def run(args, log = sys.stdout):
cmdline = mmtbx.command_line.load_model_and_data(
args = args,
master_phil = get_master_phil(),
create_fmodel = False,
out = log)
params = cmdline.params
fmodel = create_fmodel(
f_obs = cmdline.f_obs,
r_free_flags = cmdline.r_free_flags,
xray_structure = cmdline.xray_structure,
log = log,
target_name = params.refinement_target_name,
update_all_scales = params.update_all_scales)
data_weight=None
if(params.restraints == "cctbx"):
grm = restraints.get_grm(
file_name = cmdline.pdb_file_names[0]).restraints_manager
restraints_manager = restraints.from_cctbx(
geometry_restraints_manager = grm)
else:
assert params.restraints == "qm"
### check the total charge and spin
restraints_manager = restraints.from_qm(
pdb_hierarchy = cmdline.pdb_hierarchy.deep_copy(),
calculator = Mopac(label='./ase/ase',charge="0", spin=0,
job_type='1SCF GRADIENTS AUX(0,PRECISION=9)',
RELSCF=None,functional='PM7'))
states = mmtbx.utils.states(
pdb_hierarchy = cmdline.pdb_hierarchy,
xray_structure = cmdline.xray_structure)
states.add(sites_cart = cmdline.xray_structure.sites_cart())
print "params.data_weight:", params.data_weight
print "params.restraints:", params.restraints
#####
geometry_rmsd_manager=restraints.get_grm(
file_name = cmdline.pdb_file_names[0]).restraints_manager
macro_cycle.run(
fmodel = fmodel,
states = states,
pdb_hierarchy = cmdline.pdb_hierarchy,
restraints_manager = restraints_manager,
number_of_macro_cycles = params.number_of_macro_cycles,
file_label = params.restraints,
data_weight = params.data_weight,
file_out_prefix = params.file_out_prefix,
use_convergence_test = params.use_convergence_test,
max_bond_rmsd = params.max_bond_rmsd,
geometry_rmsd_manager = geometry_rmsd_manager)
def get_model_stat(file_name):
grm = restraints.get_grm(file_name = file_name)
r = model_statistics.geometry(
pdb_hierarchy = grm.pdb_hierarchy,
restraints_manager = grm.restraints_manager,
molprobity_scores = True)
# XXX very runtime inefficient
distances = flex.double()
xyz = grm.pdb_hierarchy.atoms().extract_xyz()
bond_proxies_simple = grm.restraints_manager.geometry.pair_proxies(
sites_cart = xyz).bond_proxies.simple
for i, site_i in enumerate(xyz):
for j, site_j in enumerate(xyz):
if(j>i):
bonded = False
for proxy in bond_proxies_simple:
p1 = list(proxy.i_seqs)
p2 = [i,j]
p1.sort()
p2.sort()
if(p1==p2): bonded=True
if(not bonded):
dist_ij = math.sqrt(
(site_i[0]-site_j[0])**2+
(site_i[1]-site_j[1])**2+
(site_i[2]-site_j[2])**2)
distances.append(dist_ij)
min_nonbonded_distance = flex.min(distances)
# bond(rmsd), bond(max), angle(rmsd), angle(max), etc..
#print r.b_mean, r.b_max, r.a_min, r.a_max, r.clashscore, min_nonbonded_distance
return min_nonbonded_distance, r.b_max , r.a_max
