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import datetime
from pathlib import Path
from string import Template
from typing import TYPE_CHECKING, Dict
from shelxfile.version import VERSION
from shelxfile.atoms.atoms import Atoms
if TYPE_CHECKING:
from shelxfile.shelx.shelxfile import Shelxfile
class CifFile():
"""Class for writing IUCr CIF-1.1 of DDL1 compliant Version 2.4.5 files."""
def __init__(self, shelx_file: 'Shelxfile', template: str = None):
if template is not None:
self.template = template
else:
self.template = Path(__file__).parent / "cif_template.tmpl"
self.data = shelx_file
self._cif = None
def __str__(self):
return self._cif
def __repr__(self):
return self._cif
def write_cif(self, cif_path: Path) -> None:
with open(self.template, "r") as f:
template = f.read()
cif = Template(template)
sub = cif.substitute(self._cif_dict())
cif_path.write_text(sub)
def _cif_dict(self) -> Dict[str, str]:
cif_dict = {}
cif_dict["data_name"] = self.data.titl.split()[0].lower() or "unknown"
cif_dict["version"] = VERSION
cif_dict["creation_date"] = f"{datetime.datetime.now().strftime('%Y-%m-%d %H:%M:%S')}"
cif_dict["sum_formula"] = self.data.sum_formula
cif_dict["formula_weight"] = self.data.formula_weight
cif_dict.update(self._cell_data())
cif_dict.update(self._symmetry_data())
cif_dict.update(self._atoms_data())
cif_dict.update(self._adp_data())
cif_dict.update(self._misc_dict())
return cif_dict
def _cell_data(self) -> Dict[str, float]:
cell = self.data.cell
return {
"cell_a" : cell.a,
"cell_b" : cell.b,
"cell_c" : cell.c,
"cell_alpha" : cell.alpha,
"cell_beta" : cell.beta,
"cell_gamma" : cell.gamma,
"cell_volume": round(cell.volume, 4),
"cell_z" : self.data.zerr.Z,
}
def _symmetry_data(self) -> Dict[str, str]:
symmcards_ = [f" '{sym.to_cif()}'" for sym in self.data.symmcards]
return {
"space_group" : self.data.space_group,
# "crystal_system": self.data.symmcards.crystal_system,
"symmetry_loop": '\n'.join(symmcards_),
}
def _atoms_data(self) -> Dict[str, str]:
atoms: Atoms = self.data.atoms
lines = []
loop_header = ("loop_\n"
" _atom_site_label\n"
" _atom_site_type_symbol\n"
" _atom_site_fract_x\n"
" _atom_site_fract_y\n"
" _atom_site_fract_z\n"
" _atom_site_adp_type\n"
" _atom_site_occupancy\n"
" _atom_site_disorder_group")
for atom in atoms.all_atoms:
if not atom.qpeak:
lines.append(f"{atom.fullname_short} {atom.element} "
f"{atom.x} {atom.y} {atom.z} "
f"{'Uiso' if atom.is_isotropic else 'Uani'} "
f"{atom.occupancy} {atom.part.n}")
return {
"atom_loop_header": loop_header,
"atom_loop" : '\n'.join(lines),
}
def _adp_data(self) -> Dict[str, str]:
atoms: Atoms = self.data.atoms
lines = []
loop_header = (
"loop_\n"
" _atom_site_aniso_label\n"
" _atom_site_aniso_U_11\n"
" _atom_site_aniso_U_22\n"
" _atom_site_aniso_U_33\n"
" _atom_site_aniso_U_23\n"
" _atom_site_aniso_U_13\n"
" _atom_site_aniso_U_12")
for atom in atoms.all_atoms:
if not atom.qpeak and not atom.is_isotropic:
lines.append(f"{atom.fullname_short} "
f"{atom.U11} {atom.U22} {atom.U33} "
f"{atom.U23} {atom.U13} {atom.U12} ")
return {
"aniso_loop_header": loop_header,
"aniso_loop" : '\n'.join(lines),
}
def _misc_dict(self) -> Dict[str, str]:
misc_dict = {}
misc_dict["temperature"] = round(self.data.temp_in_kelvin, 3) or '?'
misc_dict["crystal_size_max"] = self.data.size.max or '?'
misc_dict["crystal_size_mid"] = self.data.size.mid or '?'
misc_dict["crystal_size_min"] = self.data.size.min or '?'
misc_dict["wavelength"] = self.data.wavelength or '?'
misc_dict["R1"] = self.data.R1 or '?'
misc_dict["wR2"] = self.data.wr2 or '?'
misc_dict["goodness_of_fit"] = self.data.goof or '?'
return misc_dict
if __name__ == '__main__':
from shelxfile import Shelxfile
shx = Shelxfile(debug=True)
#shx.read_file('tests/resources/I-43d.res')
shx.read_file('./tests/resources/p21c.res')
#cif = CifFile(shx)
#cif.write_cif(Path('p21c-test.cif'))
shx.to_cif('p21c-test.cif')
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