def test_solvation_packmol_tip3p(self):
# Complex file name
fcomplex = "tests/data/Bace_protein.pdb"
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(fcomplex) as ifs:
oechem.OEReadMolecule(ifs, mol)
# Solvate the system
solv_complex = packmol.oesolvate(mol,
density=1.0,
padding_distance=10.0,
distance_between_atoms=2.0,
solvents='tip3p',
molar_fractions='1.0',
geometry='box',
close_solvent=True,
salt='[Na+], [Cl-]',
salt_concentration=100.0,
neutralize_solute=True)
prot, lig, wat, other = utils.split(solv_complex)
npa = prot.GetMaxAtomIdx()
nla = lig.GetMaxAtomIdx()
noa = other.GetMaxAtomIdx()
nwa = wat.GetMaxAtomIdx()
self.assertEqual(npa, 6044)
self.assertEqual(nla, 0)
# Ions added to excipients
self.assertEqual(noa, 94)
# Water molecules added
self.assertEqual(nwa, 48279)
box_vectors = solv_complex.GetData('box_vectors')
box_vectors = data_utils.decodePyObj(box_vectors)
box_vectors = box_vectors.in_units_of(unit.nanometers)
self.assertAlmostEqual(box_vectors[0][0] / unit.nanometers,
8.23,
delta=0.01)
self.assertEqual(box_vectors[0][1] / unit.nanometers, 0.0)
self.assertEqual(box_vectors[0][2] / unit.nanometers, 0.0)
self.assertAlmostEqual(box_vectors[1][1] / unit.nanometers,
8.23,
delta=0.01)
self.assertEqual(box_vectors[1][0] / unit.nanometers, 0.0)
self.assertEqual(box_vectors[1][2] / unit.nanometers, 0.0)
self.assertAlmostEqual(box_vectors[2][2] / unit.nanometers,
8.23,
delta=0.01)
self.assertEqual(box_vectors[2][0] / unit.nanometers, 0.0)
self.assertEqual(box_vectors[2][1] / unit.nanometers, 0.0)
def test_solvation_packmol_components(self):
# Complex file name
fcomplex = "tests/data/Bace_protein.pdb"
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(fcomplex) as ifs:
oechem.OEReadMolecule(ifs, mol)
# Solvate the system
solv_complex, solvent, salt, counter_ions = packmol.oesolvate(
mol,
density=1.0,
padding_distance=10.0,
distance_between_atoms=2.0,
solvents='tip3p',
molar_fractions='1.0',
geometry='box',
close_solvent=True,
salt='[Na+], [Cl-]',
salt_concentration=100.0,
neutralize_solute=True,
return_components=True)
prot, lig, wat, cofactors, lipids, metals, excipients = utils.split(
solv_complex)
npa = prot.GetMaxAtomIdx()
nla = lig.GetMaxAtomIdx()
noa = excipients.GetMaxAtomIdx()
nwa = wat.GetMaxAtomIdx()
nlpa = lipids.GetMaxAtomIdx()
nma = metals.GetMaxAtomIdx()
nca = cofactors.GetMaxAtomIdx()
self.assertEqual(npa, 6044)
self.assertEqual(nla, 0)
self.assertEqual(nlpa, 0)
self.assertEqual(nca, 0)
self.assertEqual(nma, 0)
# The Bace system has 19 water molecules
self.assertEqual(nwa, solvent.NumAtoms() + 19 * 3)
# The Bace system has the TLA excipient with 14 atoms
self.assertEqual(noa, salt.NumAtoms() + counter_ions.NumAtoms() + 14)
def process(self, solute, port):
try:
opt = dict(self.opt)
# Update cube simulation parameters with the eventually molecule SD tags
new_args = {
dp.GetTag(): dp.GetValue()
for dp in oechem.OEGetSDDataPairs(solute)
if dp.GetTag() in ["solvents", "molar_fractions", "density"]
}
if new_args:
for k in new_args:
if k == 'molar_fractions':
continue
try:
new_args[k] = float(new_args[k])
except:
pass
self.log.info(
"Updating parameters for molecule: {}\n{}".format(
solute.GetTitle(), new_args))
opt.update(new_args)
# Solvate the system
sol_system = oesolvate(solute, **opt)
self.log.info("Solvated System atom number {}".format(
sol_system.NumAtoms()))
sol_system.SetTitle(solute.GetTitle())
self.success.emit(sol_system)
except Exception as e:
# Attach error message to the molecule that failed
self.log.error(traceback.format_exc())
solute.SetData('error', str(e))
# Return failed mol
self.failure.emit(solute)
return
def test_solvation_packmol_components_None(self):
# Complex file name
fcomplex = "tests/data/Bace_protein.pdb"
# Read OEMol molecule
mol = oechem.OEMol()
with oechem.oemolistream(fcomplex) as ifs:
oechem.OEReadMolecule(ifs, mol)
# Solvate the system
solv_complex, solvent, salt, counter_ions = packmol.oesolvate(
mol,
density=1.0,
