with work_manager:
if work_manager.is_master:
# Process target states
target_states = []
if args.tstate_file:
target_states.extend(TargetState.states_from_file(args.tstate_file, system.pcoord_dtype))
if args.tstates:
tstates_strio = cStringIO.StringIO('\n'.join(args.tstates).replace(',', ' '))
target_states.extend(TargetState.states_from_file(tstates_strio, system.pcoord_dtype))
del tstates_strio
# Process basis states
basis_states = []
if args.bstate_file:
basis_states.extend(BasisState.states_from_file(args.bstate_file))
if args.bstates:
for bstate_str in args.bstates:
fields = bstate_str.split(',')
label=fields[0]
probability=float(fields[1])
try:
auxref = fields[2]
except IndexError:
auxref = None
basis_states.append(BasisState(label=label,probability=probability,auxref=auxref))
if not basis_states:
log.error('At least one basis state is required')
sys.exit(3)
if args.tstate_file:
target_states.extend(
TargetState.states_from_file(args.tstate_file,
system.pcoord_dtype))
if args.tstates:
tstates_strio = io.StringIO('\n'.join(args.tstates).replace(
',', ' '))
target_states.extend(
TargetState.states_from_file(tstates_strio,
system.pcoord_dtype))
del tstates_strio
# Process basis states
basis_states = []
if args.bstate_file:
basis_states.extend(BasisState.states_from_file(args.bstate_file))
if args.bstates:
for bstate_str in args.bstates:
fields = bstate_str.split(',')
label = fields[0]
probability = float(fields[1])
try:
auxref = fields[2]
except IndexError:
auxref = None
basis_states.append(
BasisState(label=label,
probability=probability,
auxref=auxref))
if not basis_states:
westpa.rc.process_args(args)
system = west.rc.get_system_driver()
data_manager = west.rc.get_data_manager()
h5file = data_manager.we_h5filename
try:
os.unlink(h5file)
except OSError as e:
pass
data_manager.prepare_backing()
uv = MDAnalysis.Universe(args.template_file)
bstate = BasisState('extsim',
1.0,
pcoord=[0.0, 0.0, 0.0, 0.0],
auxref=args.basis_file,
state_id=0)
data_manager.create_ibstate_group([bstate])
basis_h5 = h5py.File(args.basis_file, 'r')
bs_norm_rmsd = basis_h5['normal_rmsd'][...]
min_dist = basis_h5['mindist'][...]
bs_side_chain = basis_h5['side_rmsd'][...]
bs_ca = basis_h5['ca_rmsd'][...]
coord_ds = basis_h5['coords']
all_weight = basis_h5['weight'][...]
print('Total weight of all possible structures: {}'.format(
all_weight.sum()))
all_pcoord = numpy.column_stack(
[min_dist, bs_norm_rmsd, bs_ca, bs_side_chain])
if work_manager.is_master:
data_manager = westpa.rc.get_data_manager()
data_manager.open_backing(mode='a')
sim_manager = westpa.rc.get_sim_manager()
n_iter = data_manager.current_iteration
assert args.mode in ('show', 'replace', 'append')
if args.mode == 'show':
basis_states = data_manager.get_basis_states(n_iter)
if basis_states:
bstate_file = sys.stdout if not args.bstate_file else open(
args.bstate_file, 'wt')
bstate_file.write(
'# Basis states for iteration {:d}\n'.format(n_iter))
BasisState.states_to_file(basis_states, bstate_file)
target_states = data_manager.get_target_states(n_iter)
if target_states:
tstate_file = sys.stdout if not args.tstate_file else open(
args.tstate_file, 'wt')
tstate_file.write(
'# Target states for iteration {:d}\n'.format(n_iter))
TargetState.states_to_file(target_states, tstate_file)
elif args.mode == 'replace':
seg_index = data_manager.get_seg_index(n_iter)
if (seg_index['status'] == Segment.SEG_STATUS_COMPLETE).any():
print(
'Iteration {:d} has completed segments; applying new states to iteration {:d}'
.format(n_iter, n_iter + 1))
with work_manager:
if work_manager.is_master:
data_manager = westpa.rc.get_data_manager()
data_manager.open_backing(mode='a')
sim_manager = westpa.rc.get_sim_manager()
n_iter = data_manager.current_iteration
assert args.mode in ('show', 'replace', 'append')
if args.mode == 'show':
basis_states = data_manager.get_basis_states(n_iter)
if basis_states:
bstate_file = sys.stdout if not args.bstate_file else open(args.bstate_file, 'wt')
bstate_file.write('# Basis states for iteration {:d}\n'.format(n_iter))
BasisState.states_to_file(basis_states, bstate_file)
target_states = data_manager.get_target_states(n_iter)
if target_states:
tstate_file = sys.stdout if not args.tstate_file else open(args.tstate_file, 'wt')
tstate_file.write('# Target states for iteration {:d}\n'.format(n_iter))
TargetState.states_to_file(target_states, tstate_file)
elif args.mode == 'replace':
seg_index = data_manager.get_seg_index(n_iter)
if (seg_index['status'] == Segment.SEG_STATUS_COMPLETE).any():
print('Iteration {:d} has completed segments; applying new states to iteration {:d}'.format(n_iter,n_iter+1))
n_iter += 1
basis_states = []
if args.bstate_file:
