def get_initial_restraints_weight_scale(
initial_fmodel,
states,
restraints_manager,
sites,
data_weight,
max_bond_rmsd,
geometry_rmsd_manager):
initial_restraints_weight_scale = 1
b_rmsd = False
counter=0
while(b_rmsd is False):
counter+=1
print "Initial weight optimization conter:", counter
if(counter>10): return 1.
fmodel = initial_fmodel.deep_copy()
minimizer.run(
fmodel = fmodel,
states = states,
restraints_manager = restraints_manager,
sites = True,
data_weight = data_weight,
restraints_weight_scale = initial_restraints_weight_scale)
cctbx_rm_bonds_rmsd = geometry_rmsd_manager.energies_sites(
sites_cart = fmodel.xray_structure.sites_cart(),
compute_gradients = False).geometry.bond_deviations()[2]
if(cctbx_rm_bonds_rmsd<=max_bond_rmsd and
fmodel.r_work() < initial_fmodel.r_work()):
b_rmsd=True
else:
initial_restraints_weight_scale *= 2.
return initial_restraints_weight_scale
def run(fmodel,
restraints_manager,
states,
pdb_hierarchy,
number_of_macro_cycles,
max_bond_rmsd,
file_label,
data_weight = None,
file_out_prefix = None,
r_tolerance = 0.001,
rmsd_tolerance = 0.01,
use_convergence_test = False,
geometry_rmsd_manager = None):
cctbx_rm_bonds_rmsd = geometry_rmsd_manager.energies_sites(
sites_cart = fmodel.xray_structure.sites_cart(),
compute_gradients = False).geometry.bond_deviations()[2]
print "rmsd(b), start: %7.4f"%cctbx_rm_bonds_rmsd
conv_test = convergence(
fmodel=fmodel, r_tolerance=r_tolerance, rmsd_tolerance=rmsd_tolerance)
restraints_weight_scale = 1.0
if(not (data_weight is not None and abs(data_weight)<1.e-9)):
restraints_weight_scale = get_initial_restraints_weight_scale(
initial_fmodel = fmodel,
states = states,
restraints_manager = restraints_manager,
sites = True,
data_weight = data_weight,
max_bond_rmsd = max_bond_rmsd,
geometry_rmsd_manager = geometry_rmsd_manager)
print "initial_restraints_weight_scale", restraints_weight_scale
res = results(r=fmodel.r_work(), b=cctbx_rm_bonds_rmsd,
xrs=fmodel.xray_structure, max_bond_rmsd=max_bond_rmsd)
for macro_cycle in xrange(number_of_macro_cycles):
# refine coordinates
minimized = minimizer.run(
fmodel = fmodel,
states = states,
restraints_manager = restraints_manager,
sites = True,
data_weight = data_weight,
restraints_weight_scale = restraints_weight_scale)
#
cctbx_rm_bonds_rmsd = geometry_rmsd_manager.energies_sites(
sites_cart = fmodel.xray_structure.sites_cart(),
compute_gradients = False).geometry.bond_deviations()[2]
if(data_weight is None or abs(data_weight)>1.e-9):
if(cctbx_rm_bonds_rmsd>max_bond_rmsd*10.0):
print "the structure is distorted"
break
if(cctbx_rm_bonds_rmsd>max_bond_rmsd):
restraints_weight_scale *= 2.
if(cctbx_rm_bonds_rmsd<0.01):
restraints_weight_scale /= 2.
###
if(not (data_weight is not None and abs(data_weight)<1.e-9)):
res.update(r=fmodel.r_work(), b=cctbx_rm_bonds_rmsd, xrs=fmodel.xray_structure)
####convergence test
fmt="mc: %3d Rw: %6.4f Rf: %6.4f rmsd(b): %7.4f restraint_scale: %4.1f min_steps: %d"
print fmt%(macro_cycle, fmodel.r_work(), fmodel.r_free(), cctbx_rm_bonds_rmsd,
restraints_weight_scale, minimized.minimizer.nfun())
if(use_convergence_test and conv_test.is_converged(fmodel=fmodel)):
print "Convergence reached, stop now."
break
###
if(not (data_weight is not None and abs(data_weight)<1.e-9)):
xrs_best = res.choose_best()
if(xrs_best is not None):
fmodel.update_xray_structure(xray_structure = xrs_best, update_f_calc=True)
pdb_hierarchy.adopt_xray_structure(xrs_best)
print " r_factor (best): %7.5f"%fmodel.r_work()
else:
print " r_factor (best): None"
###
if(1):
pdb_hierarchy.adopt_xray_structure(fmodel.xray_structure)
if(file_out_prefix==None):
file_out_prefix="./pdb/"
if( os.path.exists(file_out_prefix)) !=True:
os.mkdir(file_out_prefix)
job_type= "_refined" if (data_weight==None) else "_opt"
file_out_prefix=file_out_prefix+file_label+ job_type
pdb_hierarchy.write_pdb_file(file_name=file_out_prefix+".pdb",
crystal_symmetry = fmodel.xray_structure.crystal_symmetry())
# good for debugging, useless otherwise
# states.write(file_name=file_out_prefix+"_all_states.pdb")
print "see the result structure: ", file_out_prefix+".pdb"
