecord.get_value(Fields.title)
self.assertEqual(title, 'pPRT_ltoluene')
@pytest.mark.travis
@pytest.mark.local
def test_has_tile(self):
self.assertTrue(self.mdrecord.has_title)
@pytest.mark.travis
@pytest.mark.local
def test_set_title(self):
self.mdrecord.set_title("Pippo")
self.assertEqual(self.mdrecord.get_title, 'Pippo')
@pytest.mark.travis
@pytest.mark.local
def test_get_last_stage(self):
last_stage = self.mdrecord.get_last_stage
self.assertEqual(last_stage.get_value(Fields.stage_name), 'Production')
self.assertEqual(last_stage.get_value(Fields.stage_type), 'NPT')
@pytest.mark.travis
@pytest.mark.local
def test_get_stage_by_name(self):
last_stage = self.mdrecord.get_stage_by_name()
self.assertEqual(last_stage.get_value(Fields.stage_name), 'Production')
self.assertEqual(last_stage.get_value(Fields.stage_type), 'NPT')
param_stage = self.mdrecord.get_stage_by_name(
stg_name='System Parametrization')
self.assertEqual(param_stage.get_value(Fields.stage_name),
'System Parametrization')
self.assertEqual(param_stage.get_value(Fields.stage_type), 'SETUP')
param_stage = self.mdrecord.get_stage_by_name(
stg_name='System Minimization')
self.assertEqual(param_stage.get_value(Fields.stage_name),
'System Minimization')
self.assertEqual(param_stage.get_value(Fields.stage_type),
'MINIMIZATION')
with self.assertRaises(ValueError):
self.mdrecord.get_stage_by_name('Error')
# @pytest.mark.local
# def test_delete_stage_by_name(self):
# new_record = OERecord(self.record)
# new_mdrecord = MDDataRecord(new_record)
#
# new_mdrecord.delete_stage_by_name(stg_name='System Minimization')
# self.assertFalse(new_mdrecord.has_stage_name('System Minimization'))
# self.assertEqual(len(new_mdrecord.get_stages), 2)
# TODO THIS IS GOING TO DELETE FILES LOCALLY KEEP DISABLED
@pytest.mark.travis
@pytest.mark.local
def test_has_stage_name(self):
self.assertTrue(self.mdrecord.has_stage_name('Production'))
self.assertFalse(self.mdrecord.has_stage_name('Error'))
@pytest.mark.travis
@pytest.mark.local
def test_get_stage_by_idx(self):
with self.assertRaises(ValueError):
self.mdrecord.get_stage_by_idx(5)
self.assertEqual(
self.mdrecord.get_stage_by_idx(0).get_value(Fields.stage_name),
'System Parametrization')
@pytest.mark.travis
@pytest.mark.local
def test_get_stage_state(self):
last_stage = self.mdrecord.get_last_stage
mddata_fn = os.path.join(FILE_DIR, last_stage.get_value(Fields.mddata))
with TemporaryDirectory() as out_directory:
with tarfile.open(mddata_fn) as tar:
tar.extractall(path=out_directory)
state_fn = os.path.join(out_directory, MDFileNames.state)
with open(state_fn, 'rb') as f:
md_state = pickle.load(f)
self.assertEqual(md_state.get_positions(),
self.mdrecord.get_stage_state().get_positions())
self.assertEqual(md_state.get_velocities(),
self.mdrecord.get_stage_state().get_velocities())
self.assertEqual(md_state.get_box_vectors(),
self.mdrecord.get_stage_state().get_box_vectors())
@pytest.mark.travis
@pytest.mark.local
def test_get_stage_topology(self):
par_stage = self.mdrecord.get_stage_by_idx(0)
mddata_fn = os.path.join(FILE_DIR, par_stage.get_value(Fields.mddata))
with TemporaryDirectory() as out_directory:
with tarfile.open(mddata_fn) as tar:
tar.extractall(path=out_directory)
topology_fn = os.path.join(out_directory, MDFileNames.topology)
topology_mol = oechem.OEMol()
with oechem.oemolistream(topology_fn) as ifs:
oechem.OEReadMolecule(ifs, topology_mol)
topology = self.mdrecord.get_stage_topology(
stg_name='System Parametrization')
for mol_at, top_at in zip(topology_mol.GetAtoms(),
