def test_omm_STMD_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DEV_DIR, "ShortTrajMD.py"),
run_timeout=43200,
queue_timeout=2000)
ligand_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "MCL1_lig26.oeb"))
protein_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "MCL1_protein_ACE_NMA_caps.pdb"))
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
if using_orion():
workfloe.start({
"promoted": {
"ligands": ligand_file.identifier,
"protein": protein_file.identifier,
"out": output_file.identifier,
"fail": fail_output_file.identifier
}
})
else:
workfloe.start({
"promoted": {
"ligands": ligand_file.identifier,
"protein": protein_file.identifier,
"out": output_file.identifier,
"fail": fail_output_file.identifier
},
"mp": num_proc
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
# Check output
ifs = oechem.oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)
def test_simple_run(self):
workfloe = WorkFloeWrapper.get_workfloe(
os.path.join(FLOES_DIR, "relative_binding.py"),
run_timeout=1200
)
protein_file = DatasetWrapper.get_dataset(os.path.join(FILE_DIR, "Thrombin_protein.pdb"))
reference_ligand_file = DatasetWrapper.get_dataset(os.path.join(FILE_DIR, "ligand7.sdf"))
target_ligands_file = DatasetWrapper.get_dataset(os.path.join(FILE_DIR, "ligand0.sdf"))
success_output_file = OutputDatasetWrapper(extension=".oedb")
failure_output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start(
{
"promoted": {
"n_iterations" : 20,
"n_steps_per_iteration" : 2,
"solvent_padding" : 0.0,
"protein": protein_file.identifier,
"vacuum_test": True, # test ligand in vacuum only
"reference_ligand": reference_ligand_file.identifier,
"target_ligands": target_ligands_file.identifier,
"success": success_output_file.identifier,
"failure": failure_output_file.identifier,
}
}
)
# Faked locally
self.assertEqual(workfloe.state, "complete")
# Also faked
self.assertEqual(
len(workfloe.reason),
0,
"Failed with reason {}".format(workfloe.reason)
)
ifs = oeifstream()
with open(success_output_file.path, "rb") as ifs:
records = list(OEReadRecords(ifs))
count = len(records)
self.assertEqual(count, 10)
def test_gmx_PlainMD_protein_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DIR, "PlainMD.py"),
run_timeout=43200,
queue_timeout=2000)
protein_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "4JOO_truncNoLig.pdb"))
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start({
"promoted": {
"solute": protein_file.identifier,
"md_engine": "Gromacs",
"prod_ns": 1,
"out": output_file.identifier,
"fail": fail_output_file.identifier
}
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
# Check output
ifs = oechem.oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)
def test_simple_run(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DIR, "charge_floe.py"),
run_timeout=1200)
input_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "10.ism"))
output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start({
"promoted": {
"in": input_file.identifier,
"out": output_file.identifier,
}
})
# Faked locally
self.assertEqual(workfloe.state, "complete")
# Also faked
self.assertEqual(len(workfloe.reason), 0,
"Failed with reason {}".format(workfloe.reason))
ifs = oeifstream()
with open(output_file.path, "rb") as ifs:
records = list(OEReadRecords(ifs))
count = len(records)
self.assertEqual(count, 10)
def test_omm_minimization_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DEV_DIR, "MDminimize.py"),
run_timeout=43200,
queue_timeout=2000)
system = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "pbace_lcat13a.oedb"))
# Read input record
ifs = oeifstream(system.dataset_path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)
# Calculate the initial potential energy
for record in records:
mdrecord = MDDataRecord(record)
stages = mdrecord.get_stages
self.assertEqual(len(stages), 1)
mdstate = mdrecord.get_stage_state()
parmed_structure = mdrecord.get_parmed(sync_stage_name='last')
# Calculate the initial potential energy
eng_i = calculate_eng(mdstate, parmed_structure)
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start({
"promoted": {
"system": system.identifier,
"out": output_file.identifier,
"fail": fail_output_file.identifier
},
"cube": {
"Minimize": {
"save_md_stage": True
}
}
