def check_if_loop_and_row_size_fit_together(self, gemmi_loop, row):
if gemmi_loop.width() == len(row):
gemmi_loop.add_row(row)
else:
show_general_warning(
'An author loop with different size is already in the CIF. Can not proceed.'
)
def import_equipment_from_file(self, filename='') -> None:
"""
Import an equipment entry from a cif file.
"""
if not filename:
filename = cif_file_open_dialog(
filter="CIF file (*.cif *.cif_od *.cfx)")
if not filename:
print('No file given')
return
try:
doc = cif.read_file(filename)
except RuntimeError as e:
show_general_warning(str(e))
return
block = doc.sole_block()
table_data = []
for item in block:
if item.pair is not None:
key, value = item.pair
if filename.endswith(
'.cif_od') and key not in include_equipment_imports:
continue
table_data.append([
key,
retranslate_delimiter(
cif.as_string(value).strip('\n\r ;'))
])
if filename.endswith('.cif_od'):
name = Path(filename).stem
else:
name = block.name.replace('__', ' ')
self.settings.save_settings_list('equipment', name, table_data)
self.show_equipment()
def export_equipment_template(self, filename: str = None) -> None:
"""
Exports the currently selected equipment entry to a file.
In order to export, we have to run self.edit_equipment_template() first!
"""
selected_template, table_data = self.get_equipment_entry_data()
if not selected_template:
return
blockname = '__'.join(selected_template.split())
if not filename:
filename = cif_file_save_dialog(
blockname.replace('__', '_') + '.cif')
if not filename.strip():
return
equipment_cif = CifContainer(filename, new_block=blockname)
for key, value in table_data:
equipment_cif[key] = value.strip('\n\r ')
try:
equipment_cif.save(filename)
# Path(filename).write_text(doc.as_string(cif.Style.Indent35))
except PermissionError:
if Path(filename).is_dir():
return
show_general_warning('No permission to write file to {}'.format(
Path(filename).resolve()))
def _set_external_hkl_file(self) -> None:
file = cif_file_open_dialog(filter="HKL file (*.hkl *.fcf)")
if file.endswith('.hkl'):
if self.cif.res_file_data:
hklf = self.cif.hklf_number_from_shelxl_file()
else:
hklf = 4
self.hkl_file = io.StringIO(
HKL(file, self.cif.block.name, hklf_type=hklf).hkl_as_cif)
self.hkl_file.name = Path(file).name
elif file.endswith('.fcf'):
cif = CifContainer(file)
list_code = cif['_shelx_refln_list_code']
if list_code != '4':
show_general_warning(
'Only plain hkl or fcf (LIST 4 style) files should be uploaded.'
)
return
self.hkl_file = io.StringIO(Path(file).read_text())
self.hkl_file.name = Path(file).name
elif file == '':
self.hkl_file = None
else:
show_general_warning(
'Only plain hkl or fcf (LIST 4 style) files should be uploaded.'
)
def import_author(self, filename=''):
"""
Import an author from a cif file.
"""
cif_auth_to_str = {
'_publ_contact_author_name': 'name',
'_publ_contact_author_address': 'address',
'_publ_contact_author_email': 'email',
'_publ_contact_author_phone': 'phone',
'_publ_contact_author_id_orcid': 'orcid',
#
'_publ_author_name': 'name',
'_publ_author_address': 'address',
'_publ_author_email': 'email',
'_publ_author_phone': 'phone',
'_publ_author_id_orcid': 'orcid',
'_publ_author_footnote': 'footnote',
}
if not filename:
filename = cif_file_open_dialog(filter="CIF file (*.cif)")
if not filename:
return
try:
doc = read_file(filename)
except RuntimeError as e:
show_general_warning(str(e))
return
block = doc.sole_block()
table_data = {}
for item in block:
if item.pair is not None:
key, value = item.pair
if key not in cif_auth_to_str:
continue
key = cif_auth_to_str.get(key)
table_data.update({
key:
retranslate_delimiter(as_string(value).strip('\n\r ;'))
})
name = block.name.replace('__', ' ')
if 'contact author' in name:
table_data.update({'contact': True})
if not table_data.get('name'):
return None
self.general_author_save(table_data)
self.show_author_loops()
def import_property_from_file(self, filename: str = '') -> None:
"""
Imports a cif file as entry of the property templates list.
