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])
# 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)
# Check that the total probability of basis states adds to one
tprob = sum(bstate.probability for bstate in basis_states)
if abs(1.0 - tprob) > len(basis_states) * EPS:
pscale = 1 / tprob
log.warning(
'Basis state probabilities do not add to unity; rescaling by {:g}'
.format(pscale))
for bstate in basis_states:
bstate.probability *= pscale
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:
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 basis_states:
# Check that the total probability of basis states adds to one
tprob = sum(bstate.probability for bstate in basis_states)
if abs(1.0 - tprob) > len(basis_states) * EPS:
pscale = 1/tprob
log.warning('Basis state probabilities do not add to unity; rescaling by {:g}'.format(pscale))
for bstate in basis_states:
bstate.probability *= pscale
# Assign progress coordinates to basis states
sim_manager.get_bstate_pcoords(basis_states, n_iter)
data_manager.create_ibstate_group(basis_states, n_iter)
sim_manager.report_basis_states(basis_states)
