def extract(ms, target, state_index=0, discard=0):
"""Extract configurations at the target thermodynamic state."""
# discard starting configuration from trajectory
trj = extract_trajectory(nc_path=str(ms),
to_file=str(target),
state_index=state_index,
start_frame=discard)
return trj
def extract(ms, target, state_index=0, discard=0):
"""Extract configurations at the target thermodynamic state."""
# discard starting configuration from trajectory
discard += 1
start_frame = ceil(discard / checkpoint_iterations)
trj = extract_trajectory(nc_path=str(ms),
to_file=str(target),
state_index=state_index,
start_frame=start_frame)
return trj
def extract():
"""Extract configurations at the target thermodynamic state."""
# discard starting configuration from trajectory
burnin = burnin_iterations + 1
start_frame = ceil(burnin / checkpoint_iterations)
trj = extract_trajectory(nc_path=ms_container,
to_file=target_container,
state_index=ref_state_index,
start_frame=start_frame)
return trj
def demux(self,
state_index=None,
*,
replica_index=None,
to_file=None,
**kwargs):
"""demux trajectories.
Default: extract configurations for state_index = 0.
"""
trj_file = Path(to_file) if to_file else Path('trj.nc')
trj_dir = trj_file.parent.resolve()
trj_dir.mkdir(parents=True, exist_ok=True)
if (state_index is None) and (replica_index is None):
state_index = self.ref_state
top = kwargs.pop('top', None) or self.topology
if not top:
raise ValueError('Need a topology.')
nc_path = kwargs.pop('nc_path', None) or self.reporter.filepath
trj = mmdemux.extract_trajectory(ref_system=self.ref_system,
top=top,
nc_path=nc_path,
state_index=state_index,
replica_index=replica_index,
to_file=trj_file,
**kwargs)
# save a ref pdb for topology
out_dir = trj_file.parent
filename = out_dir / 'system.pdb'
trj[-1].save(str(filename))
# save a ref pdb for topology
out_dir = trj_file.parent
filename = out_dir / 'system.pdb'
trj[-1].save(str(filename))
# save system as .xml
serialized_system = mm.openmm.XmlSerializer.serialize(self.ref_system)
with open('system.xml', 'w') as fp:
print(serialized_system, file=fp)
return trj
from mmdemux import extract_trajectory
from mmlite.gromacs import generate_gromacs_input
from mmlite.utils import multistate_reporter_metadata
burnin_iterations = 100 # number of burnin iterations (#iterations)
checkpoint_iterations = 10 # checkpoint_interval (#iterations)
ref_state_index = 0
ms_container = Path('frames/trj.nc') # trajectory filepath
target_container = Path('frames/trj.0.nc') # trajectory filepath
burnin_iterations += 1 # discard starting configuration from trajectory
start_frame = ceil(burnin_iterations / checkpoint_iterations)
reference_system, topology = multistate_reporter_metadata(
ms_container, 'reference_state.system topography.topology'.split())
# save the sampled configurations at the target thermodynamic state
trj = extract_trajectory(nc_path=ms_container,
to_file=target_container,
state_index=ref_state_index,
start_frame=start_frame)
# create gromacs .top and .gro files in the target directory
generate_gromacs_input(target_container,
topology=topology,
system=reference_system,
split='.gro')
def test_from_pdb_file():
kw = dict(kwargs)
kw['top'] = 'test_repex.pdb'
trj = extract_trajectory(state_index=0, **kw)
assert trj.n_frames == 11
def test_from_system_file():
kw = dict(kwargs)
kw['ref_system'] = 'test_repex.xml'
trj = extract_trajectory(state_index=0, **kw)
assert trj.n_frames == 11
def test_index_out_of_bounds():
trj = extract_trajectory(state_index=3, **kwargs)
assert trj.n_frames == 0
def test_replica():
trj = extract_trajectory(replica_index=0, **kwargs)
assert trj.n_frames == 11
def test_state():
trj = extract_trajectory(state_index=0, **kwargs)
assert trj.n_frames == 11