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
# Read output record
ifs = oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# The records list must have just one record
self.assertEqual(count, 1)
# Calculate the final potential energy
for record in records:
mdrecord = MDDataRecord(record)
stages = mdrecord.get_stages
self.assertEqual(len(stages), 2)
mdstate = mdrecord.get_stage_state()
parmed_structure = mdrecord.get_parmed(sync_stage_name='last')
# Calculate the final potential energy
eng_f = calculate_eng(mdstate, parmed_structure)
self.assertLess(
eng_f.in_units_of(unit.kilojoule_per_mole) /
unit.kilojoule_per_mole,
eng_i.in_units_of(unit.kilojoule_per_mole) /
unit.kilojoule_per_mole)
def test_gmx_minimization_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DEV_DIR, "MDminimize.py"),
run_timeout=43200,
queue_timeout=2000)
system = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "pbace_lcat13a.oedb"))
# Read input record
ifs = oeifstream(system.dataset_path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start({
"promoted": {
"system": system.identifier,
"md_engine": "Gromacs",
"out": output_file.identifier,
"fail": fail_output_file.identifier
},
"cube": {
"Minimize": {
"save_md_stage": True
}
}
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
# Read output record
ifs = oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# The records list must have just one record
self.assertEqual(count, 1)
def test_compex_prep_split_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DEV_DIR, "Complex_prep.py"),
run_timeout=43200,
queue_timeout=2000)
ligand_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "MCL1_lig26.oeb"))
protein_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "MCL1_protein_ACE_NMA_caps.pdb"))
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start({
"promoted": {
"ligands": ligand_file.identifier,
"protein": protein_file.identifier,
"out": output_file.identifier,
"fail": fail_output_file.identifier
}
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
ifs = oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)
# Each record should have the MD record interface
for record in records:
mdrecord = MDDataRecord(record)
self.assertTrue(record.has_value(Fields.flaskid))
self.assertTrue(record.has_value(Fields.title))
self.assertTrue(record.has_value(Fields.ligand))
self.assertTrue(record.has_value(Fields.protein))
self.assertTrue(record.has_value(Fields.primary_molecule))
self.assertTrue(record.has_value(Fields.flask))
self.assertTrue(record.has_value(Fields.md_stages))
self.assertTrue(record.has_value(Fields.pmd_structure))
self.assertEqual(mdrecord.get_flask_id, 0)
self.assertEqual(mdrecord.get_title, "pMCL1_l26")
self.assertEqual(record.get_value(Fields.ligand).NumAtoms(), 43)
self.assertEqual(record.get_value(Fields.protein).NumAtoms(), 2432)
complx = mdrecord.get_flask
protein_split, ligand_split, water, excipients = oeommutils.split(
complx)
self.assertEqual(protein_split.NumAtoms(), 2432)
self.assertEqual(ligand_split.NumAtoms(), 43)
self.assertEqual(water.NumAtoms(), 20022)
self.assertEqual(excipients.NumAtoms(), 17)
stages = mdrecord.get_stages
self.assertEqual(len(stages), 1)
stage = stages[0]
self.assertTrue(stage.has_value(Fields.stage_name))
self.assertTrue(stage.has_value(Fields.mddata))
self.assertEqual(stage.get_value(Fields.stage_type), "SETUP")
top_mol = mdrecord.get_stage_topology()
self.assertEqual(top_mol.NumAtoms(), complx.NumAtoms())
def test_compex_prep_md_comp_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DEV_DIR, "Complex_prep.py"),
run_timeout=43200,
queue_timeout=2000)
ligand_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "retigabine.oeb"))
protein_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "kcnq_fix_ARG_fc.oeb"))
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start({
"promoted": {
"ligands": ligand_file.identifier,
"protein": protein_file.identifier,
"out": output_file.identifier,
"fail": fail_output_file.identifier
}
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
ifs = oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)
for record in records:
md_components = record.get_value(Fields.md_components)
protein = md_components.get_protein
ligand = md_components.get_ligand
counter_ions = md_components.get_counter_ions
