def build_system_from_molecules(self, molecules, patchers=None,
leap_header_cmds=None):
if patchers is None:
patchers = []
if leap_header_cmds is None:
leap_header_cmds = []
if isinstance(leap_header_cmds, string_types):
leap_header_cmds = [leap_header_cmds]
with util.in_temp_dir():
leap_cmds = []
mol_ids = []
leap_cmds.extend(self._generate_leap_header())
leap_cmds.extend(leap_header_cmds)
for index, mol in enumerate(molecules):
mol_id = 'mol_{}'.format(index)
mol_ids.append(mol_id)
mol.prepare_for_tleap(mol_id)
leap_cmds.extend(mol.generate_tleap_input(mol_id))
leap_cmds.extend(self._generate_leap_footer(mol_ids))
with open('tleap.in', 'w') as tleap_file:
tleap_string = '\n'.join(leap_cmds)
tleap_file.write(tleap_string)
subprocess.check_call('tleap -f tleap.in > tleap.out', shell=True)
return load_amber_system('system.top', 'system.mdcrd', patchers)
def build_system_from_molecules(self,
molecules,
patchers=None,
leap_header_cmds=None):
if patchers is None:
patchers = []
if leap_header_cmds is None:
leap_header_cmds = []
if isinstance(leap_header_cmds, string_types):
leap_header_cmds = [leap_header_cmds]
with util.in_temp_dir():
leap_cmds = []
mol_ids = []
leap_cmds.extend(self._generate_leap_header())
leap_cmds.extend(leap_header_cmds)
for index, mol in enumerate(molecules):
mol_id = 'mol_{}'.format(index)
mol_ids.append(mol_id)
mol.prepare_for_tleap(mol_id)
leap_cmds.extend(mol.generate_tleap_input(mol_id))
leap_cmds.extend(self._generate_leap_footer(mol_ids))
with open('tleap.in', 'w') as tleap_file:
tleap_string = '\n'.join(leap_cmds)
tleap_file.write(tleap_string)
subprocess.check_call('tleap -f tleap.in > tleap.out', shell=True)
return load_amber_system('system.top', 'system.mdcrd', patchers)
def setUp(self):
with in_temp_dir():
with open("pdb.pdb", "w") as outfile:
outfile.write(pdb_string)
p = subsystem.SubSystemFromPdbFile("pdb.pdb")
b = builder.SystemBuilder(explicit_solvent=True)
self.system = b.build_system([p])
def build_system_from_molecules(self,
molecules,
patchers=None,
leap_header_cmds=None):
if patchers is None:
patchers = []
if leap_header_cmds is None:
leap_header_cmds = []
if isinstance(leap_header_cmds, str):
leap_header_cmds = [leap_header_cmds]
with util.in_temp_dir():
leap_cmds = []
mol_ids = []
leap_cmds.extend(self._generate_leap_header())
leap_cmds.extend(leap_header_cmds)
for index, mol in enumerate(molecules):
mol_id = f"mol_{index}"
mol_ids.append(mol_id)
mol.prepare_for_tleap(mol_id)
leap_cmds.extend(mol.generate_tleap_input(mol_id))
if self._explicit_solvent:
leap_cmds.extend(self._generate_solvent(mol_ids))
leap_cmds.extend(self._generate_leap_footer([f"solute"]))
else:
leap_cmds.extend(self._generate_leap_footer(mol_ids))
with open("tleap.in", "w") as tleap_file:
tleap_string = "\n".join(leap_cmds)
tleap_file.write(tleap_string)
subprocess.check_call("tleap -f tleap.in > tleap.out", shell=True)
return load_amber_system("system.top", "system.mdcrd", patchers)
def patch(self, top_string, crd_string):
INTOP = 'in.top'
INRST = 'in.rst'
OUTTOP = 'out.top'
OUTRST = 'out.rst'
with util.in_temp_dir():
with open(INTOP, 'wt') as outfile:
outfile.write(top_string)
with open(INRST, 'wt') as outfile:
outfile.write(crd_string)
topol = pmd.load_file(INTOP)
crd = pmd.load_file(INRST)
topol.coordinates = crd.coordinates
self._add_particles(topol)
topol.write_parm(OUTTOP)
topol.write_rst7(OUTRST)
with open(OUTTOP, 'rt') as infile:
top_string = infile.read()
with open(OUTRST, 'rt') as infile:
crd_string = infile.read()
return top_string, crd_string
