def debug_write_reciprocal_lattice_points_as_pdb(
points, file_name='reciprocal_lattice.pdb'):
from cctbx import crystal, xray
cs = crystal.symmetry(unit_cell=(1000,1000,1000,90,90,90), space_group="P1")
xs = xray.structure(crystal_symmetry=cs)
sel = flex.random_selection(points.size(),
min(20000, points.size()))
rsp = points.select(sel)
for site in rsp:
xs.add_scatterer(xray.scatterer("C", site=site))
xs.sites_mod_short()
with open(file_name, 'wb') as f:
print >> f, xs.as_pdb_file()
def debug_write_reciprocal_lattice_points_as_pdb(
points, file_name="reciprocal_lattice.pdb"
):
from cctbx import crystal, xray
cs = crystal.symmetry(unit_cell=(1000, 1000, 1000, 90, 90, 90), space_group="P1")
xs = xray.structure(crystal_symmetry=cs)
sel = flex.random_selection(points.size(), min(20000, points.size()))
rsp = points.select(sel)
for site in rsp:
xs.add_scatterer(xray.scatterer("C", site=site))
xs.sites_mod_short()
with open(file_name, "wb") as f:
print(xs.as_pdb_file(), file=f)
def select_random_den_restraints(self):
from cctbx.array_family import flex
print("Selecting random DEN pairs...", file=self.log)
random_pairs = {}
for chain in self.ref_atom_pairs.keys():
random_pairs[chain] = []
pair_list_size = len(self.ref_atom_pairs[chain])
num_restraints = round(self.atoms_per_chain_ref[chain] *
self.ndistance_ratio)
if num_restraints > pair_list_size:
num_restraints = pair_list_size
random_selection = \
flex.random_selection(pair_list_size, int(num_restraints))
for i in random_selection:
random_pairs[chain].append(self.ref_atom_pairs[chain][i])
return random_pairs
def select_random_den_restraints(self):
from cctbx.array_family import flex
print >> self.log, "Selecting random DEN pairs..."
random_pairs = {}
for chain in self.ref_atom_pairs.keys():
random_pairs[chain] = []
pair_list_size = len(self.ref_atom_pairs[chain])
num_restraints = round(self.atoms_per_chain_ref[chain] *
self.ndistance_ratio)
if num_restraints > pair_list_size:
num_restraints = pair_list_size
random_selection = \
flex.random_selection(pair_list_size, int(num_restraints))
for i in random_selection:
random_pairs[chain].append(self.ref_atom_pairs[chain][i])
return random_pairs