"""
if not filename:
filename = cif_file_open_dialog(filter="CIF file (*.cif)")
if not filename:
return
try:
doc = cif.read_file(filename)
except RuntimeError as e:
show_general_warning(str(e))
return
property_list = self.settings.settings.value('property_list')
if not property_list:
property_list = ['']
block = doc.sole_block()
template_list = []
loop_column_name = ''
for i in block:
if i.loop is not None:
if len(i.loop.tags) > 0:
loop_column_name = i.loop.tags[0]
for n in range(i.loop.length()):
value = i.loop.val(n, 0)
template_list.append(
retranslate_delimiter(
cif.as_string(value).strip("\n\r ;")))
block_name = block.name.replace('__', ' ')
# This is the list shown in the Main menu:
property_list.append(block_name)
table = self.app.ui.PropertiesEditTableWidget
table.setRowCount(0)
self.app.ui.cifKeywordLineEdit.setText(loop_column_name)
newlist = [x for x in list(set(property_list)) if x]
newlist.sort()
# this list keeps track of the property items:
self.settings.save_template_list('property_list', newlist)
template_list.insert(0, '')
template_list = list(set(template_list))
# save as dictionary for properties to have "_cif_key : itemlist"
# for a table item as dropdown menu in the main table.
table_data = [loop_column_name, template_list]
self.settings.save_template_list('property/' + block_name, table_data)
self.show_properties()
def export_property_template(self, filename: str = '') -> None:
"""
Exports the currently selected property entry to a file.
"""
selected_row_text = self.app.ui.PropertiesTemplatesListWidget.currentIndex(
).data()
if not selected_row_text:
return
prop_data = self.settings.load_settings_list('property',
selected_row_text)
table_data = []
cif_key = ''
if prop_data:
cif_key = prop_data[0]
with suppress(Exception):
table_data = prop_data[1]
if not cif_key:
return
doc = cif.Document()
blockname = '__'.join(selected_row_text.split())
block = doc.add_new_block(blockname)
try:
loop = block.init_loop(cif_key, [''])
except RuntimeError:
# Not a valid loop key
show_general_warning(
'"{}" is not a valid cif keyword.'.format(cif_key))
return
for value in table_data:
if value:
loop.add_row([cif.quote(utf8_to_str(value))])
if not filename:
filename = cif_file_save_dialog(
blockname.replace('__', '_') + '.cif')
if not filename.strip():
return
try:
doc.write_file(filename, style=cif.Style.Indent35)
# Path(filename).write_text(doc.as_string(cif.Style.Indent35))
except PermissionError:
if Path(filename).is_dir():
return
show_general_warning('No permission to write file to {}'.format(
Path(filename).resolve()))
def save_equipment_template(self) -> None:
"""
Saves the currently selected equipment template to the config file.
"""
selected_template_text, table_data = self.get_equipment_entry_data()
# warn if key is not official:
for key, _ in table_data:
if key not in cif_all_dict:
if not key.startswith('_'):
show_general_warning(
'"{}" is not a valid keyword! '
'\nChange the name in order to save.\n'
'Keys must start with an underscore.'.format(key))
return
show_general_warning(
'"{}" is not an official CIF keyword!'.format(key))
self.settings.save_settings_list('equipment', selected_template_text,
table_data)
self.app.ui.EquipmentTemplatesStackedWidget.setCurrentIndex(0)
print('saved')
def export_author_template(self, filename: str = None) -> None:
"""
Exports the currently selected author to a file.
"""
author = self.get_author_info()
selected_template = self.ui.LoopTemplatesListWidget.currentIndex(
).data()
if not selected_template:
return
blockname = '__'.join(selected_template.split())
if not filename:
filename = cif_file_save_dialog(
blockname.replace('__', '_') + '.cif')
if not filename.strip():
return
author_cif = CifContainer(filename, new_block=blockname)
contact_author: bool = author.get('contact')
loop = self.get_author_loop(contact_author)
data = [
author.get('name'),
author.get('address'),
author.get('email'),
author.get('phone'),
author.get('orcid'),
author.get('footnote')
]
if contact_author:
del data[-1]
for key, value in zip(loop, data):
author_cif.set_pair_delimited(key, as_string(value))
try:
author_cif.save(filename)
except PermissionError:
if Path(filename).is_dir():
return
show_general_warning('No permission to write file to {}'.format(
Path(filename).resolve()))
def __init__(self, app, cif: CifContainer):
super(BrukerData, self).__init__()
self.cif = cif
self.app = app
self.basename = cif.fileobj.stem.split('_0m')[0]
self.saint_data = SaintListFile(name_patt='*_0*m._ls')
# This is only in this list file, not in the global:
saint_first_ls = SaintListFile(name_patt='*_01._ls')
sol = SolutionProgram(cif)
solution_program = None
if 'shelx' in self.cif.block.find_value('_audit_creation_method').lower():
shelx = 'Sheldrick, G.M. (2015). Acta Cryst. A71, 3-8.\nSheldrick, G.M. (2015). Acta Cryst. C71, 3-8.\n'
else:
shelx = ''
if cif.res_file_data:
if cif.dsr_used:
dsr = 'The program DSR was used for model building:\n' \
'D. Kratzert, I. Krossing, J. Appl. Cryst. 2018, 51, 928-934. doi: 10.1107/S1600576718004508'
shelx += dsr
abstype = '?'
t_min = '?'
t_max = '?'