def patch(self, top_string, crd_string):
INTOP = "in.top"
INRST = "in.rst"
OUTTOP = "out.top"
OUTRST = "out.rst"
with util.in_temp_dir():
with open(INTOP, "wt") as outfile:
outfile.write(top_string)
with open(INRST, "wt") as outfile:
outfile.write(crd_string)
topol = pmd.load_file(INTOP)
crd = pmd.load_file(INRST)
topol.coordinates = crd.coordinates
self._add_particles(topol)
topol.write_parm(OUTTOP)
topol.write_rst7(OUTRST)
with open(OUTTOP, "rt") as infile:
top_string = infile.read()
with open(OUTRST, "rt") as infile:
crd_string = infile.read()
return top_string, crd_string
def build_system_from_molecules(
self, molecules, patchers=None, leap_header_cmds=None
):
if patchers is None:
patchers = []
if leap_header_cmds is None:
leap_header_cmds = []
if isinstance(leap_header_cmds, str):
leap_header_cmds = [leap_header_cmds]
with util.in_temp_dir():
leap_cmds = []
mol_ids = []
leap_cmds.extend(self._generate_leap_header())
leap_cmds.extend(leap_header_cmds)
for index, mol in enumerate(molecules):
mol_id = f"mol_{index}"
mol_ids.append(mol_id)
mol.prepare_for_tleap(mol_id)
leap_cmds.extend(mol.generate_tleap_input(mol_id))
if self._explicit_solvent:
leap_cmds.extend(self._generate_solvent(mol_ids))
leap_cmds.extend(self._generate_leap_footer([f"solute"]))
else:
leap_cmds.extend(self._generate_leap_footer(mol_ids))
with open("tleap.in", "w") as tleap_file:
tleap_string = "\n".join(leap_cmds)
tleap_file.write(tleap_string)
subprocess.check_call("tleap -f tleap.in > tleap.out", shell=True)
return load_amber_system("system.top", "system.mdcrd", patchers)
def test_init_mode_w_creates_results(self):
"calling initialize should create the results.h5 file"
with in_temp_dir():
pdb_writer = object() # dummy pdb writer; can't use a mock because they can't be pickled
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode='w')
self.assertTrue(os.path.exists('Data/Blocks/block_000000.nc'), 'results_000000.nc not created')
def test_load_datastore(self):
"should call load the datastore"
with in_temp_dir():
os.mkdir("Logs")
launch.launch("Reference", self.log_handler)
self.MockDataStore.load_data_store.assert_called_once_with()
def test_should_init_store(self):
"should initialize the store"
with in_temp_dir():
os.mkdir("Logs")
launch.launch("Reference", self.log_handler)
self.mock_store.initialize.assert_called_once_with(mode="a")
def test_should_init_comm(self):
"should initialize the communicator"
with in_temp_dir():
os.mkdir("Logs")
launch.launch("Reference", self.log_handler)
self.mock_comm.initialize.assert_called_once_with()
def test_init_mode_w_creates_directories(self):
"calling initialize should create the Data and Data/Backup directories"
with in_temp_dir():
pdb_writer = object() # dummy pdb writer; can't use a mock because they can't be pickled
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode='w')
self.assertTrue(os.path.exists('Data'), 'Data directory does not created')
self.assertTrue(os.path.exists('Data/Backup'), 'Backup directory not created')
def test_should_run(self):
"should run remd runner with correct parameters"
with in_temp_dir():
os.mkdir("Logs")
launch.launch("Reference", self.log_handler)
self.mock_remd_leader.run.assert_called_once_with(
self.mock_comm, self.mock_runner, self.mock_store)
def test_init_mode_w_raises_when_dirs_exist(self):
"calling initialize should raise RuntimeError when Data and Data/Backup directories exist"
with in_temp_dir():
os.mkdir('Data')
os.mkdir('Data/Backup')
pdb_writer = object() # dummy pdb writer; can't use a mock because they can't be pickled