padding_distance=10.0,
distance_between_atoms=2.0,
solvents='tip3p',
molar_fractions='1.0',
geometry='box',
close_solvent=True,
salt='[Na+], [Cl-]',
salt_concentration=0.0,
neutralize_solute=False,
return_components=True)
prot, lig, wat, cofactors, lipids, metals, excipients = utils.split(
solv_complex)
npa = prot.GetMaxAtomIdx()
nla = lig.GetMaxAtomIdx()
self.assertEqual(npa, 6044)
self.assertEqual(nla, 0)
assert salt is None
assert counter_ions is None
def process(self, record, port):
try:
opt = dict(self.opt)
if not record.has_value(Fields.md_components):
raise ValueError("Missing the MD Components Field")
md_components = record.get_value(Fields.md_components)
solute, map_comp = md_components.create_flask
if not record.has_value(Fields.title):
self.log.warn("Missing Title field")
solute_title = solute.GetTitle()[0:12]
else:
solute_title = record.get_value(Fields.title)
self.log.info("[{}] solvating flask {}".format(
self.title, solute_title))
# Update cube simulation parameters
for field in record.get_fields(include_meta=True):
field_name = field.get_name()
if field_name in ['molar_fractions', 'density', 'solvents']:
rec_value = record.get_value(field)
if field_name == 'molar_fractions':
opt[field_name] = str(rec_value)
else:
opt[field_name] = rec_value
opt['Logger'].info(
"{} Updating parameters for molecule: {} {} = {}".
format(self.title, solute.GetTitle(), field_name,
rec_value))
# Set the flag to return the solvent molecule components
opt['return_components'] = True
# Solvate the system
sol_system, solvent, salt, counter_ions = packmol.oesolvate(
solute, **opt)
# Separate the Water from the solvent
pred_water = oechem.OEIsWater(checkHydrogens=True)
water = oechem.OEMol()
oechem.OESubsetMol(water, solvent, pred_water)
if water.NumAtoms():
if md_components.has_water:
water_comp = md_components.get_water
if not oechem.OEAddMols(water_comp, water):
raise ValueError(
"Cannot add the MD Component Water and the Packmol Water"
)
md_components.set_water(water_comp)
else:
md_components.set_water(water)
pred_not_water = oechem.OENotAtom(
oechem.OEIsWater(checkHydrogens=True))
solvent_not_water = oechem.OEMol()
oechem.OESubsetMol(solvent_not_water, solvent, pred_not_water)
if solvent_not_water.NumAtoms():
solvent = solvent_not_water
else:
solvent = oechem.OEMol()
self.log.info(
"[{}] Solvated simulation flask {} yielding {} atoms overall".
format(self.title, solute_title, sol_system.NumAtoms()))
sol_system.SetTitle(solute.GetTitle())
if salt is not None and counter_ions is not None:
if not oechem.OEAddMols(counter_ions, salt):
raise ValueError(
"Cannot add the salt component and the counter ion component"
)
elif salt is not None:
counter_ions = salt
else:
pass
if md_components.has_solvent:
solvent_comp = md_components.get_solvent
if not oechem.OEAddMols(solvent_comp, solvent):
raise ValueError(
"Cannot add the MD Component solvent and the Packmol Solvent"
)
else:
solvent_comp = solvent
if solvent_comp.NumAtoms():
md_components.set_solvent(solvent_comp)
if counter_ions is not None:
if md_components.has_counter_ions:
counter_ions_comp = md_components.get_counter_ions
if not oechem.OEAddMols(counter_ions_comp, counter_ions):
raise ValueError(
"Cannot add the MD Component counter ions and the Packmol counter ions"
)
else:
counter_ions_comp = counter_ions
md_components.set_counter_ions(counter_ions_comp)
# Set Box Vectors
vec_data = pack_utils.getData(sol_system, tag='box_vectors')
box_vec = pack_utils.decodePyObj(vec_data)
md_components.set_box_vectors(box_vec)
flask, map_comp = md_components.create_flask
record.set_value(Fields.md_components, md_components)
record.set_value(Fields.flask, flask)
record.set_value(Fields.title, solute_title)
self.success.emit(record)
except Exception as e:
print("Failed to complete", str(e), flush=True)
self.opt['Logger'].info('Exception {} {}'.format(
str(e), self.title))
self.log.error(traceback.format_exc())
self.failure.emit(record)
return