def run(args):
if (len(args) == 0): args = ["--help"]
command_line = (option_parser(
usage="%s [OPTIONS] FILE..." % libtbx.env.dispatcher_name)
.option(None, "--niggli_cell",
action="store_true")
).process(args=args)
if (len(command_line.args) == 0):
command_line.parser.show_help()
return
co = command_line.options
for arg in command_line.args:
crystal_symmetry = crystal_symmetry_from_any.extract_from(arg)
if (crystal_symmetry is None):
raise RuntimeError, \
"Unknown file format or unit cell and space group missing from file."
if (co.niggli_cell
and crystal_symmetry.unit_cell() is not None
and crystal_symmetry.space_group_info() is not None):
crystal_symmetry = crystal_symmetry.niggli_cell()
format.crystal_symmetry(crystal_symmetry)
print
print "\n".join(
crystal_symmetry_as_cns_inp_defines(crystal_symmetry=crystal_symmetry))
print
print format_cryst1_and_scale_records(
crystal_symmetry=crystal_symmetry,
write_scale_records=True)
print
def run(args):
if (len(args) == 0): args = ["--help"]
command_line = (option_parser(usage="%s [OPTIONS] FILE..." %
libtbx.env.dispatcher_name).option(
None,
"--niggli_cell",
action="store_true")).process(args=args)
if (len(command_line.args) == 0):
command_line.parser.show_help()
return
co = command_line.options
for arg in command_line.args:
crystal_symmetry = crystal_symmetry_from_any.extract_from(arg)
if (crystal_symmetry is None):
raise RuntimeError, \
"Unknown file format or unit cell and space group missing from file."
if (co.niggli_cell and crystal_symmetry.unit_cell() is not None
and crystal_symmetry.space_group_info() is not None):
crystal_symmetry = crystal_symmetry.niggli_cell()
format.crystal_symmetry(crystal_symmetry)
print
print "\n".join(
crystal_symmetry_as_cns_inp_defines(
crystal_symmetry=crystal_symmetry))
print
print format_cryst1_and_scale_records(
crystal_symmetry=crystal_symmetry, write_scale_records=True)
print
def SaveSites (self, file_name) :
if (self._atoms is None) or (len(self._atoms) == 0) :
raise Sorry("No atoms loaded!")
from scitbx.array_family import flex
selection = flex.bool(self._atoms.size(), False)
assert (len(selection) == self.GetItemCount())
for item in range(self.GetItemCount()) :
if (self.IsChecked(item)) :
selection[item] = True
atoms_selected = self._atoms.select(selection)
if (len(atoms_selected) == 0) :
raise Sorry("No atoms selected!")
f = open(file_name, "w")
if (self._symm is not None) :
from iotbx.pdb import format_cryst1_and_scale_records
f.write(format_cryst1_and_scale_records(self._symm) + "\n")
for atom in atoms_selected :
f.write(atom.format_atom_record() + "\n")
f.close()
wx.MessageBox(("%d atoms saved to %s.") % (len(atoms_selected), file_name))