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
with self.assertRaises(RuntimeError):
store.initialize(mode='w')
def test_init_mode_w_creates_results(self):
"calling initialize should create the results.h5 file"
with in_temp_dir():
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode='w')
self.assertTrue(os.path.exists('Data/Blocks/block_000000.nc'),
'results_000000.nc not created')
def test_init_mode_w_raises_when_dirs_exist(self):
"calling initialize should raise RuntimeError when Data directories exist"
with in_temp_dir():
os.mkdir("Data")
os.mkdir("Data/Backup")
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
with self.assertRaises(RuntimeError):
store.initialize(mode="w")
def test_save_and_load_run_options(self):
"should be able to save and load run options"
with in_temp_dir():
pdb_writer = object() # dummy pdb writer; can't use a mock because they can't be pickled
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode='w')
fake_run_options = object()
store.save_run_options(fake_run_options)
store.load_run_options()
self.assertTrue(os.path.exists('Data/run_options.dat'))
def test_init_mode_w_creates_directories(self):
"calling initialize should create the Data and Data/Backup directories"
with in_temp_dir():
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode="w")
self.assertTrue(os.path.exists("Data"),
"Data directory does not created")
self.assertTrue(os.path.exists("Data/Backup"),
"Backup directory not created")
def test_save_and_load_run_options(self):
"should be able to save and load run options"
with in_temp_dir():
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode="w")
fake_run_options = system.RunOptions()
store.save_run_options(fake_run_options)
store.load_run_options()
self.assertTrue(os.path.exists("Data/run_options.dat"))
def test_save_and_load_system(self):
"should be able to save and load a System"
with in_temp_dir():
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode='w')
fake_system = object()
store.save_system(fake_system)
store.load_system()
self.assertTrue(os.path.exists('Data/system.dat'))
def test_save_and_load_system(self):
"should be able to save and load a System"
with in_temp_dir():
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.state_template, self.N_REPLICAS, pdb_writer)
store.initialize(mode="w")
fake_system = object()
store.save_system(fake_system)
store.load_system()
self.assertTrue(os.path.exists("Data/system.dat"))
def test_save_and_load_data_store(self):
"should be able to save and then reload the DataStore"
with in_temp_dir():
pdb_writer = object() # dummy pdb writer; can't use a mock because they can't be pickled
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode='w')
store.save_data_store()
store2 = vault.DataStore.load_data_store()
self.assertEqual(store.n_atoms, store2.n_atoms)
self.assertEqual(store.n_replicas, store2.n_replicas)
self.assertIsNone(store2._cdf_data_set)
self.assertTrue(os.path.exists('Data/data_store.dat'))
def test_save_and_load_data_store(self):
"should be able to save and then reload the DataStore"
with in_temp_dir():
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode="w")
store.save_data_store()
store2 = vault.DataStore.load_data_store()
self.assertEqual(store.n_atoms, store2.n_atoms)
self.assertEqual(store.n_replicas, store2.n_replicas)
self.assertIsNone(store2._cdf_data_set)
self.assertTrue(os.path.exists("Data/data_store.dat"))
def test_save_and_load_remd_runner(self):
"should be able to save and reload an remd runner"