# Going back from last dataset:
for n in range(1, len(self.sadabs.datasets) + 1):
try:
abstype = 'numerical' if self.sadabs.dataset(-n).numerical else 'multi-scan'
t_min = min(self.sadabs.dataset(-n).transmission)
t_max = max(self.sadabs.dataset(-n).transmission)
if all([abstype, t_min, t_max]):
break
except (KeyError, AttributeError, TypeError):
pass
# print('No .abs file found.')
# no abs file found
# the lower temp is more likely:
try:
temp1 = self.frame_header.temperature
except (AttributeError, KeyError, FileNotFoundError):
temp1 = 293
try:
kilovolt = self.frame_header.kilovolts
except (AttributeError, KeyError, FileNotFoundError):
kilovolt = ''
try:
milliamps = self.frame_header.milliamps
except (AttributeError, KeyError, FileNotFoundError):
milliamps = ''
try:
frame_name = self.frame_header.filename.name
except FileNotFoundError:
frame_name = ''
if self.cif.solution_program_details:
solution_program = (self.cif.solution_program_details, self.cif.fileobj.name)
if self.cif['_computing_structure_solution']:
solution_program = (gcif.as_string(self.cif['_computing_structure_solution']), self.cif.fileobj.name)
if not solution_program:
solution_program = (sol.program.version, Path(sol.program.filename).name)
if self.cif.absorpt_process_details:
absdetails = (self.cif.absorpt_process_details, self.cif.fileobj.name)
else:
absdetails = (self.sadabs.version, self.sadabs.filename.name)
if self.cif.absorpt_correction_type:
abscorrtype = (self.cif.absorpt_correction_type, self.cif.fileobj.name)
else:
abscorrtype = (abstype, self.sadabs.filename.name)
if self.cif.absorpt_correction_t_max:
abs_tmax = (self.cif.absorpt_correction_t_max, self.cif.fileobj.name)
else:
abs_tmax = (str(t_max), self.sadabs.filename.name)
if self.cif.absorpt_correction_t_min:
abs_tmin = (self.cif.absorpt_correction_t_min, self.cif.fileobj.name)
else:
abs_tmin = (str(t_min), self.sadabs.filename.name)
if self.sadabs.Rint:
rint = (self.sadabs.Rint, self.sadabs.filename.name)
self.sources['_diffrn_reflns_av_R_equivalents'] = rint
temp2 = self.p4p.temperature
temperature = round(min([temp1, temp2]), 1)
if temperature < 0.01:
temperature = ''
if (self.cif['_diffrn_ambient_temperature'].split('(')[0] or
self.cif['_cell_measurement_temperature']).split('(')[0] == '0':
show_general_warning('<b>Warning of impossible temperature specification</b>:<br>'
'You probably entered −273.15 °C instead '
'of −173.15 °C into the SHELX instruction file.<br>'
'A temperature of 0 K is likely to be wrong.')
try:
if abs(int(self.cif['_diffrn_ambient_temperature'].split('(')[0]) - int(temperature)) >= 2 and \
not self.app.temperature_warning_displayed:
self.app.temperature_warning_displayed = True
show_general_warning('<b>Warning</b>: The temperature from the measurement and '
'from SHELX differ. Please double-check for correctness.<br><br>'
'SHELX says: {} K<br>'
'The P4P file says: {} K<br>'
'Frame header says: {} K<br><br>'
'You may add a '
'<a href="http://shelx.uni-goettingen.de/shelxl_html.php#TEMP">TEMP</a> '
'instruction to your SHELX file (in °C).'
.format(self.cif['_diffrn_ambient_temperature'].split('(')[0],
round(temp2, 1),
round(temp1, 1)))
except ValueError:
# most probably one value is '?'
pass
if not self.cif['_space_group_name_H-M_alt']:
try:
self.sources['_space_group_name_H-M_alt'] = (
self.cif.space_group, 'Calculated by gemmi: https://gemmi.readthedocs.io')
except AttributeError:
pass
if not self.cif['_space_group_name_Hall']:
with suppress(AttributeError):
self.sources['_space_group_name_Hall'] = (
self.cif.hall_symbol, 'Calculated by gemmi: https://gemmi.readthedocs.io')
if not self.cif['_space_group_IT_number']:
with suppress(AttributeError):
self.sources['_space_group_IT_number'] = (
self.cif.spgr_number_from_symmops, 'Calculated by gemmi: https://gemmi.readthedocs.io')
if not self.cif['_space_group_crystal_system']:
with suppress(AttributeError):
csystem = self.cif.crystal_system
self.sources['_space_group_crystal_system'] = (
csystem, 'calculated by gemmi: https://gemmi.readthedocs.io')
if not self.cif.symmops and self.cif.symmops_from_spgr:
loop = self.cif.block.init_loop('_space_group_symop_operation_', ['xyz'])
for symmop in reversed(self.cif.symmops_from_spgr):
loop.add_row([gcif.quote(symmop)])
# All sources that are not filled with data will be yellow in the main table
# data tooltip
self.sources['_cell_measurement_reflns_used'] = (
self.saint_data.cell_reflections, self.saint_data.filename.name)
self.sources['_cell_measurement_theta_min'] = (
self.saint_data.cell_res_min_theta or '', self.saint_data.filename.name)
self.sources['_cell_measurement_theta_max'] = (
self.saint_data.cell_res_max_theta or '', self.saint_data.filename.name)
self.sources['_computing_data_collection'] = (saint_first_ls.aquire_software, saint_first_ls.filename.name)
self.sources['_computing_cell_refinement'] = (self.saint_data.version, self.saint_data.filename.name)
self.sources['_computing_data_reduction'] = (self.saint_data.version, self.saint_data.filename.name)
self.sources['_exptl_absorpt_correction_type'] = abscorrtype
self.sources['_exptl_absorpt_correction_T_min'] = abs_tmin
self.sources['_exptl_absorpt_correction_T_max'] = abs_tmax
self.sources['_exptl_absorpt_process_details'] = absdetails
self.sources['_cell_measurement_temperature'] = (temperature, self.p4p.filename.name)
self.sources['_diffrn_ambient_temperature'] = (temperature, self.p4p.filename.name)
self.sources['_exptl_crystal_colour'] = (self.p4p.crystal_color, self.p4p.filename.name)
self.sources['_exptl_crystal_description'] = (self.p4p.morphology, self.p4p.filename.name)
self.sources['_exptl_crystal_size_min'] = (self.p4p.crystal_size[0] or '', self.p4p.filename.name)
self.sources['_exptl_crystal_size_mid'] = (self.p4p.crystal_size[1] or '', self.p4p.filename.name)
self.sources['_exptl_crystal_size_max'] = (self.p4p.crystal_size[2] or '', self.p4p.filename.name)
self.sources['_computing_structure_solution'] = solution_program
self.sources['_atom_sites_solution_primary'] = (sol.method, 'Inherited from solution program.')
self.sources['_diffrn_source_voltage'] = (kilovolt or '', frame_name)
self.sources['_diffrn_source_current'] = (milliamps or '', frame_name)
self.sources['_chemical_formula_moiety'] = ('', '')
self.sources['_publ_section_references'] = (shelx, '')
self.sources['_refine_special_details'] = ('', '')
self.sources['_exptl_crystal_recrystallization_method'] = ('', '')
if not self.cif.is_centrosymm:
self.sources['_chemical_absolute_configuration'] = ('', '')
if self.saint_data.is_twin and self.saint_data.components_firstsample == 2:
with suppress(Exception):
law = self.saint_data.twinlaw[list(self.saint_data.twinlaw.keys())[0]]
self.sources['_twin_individual_twin_matrix_11'] = (str(law[0][1]), self.saint_data.filename.name)
self.sources['_twin_individual_twin_matrix_12'] = (str(law[0][2]), self.saint_data.filename.name)
self.sources['_twin_individual_twin_matrix_13'] = (str(law[0][0]), self.saint_data.filename.name)
self.sources['_twin_individual_twin_matrix_21'] = (str(law[1][1]), self.saint_data.filename.name)
self.sources['_twin_individual_twin_matrix_22'] = (str(law[1][2]), self.saint_data.filename.name)
self.sources['_twin_individual_twin_matrix_23'] = (str(law[1][0]), self.saint_data.filename.name)
self.sources['_twin_individual_twin_matrix_31'] = (str(law[2][1]), self.saint_data.filename.name)
self.sources['_twin_individual_twin_matrix_32'] = (str(law[2][2]), self.saint_data.filename.name)
self.sources['_twin_individual_twin_matrix_33'] = (str(law[2][0]), self.saint_data.filename.name)
self.sources['_twin_individual_id'] = (
str(self.saint_data.components_firstsample), self.saint_data.filename.name)
self.sources['_twin_special_details'] = (
'The data was integrated as a 2-component twin.', self.saint_data.filename.name)
