def add_r_int_value(cif: CifContainer, rint_p: Paragraph):
reflns_number_total = cif['_reflns_number_total']
reflns_av_R_equivalents = cif['_diffrn_reflns_av_R_equivalents']
reflns_av_unetI = cif['_diffrn_reflns_av_unetI/netI']
rint_p.add_run(this_or_quest(reflns_number_total) + '\n')
rint_p.add_run('R').font.italic = True
rint_p.add_run('int').font.subscript = True
rint_p.add_run(' = ' + this_or_quest(reflns_av_R_equivalents) + '\n')
rint_p.add_run('R').font.italic = True
rint_p.add_run('sigma').font.subscript = True
rint_p.add_run(' = ' + this_or_quest(reflns_av_unetI))
def add_r1sig_and_wr2full(cif, r2sig_p, rfull_p):
ls_R_factor_gt = cif['_refine_ls_R_factor_gt']
ls_wR_factor_gt = cif['_refine_ls_wR_factor_gt']
ls_R_factor_all = cif['_refine_ls_R_factor_all']
ls_wR_factor_ref = cif['_refine_ls_wR_factor_ref']
r2sig_p.add_run('R').font.italic = True
r2sig_p.add_run('1').font.subscript = True
r2sig_p.add_run(' = ' + this_or_quest(ls_R_factor_gt))
r2sig_p.add_run('\nw')
r2sig_p.add_run('R').font.italic = True
r2sig_p.add_run('2').font.subscript = True
r2sig_p.add_run(' = ' + this_or_quest(ls_wR_factor_gt))
rfull_p.add_run('R').font.italic = True
rfull_p.add_run('1').font.subscript = True
rfull_p.add_run(' = ' + this_or_quest(ls_R_factor_all))
rfull_p.add_run('\nw')
rfull_p.add_run('R').font.italic = True
rfull_p.add_run('2').font.subscript = True
rfull_p.add_run(' = ' + ls_wR_factor_ref)
def make_templated_report(self, options: Options, file_obj: Path, output_filename: str, picfile: Path,
template_path: Path):
cif = CifContainer(file_obj)
tpl_doc = DocxTemplate(Path(__file__).parent.parent.joinpath(template_path))
ba = BondsAndAngles(cif, without_h=options.without_h)
t = TorsionAngles(cif, without_h=options.without_h)
h = HydrogenBonds(cif)
context = {'options' : options,
# {'without_h': True, 'atoms_table': True, 'text': True, 'bonds_table': True},
'cif' : cif,
'space_group' : self.space_group_subdoc(tpl_doc, cif),
'structure_figure' : self.make_picture(options, picfile, tpl_doc),
'crystallization_method': remove_line_endings(retranslate_delimiter(
cif['_exptl_crystal_recrystallization_method'])) or '[No crystallization method given!]',
'sum_formula' : self.format_sum_formula(cif['_chemical_formula_sum'].replace(" ", "")),
'itnum' : cif['_space_group_IT_number'],
'crystal_size' : this_or_quest(cif['_exptl_crystal_size_min']) + timessym +
this_or_quest(cif['_exptl_crystal_size_mid']) + timessym +
this_or_quest(cif['_exptl_crystal_size_max']),
'crystal_colour' : this_or_quest(cif['_exptl_crystal_colour']),
'crystal_shape' : this_or_quest(cif['_exptl_crystal_description']),
'radiation' : self.get_radiation(cif),
'wavelength' : cif['_diffrn_radiation_wavelength'],
'theta_range' : self.get_from_to_theta_range(cif),
'diffr_type' : gstr(cif['_diffrn_measurement_device_type'])
or '[No measurement device type given]',