with in_temp_dir():
pdb_writer = object() # dummy pdb writer; can't use a mock because they can't be pickled
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode='w')
l = ladder.NearestNeighborLadder(n_trials=100)
policy = adaptor.AdaptationPolicy(1.0, 50, 100)
a = adaptor.EqualAcceptanceAdaptor(n_replicas=self.N_REPLICAS, adaptation_policy=policy)
runner = master_runner.MasterReplicaExchangeRunner(self.N_REPLICAS, max_steps=100, ladder=l, adaptor=a)
store.save_remd_runner(runner)
runner2 = store.load_remd_runner()
self.assertEqual(runner.n_replicas, runner2.n_replicas)
self.assertTrue(os.path.exists('Data/remd_runner.dat'))
def test_save_and_load_communicator(self):
"should be able to save and reload the communicator"
with in_temp_dir():
pdb_writer = object() # dummy pdb writer; can't use a mock because they can't be pickled
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode='w')
c = comm.MPICommunicator(self.N_ATOMS, self.N_REPLICAS)
# set _mpi_comm to something
# this should not be saved
c._mpi_comm = 'foo'
store.save_communicator(c)
c2 = store.load_communicator()
self.assertEqual(c.n_atoms, c2.n_atoms)
self.assertEqual(c.n_replicas, c2.n_replicas)
self.assertIsNone(c2._mpi_comm, '_mpi_comm should not be saved')
self.assertTrue(os.path.exists('Data/communicator.dat'))
def test_save_and_load_communicator(self):
"should be able to save and reload the communicator"
with in_temp_dir():
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode="w")
c = comm.MPICommunicator(self.N_ATOMS, self.N_REPLICAS)
# set _mpi_comm to something
# this should not be saved
c._mpi_comm = "foo"
store.save_communicator(c)
c2 = store.load_communicator()
self.assertEqual(c.n_atoms, c2.n_atoms)
self.assertEqual(c.n_replicas, c2.n_replicas)
self.assertTrue(os.path.exists("Data/communicator.dat"))
def test_save_and_load_remd_runner(self):
"should be able to save and reload an remd runner"
with in_temp_dir():
# dummy pdb writer; can't use a mock because they can't be pickled
pdb_writer = object()
store = vault.DataStore(self.N_ATOMS, self.N_REPLICAS, pdb_writer)
store.initialize(mode="w")
l = ladder.NearestNeighborLadder(n_trials=100)
policy = adaptor.AdaptationPolicy(1.0, 50, 100)
a = adaptor.EqualAcceptanceAdaptor(n_replicas=self.N_REPLICAS,
adaptation_policy=policy)
runner = master_runner.MasterReplicaExchangeRunner(self.N_REPLICAS,
max_steps=100,
ladder=l,
adaptor=a)
store.save_remd_runner(runner)
runner2 = store.load_remd_runner()
self.assertEqual(runner.n_replicas, runner2.n_replicas)
self.assertTrue(os.path.exists("Data/remd_runner.dat"))
def build_system_from_molecules(self, molecules):
with util.in_temp_dir():
leap_cmds = []
mol_ids = []
leap_cmds.extend(self._generate_leap_header())
for index, mol in enumerate(molecules):
mol_id = 'mol_{}'.format(index)
mol_ids.append(mol_id)
mol.prepare_for_tleap(mol_id)
leap_cmds.extend(mol.generate_tleap_input(mol_id))
leap_cmds.extend(self._generate_leap_footer(mol_ids))
with open('tleap.in', 'w') as tleap_file:
tleap_string = '\n'.join(leap_cmds)
tleap_file.write(tleap_string)
print tleap_string
subprocess.check_call('tleap -f tleap.in > tleap.out', shell=True)
with open('system.top') as top_file:
top = top_file.read()
with open('system.mdcrd') as crd_file:
crd = crd_file.read()
return System(top, crd)
def build_system(
self,
subsystems: List[subsystem._SubSystem],
patchers: Optional[List[patchers.PatcherBase]] = None,
leap_header_cmds: Optional[List[str]] = None,
) -> interfaces.ISystem:
"""
Build the system from SubSystems