excipients = md_components.get_excipients
water = md_components.get_water
self.assertEqual(protein.NumAtoms(), 7353)
self.assertEqual(ligand.NumAtoms(), 40)
self.assertEqual(water.NumAtoms(), 58308)
self.assertEqual(excipients.NumAtoms(), 44)
self.assertEqual(counter_ions.NumAtoms(), 54)
def test_gmx_npt_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DEV_DIR, "MDnpt.py"),
run_timeout=43200,
queue_timeout=2000)
system = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "pP38_lig38a_2n_npt_5ns.oedb"))
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start({
"promoted": {
"system": system.identifier,
"md_engine": "Gromacs",
"nanoseconds": 0.01,
"temperature": 300.0,
"pressure": 1.0,
"trajectory_interval": 0.0,
"reporter_interval": 0.0,
"out": output_file.identifier,
"fail": fail_output_file.identifier
},
"cube": {
"npt": {
"save_md_stage": True,
"constraints": "H-Bonds",
"restraints": "",
"nonbondedCutoff": 10.0
}
}
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
ifs = oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)
for record in records:
mdrecord = MDDataRecord(record)
stages = mdrecord.get_stages
self.assertEqual(len(stages), 3)
def test_omm_npt_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DEV_DIR, "MDnpt.py"),
run_timeout=43200,
queue_timeout=2000)
system = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "pP38_lig38a_2n_npt_5ns.oedb"))
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
workfloe.start({
"promoted": {
"system": system.identifier,
"nanoseconds": 0.01,
"temperature": 300.0,
"pressure": 1.0,
"trajectory_interval": 0.0,
"reporter_interval": 0.0,
"out": output_file.identifier,
"fail": fail_output_file.identifier
},
"cube": {
"npt": {
"save_md_stage": True,
"constraints": "H-Bonds",
"restraints": "",
"nonbondedCutoff": 10.0
}
}
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
ifs = oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)
for record in records:
mdrecord = MDDataRecord(record)
stages = mdrecord.get_stages
self.assertEqual(len(stages), 3)
mdstate = mdrecord.get_stage_state()
parmed_structure = mdrecord.get_parmed(sync_stage_name='last')
# Calculate final volume and temperature
vol_f, temp_f = calculate_VT(mdstate, parmed_structure)
# Check 3*std volume
# Average volume and its standard deviation (in nm^3) measured along
# one 5ns run for the selected system
avg_volume = 632.4198167 * (unit.nanometers**3)
std_volume = 1.201609662
self.assertAlmostEqual(avg_volume / (unit.nanometers**3),
vol_f.in_units_of(unit.nanometers**3) /
(unit.nanometers**3),
delta=3 * std_volume)
# Check temperature
# Average temperature and its standard deviation (in K) measured along
# one 5ns run for the selected system
avg_temperature = 299.9852145 * unit.kelvin
std_temperature = 2.021052471
self.assertAlmostEqual(avg_temperature / unit.kelvin,
temp_f.in_units_of(unit.kelvin) /
unit.kelvin,
delta=3 * std_temperature)
def test_gmx_STMD_Analysis_large_sys_floe(self):
workfloe = WorkFloeWrapper.get_workfloe(os.path.join(
FLOES_DIR, "ShortTrajMDWithAnalysis.py"),
run_timeout=43200,
queue_timeout=2000)
ligand_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "Hunt13_lig13.oeb"))
protein_file = DatasetWrapper.get_dataset(
os.path.join(FILE_DIR, "4JOO_truncNoLig.pdb"))
output_file = OutputDatasetWrapper(extension=".oedb")
fail_output_file = OutputDatasetWrapper(extension=".oedb")
if using_orion:
workfloe.start({
"promoted": {
"ligands": ligand_file.identifier,
"protein": protein_file.identifier,
"md_engine": "Gromacs",
"out": output_file.identifier,
"fail": fail_output_file.identifier
}
})
else:
workfloe.start({
"promoted": {
"ligands": ligand_file.identifier,
"protein": protein_file.identifier,
"md_engine": "Gromacs",
"out": output_file.identifier,
"fail": fail_output_file.identifier
},
"mp": num_proc
})
self.assertWorkFloeComplete(workfloe)
fail_ifs = oechem.oeifstream()
records_fail = []
for rec_fail in read_records(fail_ifs):
records_fail.append(rec_fail)
fail_ifs.close()
count = len(records_fail)
# The fail record must be empty
self.assertEqual(count, 0)
# Check output
ifs = oechem.oeifstream(output_file.path)
records = []
for rec in read_records(ifs):
records.append(rec)
ifs.close()
count = len(records)
# Check the out record list
self.assertEqual(count, 1)