def run(args):
assert len(args) > 0
import iotbx.poscar
for file_name in args:
print(file_name)
poscar = iotbx.poscar.reader(lines=open(file_name).read().splitlines(),
source_info=file_name)
poscar.make_up_types_if_necessary()
poscar.xray_structure(u_iso=0.05).show_summary().show_scatterers()
print()
def run(args):
assert len(args) > 0
import iotbx.poscar
for file_name in args:
print file_name
poscar = iotbx.poscar.reader(
lines=open(file_name).read().splitlines(),
source_info=file_name)
poscar.make_up_types_if_necessary()
poscar.xray_structure(u_iso=0.05).show_summary().show_scatterers()
print
def exercise():
import libtbx.load_env
import os
op = os.path
inp_dir = libtbx.env.find_in_repositories(
relative_path="phenix_regression/poscar", test=op.isdir)
if (inp_dir is None):
print("Skipping POSCAR tests: input files not available")
return
import iotbx.poscar
for node in os.listdir(inp_dir):
if (not node.startswith("POSCAR-")): continue
file_name = op.join(inp_dir, node)
poscar = iotbx.poscar.reader(lines=open(file_name).read().splitlines())
assert poscar.make_up_types_if_necessary() is poscar
xs = poscar.xray_structure(u_iso=0.1)
assert str(xs.space_group_info()) == "P 1"
assert xs.scatterers().size() == len(poscar.sites)
def exercise():
import libtbx.load_env
import os
op = os.path
inp_dir = libtbx.env.find_in_repositories(
relative_path="phenix_regression/poscar",
test=op.isdir)
if (inp_dir is None):
print "Skipping POSCAR tests: input files not available"
return
import iotbx.poscar
for node in os.listdir(inp_dir):
if (not node.startswith("POSCAR-")): continue
file_name = op.join(inp_dir, node)
poscar = iotbx.poscar.reader(lines=open(file_name).read().splitlines())
assert poscar.make_up_types_if_necessary() is poscar
xs = poscar.xray_structure(u_iso=0.1)
assert str(xs.space_group_info()) == "P 1"
assert xs.scatterers().size() == len(poscar.sites)
def run(args):
import iotbx.phil
pcl = iotbx.phil.process_command_line(args=args, master_string="""\
symmetry_search {
structure_factor_d_min = 2
.type = float
}
""")
if (len(pcl.remaining_args) != 1):
from libtbx.utils import Usage
import libtbx.load_env
print
pcl.master.show()
print
raise Usage(
"%s pdb_file|poscar_file [parameters]" % libtbx.env.dispatcher_name)
inp_file = pcl.remaining_args[0]
from libtbx.str_utils import show_string
import iotbx.pdb
if (iotbx.pdb.is_pdb_file(inp_file)):
print "PDB file:", show_string(inp_file)
pdb_inp = iotbx.pdb.input(file_name=inp_file)
xs = pdb_inp.xray_structure_simple()
else:
print "POSCAR file:", show_string(inp_file)
import iotbx.poscar
poscar = iotbx.poscar.reader(lines=open(inp_file).read().splitlines())
poscar.make_up_types_if_necessary()
xs = poscar.xray_structure()
print
pcl.work.show()
print
params = pcl.work.extract().symmetry_search
print "Unit cell:", xs.unit_cell()
print
fc_p1 = xs.structure_factors(
d_min=params.structure_factor_d_min).f_calc().expand_to_p1()
from cctbx import symmetry_search
sf_symm = symmetry_search.structure_factor_symmetry(f_in_p1=fc_p1)
print sf_symm
print
print sf_symm.space_group_info
print