topology.GetAtoms()):
self.assertEqual(mol_at.GetAtomicNum(), top_at.GetAtomicNum())
@pytest.mark.travis
@pytest.mark.local
def test_get_stage_info(self):
last_stage = self.mdrecord.get_last_stage
info = last_stage.get_value(Fields.log_data)
self.assertEqual(info, self.mdrecord.get_stage_info())
min_stage = self.mdrecord.get_stage_by_name(
stg_name='System Minimization')
info = min_stage.get_value(Fields.log_data)
self.assertEqual(
info, self.mdrecord.get_stage_info(stg_name='System Minimization'))
@pytest.mark.travis
@pytest.mark.local
def test_get_stage_trajectory(self):
self.assertTrue(os.path.isfile(self.mdrecord.get_stage_trajectory()))
@pytest.mark.travis
@pytest.mark.local
def test_add_new_stage(self):
new_record = OERecord(self.record)
new_mdrecord = MDDataRecord(new_record)
topology = self.mdrecord.get_stage_topology()
md_state = self.mdrecord.get_stage_state()
self.assertTrue(
new_mdrecord.add_new_stage("Testing",
MDStageTypes.FEC,
topology,
md_state,
"test.tar.gz",
log='TestingLogs'))
self.assertEqual(len(new_mdrecord.get_value(Fields.md_stages)), 4)
new_last_stage = new_mdrecord.get_stage_by_name(stg_name='Testing')
self.assertEqual(new_last_stage.get_value(Fields.stage_name),
'Testing')
self.assertEqual(new_last_stage.get_value(Fields.stage_type),
MDStageTypes.FEC)
@pytest.mark.travis
@pytest.mark.local
def test_get_stages(self):
stages = self.mdrecord.get_stages
self.assertEqual(len(stages), 3)
@pytest.mark.travis
@pytest.mark.local
def test_get_stages_names(self):
ls_names = [
'System Parametrization', 'System Minimization', 'Production'
]
stg_names = self.mdrecord.get_stages_names
self.assertEqual(stg_names, ls_names)
@pytest.mark.travis
@pytest.mark.local
def test_has_stages(self):
self.assertTrue(self.mdrecord.has_stages)
@pytest.mark.travis
@pytest.mark.local
def test_get_parmed(self):
pmd = self.mdrecord.get_parmed(sync_stage_name='last')
self.assertEqual(len(pmd.atoms), 30439)
self.assertEqual((len(pmd.residues)), 9446)
self.assertEqual((len(pmd.bonds)), 21178)
self.assertEqual((len(pmd.angles)), 14069)
self.assertEqual((len(pmd.dihedrals)), 8028)
@pytest.mark.travis
@pytest.mark.local
def test_set_parmed(self):
new_record = OERecord(self.record)
new_mdrecord = MDDataRecord(new_record)
pmd = new_mdrecord.get_parmed()
new_mdrecord.delete_field(Fields.pmd_structure)
self.assertFalse(new_mdrecord.has_parmed)
new_mdrecord.set_parmed(pmd, sync_stage_name='last')
self.assertTrue(new_mdrecord.has_parmed)
@pytest.mark.travis
@pytest.mark.local
def test_has_parmed(self):
self.assertTrue(self.mdrecord.has_parmed)
@pytest.mark.travis
@pytest.mark.local
def test_delete_parmed(self):
new_record = OERecord(self.record)
new_mdrecord = MDDataRecord(new_record)
new_mdrecord.delete_parmed
self.assertFalse(new_mdrecord.has_parmed)
@pytest.mark.travis
@pytest.mark.local
def test_protein_traj(self):
oetraj_record = self.record.get_value(OEField('OETraj', Types.Record))
prot_mol = oetraj_record.get_value(Fields.protein_traj_confs)
mdrecord = MDDataRecord(oetraj_record)
mdprot = mdrecord.get_protein_traj
self.assertEqual(prot_mol.NumAtoms(), mdprot.NumAtoms())
@pytest.mark.travis
@pytest.mark.local
def test_set_protein_traj(self):
oetraj_record = self.record.get_value(OEField('OETraj', Types.Record))
prot_mol = oetraj_record.get_value(Fields.protein_traj_confs)
mdrecord = MDDataRecord(oetraj_record)
oetraj_record.delete_field(Fields.protein_traj_confs)
with self.assertRaises(ValueError):
mdrecord.get_protein_traj
self.assertTrue(mdrecord.set_protein_traj(prot_mol))