'diffr_device' : gstr(cif['_diffrn_measurement_device'])
or '[No measurement device given]',
'diffr_source' : gstr(cif['_diffrn_source']).strip('\n\r')
or '[No radiation source given]',
'monochromator' : gstr(cif['_diffrn_radiation_monochromator']) \
or '[No monochromator type given]',
'detector' : gstr(cif['_diffrn_detector_type']) \
or '[No detector type given]',
'lowtemp_dev' : gstr(cif['_olex2_diffrn_ambient_temperature_device']) \
or '',
'index_ranges' : self.hkl_index_limits(cif),
'indepentent_refl' : this_or_quest(cif['_reflns_number_total']),
'r_int' : this_or_quest(cif['_diffrn_reflns_av_R_equivalents']),
'r_sigma' : this_or_quest(cif['_diffrn_reflns_av_unetI/netI']),
'completeness' : self.get_completeness(cif),
'theta_full' : cif['_diffrn_reflns_theta_full'],
'data' : this_or_quest(cif['_refine_ls_number_reflns']),
'restraints' : this_or_quest(cif['_refine_ls_number_restraints']),
'parameters' : this_or_quest(cif['_refine_ls_number_parameters']),
'goof' : this_or_quest(cif['_refine_ls_goodness_of_fit_ref']),
'ls_R_factor_gt' : this_or_quest(cif['_refine_ls_R_factor_gt']),
'ls_wR_factor_gt' : this_or_quest(cif['_refine_ls_wR_factor_gt']),
'ls_R_factor_all' : this_or_quest(cif['_refine_ls_R_factor_all']),
'ls_wR_factor_ref' : this_or_quest(cif['_refine_ls_wR_factor_ref']),
'diff_dens_min' : self.get_diff_density_min(cif).replace('-', minus_sign),
'diff_dens_max' : self.get_diff_density_max(cif).replace('-', minus_sign),
'exti' : self.get_exti(cif),
'flack_x' : self.get_flackx(cif),
'integration_progr' : self.get_integration_program(cif),
'abstype' : gstr(cif['_exptl_absorpt_correction_type']) or '??',
'abs_details' : self.get_absortion_correction_program(cif),
'solution_method' : self.solution_method(cif),
'solution_program' : self.solution_program(cif),
'refinement_prog' : self.refinement_prog(cif),
'atomic_coordinates' : self.get_atomic_coordinates(cif),
'bonds' : ba.bonds,
'angles' : ba.angles,
'ba_symminfo' : ba.symminfo,
'torsions' : t.torsion_angles,
'torsion_symminfo' : t.symminfo,
'hydrogen_bonds' : h.hydrogen_bonds,
'hydrogen_symminfo' : h.symminfo,
'literature' : self.literature
}
# Filter definition for {{foobar|filter}} things:
jinja_env = jinja2.Environment()
jinja_env.filters['inv_article'] = get_inf_article
tpl_doc.render(context, jinja_env=jinja_env, autoescape=True)
tpl_doc.save(output_filename)
def test_this_or_quest_zeropzero(self):
self.assertEqual(0.0, this_or_quest(0.0))
def test_this_or_quest_emptystring(self):
self.assertEqual('?', this_or_quest(''))
def test_this_or_quest_stringzero(self):
self.assertEqual('0', this_or_quest('0'))
def test_this_or_quest_None(self):
self.assertEqual('?', this_or_quest(None))
def test_this_or_quest_integer(self):
self.assertEqual(12, this_or_quest(12))
def populate_main_table_values(main_table: Table, cif: CifContainer):
"""
Fills the main table with residuals. Column, by column.