Args:
subsystems: component subsystems that make up the system
patchers: an optional list of patchers to modify system
leap_header_cmds: an optional list of leap commands
Returns:
the MELD system
"""
if not subsystems:
raise ValueError("len(subsystems) must be > 0")
if patchers is None:
patchers = []
if leap_header_cmds is None:
leap_header_cmds = []
if isinstance(leap_header_cmds, str):
leap_header_cmds = [leap_header_cmds]
with util.in_temp_dir():
mol_ids = []
chains = []
current_res_index = 0
leap_cmds = []
leap_cmds.extend(self._generate_leap_header())
leap_cmds.extend(leap_header_cmds)
for index, sub in enumerate(subsystems):
# First we'll update the indexing for this subsystem
for chain in sub._info.chains:
residues_with_offset = {
k: v + current_res_index
for k, v in chain.residues.items()
}
chains.append(indexing._ChainInfo(residues_with_offset))
current_res_index += sub._info.n_residues
# now add the leap commands for this subsystem
mol_id = f"mol_{index}"
mol_ids.append(mol_id)
sub.prepare_for_tleap(mol_id)
leap_cmds.extend(sub.generate_tleap_input(mol_id))
if self._explicit_solvent:
leap_cmds.extend(self._generate_solvent(mol_ids))
leap_cmds.extend(self._generate_leap_footer([f"solute"]))
else:
leap_cmds.extend(self._generate_leap_footer(mol_ids))
with open("tleap.in", "w") as tleap_file:
tleap_string = "\n".join(leap_cmds)
tleap_file.write(tleap_string)
try:
subprocess.check_call("tleap -f tleap.in > tleap.out",
shell=True)
except subprocess.CalledProcessError:
print("Call to tleap failed.")
print()
print()
print()
print("=========")
print("tleap.in")
print("=========")
print(open("tleap.in").read())
print()
print()
print()
print("=========")
print("tleap.out")
print("=========")
print(open("tleap.out").read())
print()
print()
print()
print("========")
print("leap.log")
print("========")
print(open("leap.log").read())
print()
print()
print()
raise
return meld_system._load_amber_system("system.top", "system.mdcrd",
chains, patchers)
def patch(self, top_string, crd_string):
INTOP = "in.top"
INRST = "in.rst"
OUTTOP = "out.top"
OUTRST = "out.rst"
with util.in_temp_dir():
with open(INTOP, "wt") as outfile:
outfile.write(top_string)
with open(INRST, "wt") as outfile:
outfile.write(crd_string)
base = pmd.load_file(INTOP)
crd = pmd.load_file(INRST)
base.coordinates = crd.coordinates
# create a new structure to add our dummy atoms to
parm = pmd.Structure()
# add in atom type for our dummy particles
atype = pmd.AtomType("SDUM", 0, mass=12.0, charge=0.0)
atype.set_lj_params(0.0, 0.0)
for i in range(self.n_tensors):
a1 = pmd.Atom(
name="S1",
atomic_number=atype.atomic_number,
type=str(atype),
charge=atype.charge,
mass=atype.mass,
solvent_radius=1.0,
screen=0.5,
)
a1.atom_type = atype
a2 = pmd.Atom(
name="S2",
atomic_number=atype.atomic_number,
type=str(atype),
charge=atype.charge,
mass=atype.mass,
solvent_radius=1.0,
screen=0.5,
)
a2.atom_type = atype
parm.add_atom(a1, resname="SDM", resnum=i)
parm.add_atom(a2, resname="SDM", resnum=i)
# we add noise here because we'll get NaN if the particles ever
# end up exactly on top of each other
parm.positions = np.zeros((2 * self.n_tensors, 3))
# combine the old system with the new dummy atoms
comb = base + parm
last_index = comb.residues[-1].idx
self.resids = list(range(last_index - self.n_tensors + 2, last_index + 2))
comb.write_parm(OUTTOP)
comb.write_rst7(OUTRST)
with open(OUTTOP, "rt") as infile:
top_string = infile.read()
with open(OUTRST, "rt") as infile:
crd_string = infile.read()
return top_string, crd_string