def run(args):
params = get_input(args, master_params, "zrefine", banner, help)
if params is None:
return
np = 30
nmax = params.zrefine.nmax
start_file = params.zrefine.start
target_file = params.zrefine.target
rmax = params.zrefine.rmax
qmax = params.zrefine.qmax
prefix = params.zrefine.prefix
splat_range = params.zrefine.splat_range
pdb = params.zrefine.pdb
n_trial = params.zrefine.n_trial
if pdb is not None:
pdb_obj = model_interface.container(pdbfile=pdb, rmax=rmax, nmax=nmax)
pdb_nlm = pdb_obj.nlm_array
else:
pdb_nlm = None
data = saxs_read_write.read_standard_ascii_qis(target_file)
refine_obj = zm_xplor_refine(data,
start_file,
rmax,
qmax=qmax,
nmax=nmax,
np_on_grid=np,
prefix=prefix,
splat_range=splat_range,
pdb_nlm=pdb_nlm,
n_trial=n_trial)
if pdb is not None:
out_pdb_filename = pdb.split('.')[0] + '_shift.pdb'
pdb_obj.write_pdb(rmax=refine_obj.rmax, filename=out_pdb_filename)
def process(pdb_files, nmax, rmax=50.0, fraction=0.9):
pdb_models = []
rmax_over_fraction = rmax / fraction
shift = (rmax_over_fraction, rmax_over_fraction, rmax_over_fraction)
for file in pdb_files:
model = model_interface.container(pdbfile=file, rmax=rmax, nmax=nmax)
if (model is not None):
if (len(pdb_models) == 0):
ref_nlm_array = model.nlm_array
pdb_models.append(
pdb_model(ref_nlm_array.coefs(), file, model.rmax, model))
ea = (0, 0, 0)
outname = model.id + '_sa.pdb'
model.write_pdb(rmax=rmax_over_fraction,
rotation=ea,
filename=outname)
else:
mov_nlm_array = model.nlm_array
align_obj = fft_align.align(ref_nlm_array,
mov_nlm_array,
nmax=nmax,
refine=True)
pdb_models.append(
pdb_model(align_obj.moving_nlm.coefs(), file, model.rmax,
model))
ea = align_obj.best_ea
outname = model.id + '_sa.pdb'
model.write_pdb(rmax=rmax_over_fraction,
rotation=ea,
filename=outname)
return pdb_models
def run(args):
params = get_input(args, master_params, "zrefine", banner, help)
if params is None:
return
nmax = params.zrefine.nmax
start_file = params.zrefine.start
target_file = params.zrefine.target
rmax = params.zrefine.rmax
qmax = params.zrefine.qmax
np_on_grid = params.zrefine.np_on_grid # number of grids covering [0,1]
nbr_dist = params.zrefine.nbr_dist
prefix = params.zrefine.prefix
splat_range = params.zrefine.splat_range
pdb = params.zrefine.pdb
n_trial = params.zrefine.n_trial
if pdb is not None:
pdb_nlm = model_interface.container(pdbfile=pdb, rmax=rmax,
nmax=nmax).nlm_array
else:
pdb_nlm = None
data = saxs_read_write.read_standard_ascii_qis(target_file)
zm_xplor_refine(data,
start_file,
rmax,
qmax=qmax,
nmax=nmax,
np_on_grid=np_on_grid,
prefix=prefix,
splat_range=splat_range,
pdb_nlm=pdb_nlm,
n_trial=n_trial,
nbr_dist=nbr_dist)
def run(args):
params = get_input(args, master_params, "zrefine", banner, help)
if params is None:
return
nmax=params.zrefine.nmax
lmax=params.zrefine.lmax
if( lmax is None ): lmax=nmax
start_file=params.zrefine.start
target_file=params.zrefine.target
rmax = params.zrefine.rmax
qmax = params.zrefine.qmax
prefix = params.zrefine.prefix
splat_range = params.zrefine.splat_range
pdb = params.zrefine.pdb
np_on_grid = params.zrefine.np_on_grid
n_trial = params.zrefine.n_trial
nbr_dist = params.zrefine.nbr_dist
if pdb is not None:
pdb_nlm = model_interface.container( pdbfile=pdb, rmax=rmax, nmax=nmax ).nlm_array
else:
pdb_nlm = None
data = fxs_tools.read_blq( target_file,lmax=lmax )
data.print_out(data=data.blq/data.blq[0], out=open(target_file+'_n', 'w') )
zm_xplor_refine( data, start_file, rmax, qmax=qmax, nmax=nmax, lmax=lmax, np_on_grid=np_on_grid, prefix=prefix, splat_range=splat_range, pdb_nlm=pdb_nlm, n_trial=n_trial, nbr_dist=nbr_dist )