"""
main_table.cell(0, 1).paragraphs[0].add_run(
cif['_database_code_depnum_ccdc_archive'])
# Set text for all usual cif keywords by a lookup table:
add_regular_key_value_pairs(cif, main_table)
# Now the special handling:
formula_paragraph = main_table.cell(1, 1).paragraphs[0]
sum_formula = cif['_chemical_formula_sum'].replace(" ", "")
add_sum_formula(formula_paragraph, sum_formula)
spgr_paragraph = main_table.cell(5, 1).paragraphs[0]
space_group = cif.space_group
try:
it_number = str(cif.spgr_number)
except AttributeError:
it_number = ''
format_space_group(spgr_paragraph, space_group, it_number)
radiation_type = cif['_diffrn_radiation_type']
radiation_wavelength = cif['_diffrn_radiation_wavelength']
crystal_size_min = cif['_exptl_crystal_size_min']
crystal_size_mid = cif['_exptl_crystal_size_mid']
crystal_size_max = cif['_exptl_crystal_size_max']
theta_min = cif['_diffrn_reflns_theta_min']
theta_max = cif['_diffrn_reflns_theta_max']
limit_h_min = cif['_diffrn_reflns_limit_h_min']
limit_h_max = cif['_diffrn_reflns_limit_h_max']
limit_k_min = cif['_diffrn_reflns_limit_k_min']
limit_k_max = cif['_diffrn_reflns_limit_k_max']
limit_l_min = cif['_diffrn_reflns_limit_l_min']
limit_l_max = cif['_diffrn_reflns_limit_l_max']
ls_number_reflns = cif['_refine_ls_number_reflns']
ls_number_restraints = cif['_refine_ls_number_restraints']
ls_number_parameters = cif['_refine_ls_number_parameters']
goof = cif['_refine_ls_goodness_of_fit_ref']
try:
completeness = "{0:.1f} %".format(
round(float(cif['_diffrn_measured_fraction_theta_full']) * 100, 1))
except ValueError:
completeness = '?'
try:
diff_density_min = "{0:.2f}".format(
round(float(cif['_refine_diff_density_min']), 2))
except ValueError:
diff_density_min = '?'
try:
diff_density_max = "{0:.2f}".format(
round(float(cif['_refine_diff_density_max']), 2))
except ValueError:
diff_density_max = '?'
# now prepare & write all the concatenated & derived cell contents:
main_table.cell(17, 1).text = this_or_quest(crystal_size_max) + timessym + \
this_or_quest(crystal_size_mid) + timessym + \
this_or_quest(crystal_size_min)
wavelength = str(' ({} ='.format(lambdasym) +
this_or_quest(radiation_wavelength) +
'{}{})'.format(protected_space, angstrom)).replace(
' ', '')
# radtype: ('Mo', 'K', '\\a')
radtype = format_radiation(radiation_type)
radrun = main_table.cell(20, 1).paragraphs[0]
# radiation type e.g. Mo:
radrun.add_run(radtype[0])
# K line:
radrunita = radrun.add_run(radtype[1])
radrunita.font.italic = True
alpha = radrun.add_run(radtype[2])
alpha.font.italic = True
alpha.font.subscript = True
# wavelength lambda:
radrun.add_run(' ' + wavelength)
try:
d_max = ' ({:.2f}{}{})'.format(
float(radiation_wavelength) / (2 * sin(radians(float(theta_max)))),
protected_space, angstrom)
# 2theta range:
main_table.cell(21, 1).text = "{:.2f} to {:.2f}{}".format(
2 * float(theta_min), 2 * float(theta_max), d_max)
except ValueError:
main_table.cell(21, 1).text = '? to ?'
main_table.cell(22, 1).text = limit_h_min + ' {} h {} '.format(less_or_equal, less_or_equal) + limit_h_max + '\n' \
+ limit_k_min + ' {} k {} '.format(less_or_equal, less_or_equal) + limit_k_max + '\n' \
+ limit_l_min + ' {} l {} '.format(less_or_equal, less_or_equal) + limit_l_max
rint_p = main_table.cell(24, 1).paragraphs[0]
add_r_int_value(cif, rint_p)
main_table.cell(25, 1).paragraphs[0].add_run(completeness)
main_table.cell(26, 1).text = this_or_quest(ls_number_reflns) + '/' \
+ this_or_quest(ls_number_restraints) + '/' \
+ this_or_quest(ls_number_parameters)
main_table.cell(27, 1).paragraphs[0].add_run(goof)
r1sig_p = main_table.cell(28, 1).paragraphs[0]
rfull_p = main_table.cell(29, 1).paragraphs[0]
add_r1sig_and_wr2full(cif, r1sig_p, rfull_p)
main_table.cell(30, 1).text = diff_density_max + '/' + diff_density_min
if not cif.is_centrosymm:
main_table.cell(31,
1).text = cif['_refine_ls_abs_structure_Flack'] or '?'
exti = cif['_refine_ls_extinction_coef']
if exti not in ['.', "'.'", '?', '']:
num = len(main_table.columns[0].cells)
main_table.columns[1].cells[num - 1].text = exti