finalcif 153__tar.gz → 154__tar.gz

{finalcif-153 → finalcif-154}/.gitignore

@@ -226,3 +226,4 @@ tests/examples/report_multi-finalcif.docx
 tests/examples/work/cu_BruecknerJK_153F40_0m.lxt
 finalcif_keys_order.cif
 !/.python-version
+/platon/*.mod

{finalcif-153 → finalcif-154}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 153
+Version: 154
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues

finalcif-154/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 154

{finalcif-153 → finalcif-154}/finalcif/appwindow.py

@@ -127,6 +127,25 @@ class AppWindow(QMainWindow):
         if file:
             self.load_cif_file(file)
         self.load_recent_cifs_list()
+        self.ui.CheckcifPlaintextEdit.insertPlainText(
+            "\n"
+            "  Offline CheckCIF uses PLATON from Anthony L. Spek, Utrecht University, The Netherlands."
+            "\n"
+            "  https://platonsoft.nl\n"
+            "  \n"
+            "  Please cite PLATON in your publication if you use it.\n"
+            "  \n"
+            "  - PLATON References : \n"
+            "            Spek, A.L. (2003). J. Appl. Cryst. 36, 7-13.\n"
+            "            Spek, A.L. (2009). Acta Cryst. D65, 148-155.\n"
+            "            Spek, A.L. (2015). Acta Cryst. C71, 9-18.\n"
+            "            Spek, A.L. (2018). Inorg. Chim. Acta, 470, 232-237.\n"
+            "            Spek, A.L. (2020). Acta Cryst. E76, 1-11.\n"
+            "  \n"
+            "  \n"
+            "  - Recent versions of PLATON may be obtained from: https://platonsoft.nl/xraysoft\n"
+            "  "
+        )
         self.set_checkcif_output_font(self.ui.CheckcifPlaintextEdit)
         # To make file drag&drop working:
         self.setAcceptDrops(True)
@@ -1073,6 +1092,7 @@ class AppWindow(QMainWindow):
         runner.finished.connect(lambda: self.ui.CheckcifButton.setEnabled(True))
         runner.run_process()
         runner.formula.connect(self.add_moiety_furmula)
+        return None
 
     def add_moiety_furmula(self, formula_moiety):
         moiety = self.ui.cif_main_table.getTextFromKey(key='_chemical_formula_moiety', col=Column.CIF)

{finalcif-153 → finalcif-154}/finalcif/cif/atoms.py

@@ -816,7 +816,7 @@ def get_atomlabel(input_atom: str) -> str:
         else:
             # print('*** {} is not a valid atom!! ***'.format(atom))
             raise KeyError
-    except(IndexError):
+    except IndexError:
         # print('*** {} is not a valid atom! ***'.format(atom))
         raise KeyError
 
@@ -826,6 +826,6 @@ if __name__ == '__main__':
 
     failed, attempted = doctest.testmod()  # verbose=True)
     if failed == 0:
-        print('passed all {} tests!'.format(attempted))
+        print(f'passed all {attempted} tests!')
     else:
-        print('{} of {} tests failed'.format(failed, attempted))
+        print(f'{failed} of {attempted} tests failed')

{finalcif-153 → finalcif-154}/finalcif/cif/cif_file_io.py

@@ -5,6 +5,7 @@
 #  and you think this stuff is worth it, you can buy me a beer in return.
 #  Dr. Daniel Kratzert
 #  ----------------------------------------------------------------------------
+import os
 import re
 from collections import namedtuple
 from collections.abc import Generator
@@ -13,6 +14,8 @@ from pathlib import Path
 
 import gemmi
 
+from finalcif.cif import atoms
+
 if hasattr(gemmi, 'set_leak_warnings'):
     gemmi.set_leak_warnings(False)
 
@@ -24,8 +27,7 @@ from finalcif.cif.cif_order import order, special_keys, essential_keys, non_cent
 from finalcif.cif.hkl import HKL, Limit
 from finalcif.cif.text import utf8_to_str, quote, retranslate_delimiter
 from finalcif.datafiles.utils import DSRFind
-from finalcif.tools.misc import isnumeric, grouper, strip_finalcif_of_name, \
-    _angstrom_to_x
+from finalcif.tools.misc import isnumeric, grouper, strip_finalcif_of_name, _angstrom_to_x
 
 
 class GemmiError(Exception):
@@ -45,6 +47,7 @@ class CifContainer:
             new_block: Create a new block (new file) if a name is given. Otherwise, just
                        the existing document is opened.
         """
+        self.chars_ok = True
         self.picometer: bool = False
         self._abs_hkl_details: dict[str, str] = {}
         if isinstance(file, str):
@@ -72,6 +75,7 @@ class CifContainer:
         self._on_load()
         self.order = []
         self.essential_keys = []
+        # May be overwritten later:
         self.set_order_keys(order)
         self.set_essential_keys(essential_keys)
 
@@ -123,7 +127,7 @@ class CifContainer:
         for num, line in enumerate(filepath.read_bytes().splitlines(keepends=True)):
             try:
                 line.decode('ascii')
-            except(UnicodeDecodeError):
+            except UnicodeDecodeError:
                 line_numbers.append(num)
         return line_numbers
 
@@ -155,9 +159,8 @@ class CifContainer:
         self.dsr_used = DSRFind(self.res_file_data).dsr_used
         self.atomic_struct: gemmi.SmallStructure = gemmi.make_small_structure_from_block(self.block)
         # A dictionary to convert Atom names like 'C1_2' or 'Ga3' into Element names like 'C' or 'Ga'
-        self._name2elements = dict(
-            zip([x.upper() for x in self.block.find_loop('_atom_site_label')],
-                [x.upper() for x in self.block.find_loop('_atom_site_type_symbol')], strict=True))
+        self._name2elements = dict(zip([x.upper() for x in self.block.find_loop('_atom_site_label')],
+                                       [y.upper() for y in self.block.find_loop('_atom_site_type_symbol')], strict=False))
         self.check_hkl_min_max()
 
     @property
@@ -211,8 +214,8 @@ class CifContainer:
         return doc
 
     def cif_as_string(self, without_hkl=False) -> str:
-        opt = gemmi.cif.WriteOptions(gemmi.cif.Style.Indent35)
-
+        opt = gemmi.cif.WriteOptions()
+        opt.align_pairs = 33
         if without_hkl:
             # return a copy, do not delete hkl from original:
             doc = gemmi.cif.Document()
@@ -257,7 +260,6 @@ class CifContainer:
                 f", {self.nangles()} angles")
 
     def file_is_there_and_writable(self) -> bool:
-        import os
         return self.fileobj.exists() and self.fileobj.is_file() and os.access(self.fileobj, os.W_OK)
 
     def set_pair_delimited(self, key: str, txt: str):
@@ -278,13 +280,13 @@ class CifContainer:
 
     def save(self, filename: Path | None = None) -> None:
         """
-        Saves the current cif file.
-        :param filename:  Name to save cif file to.
+        Saves the current cif file. It uses the '[basename]-finalcif.cif' suffix by default.
+        :param filename:  Name to save cif file to if the default is not sufficient.
         """
         if not filename:
             filename = self.finalcif_file
         if self.is_empty():
-            print(f'File {filename} is empty.')
+            print(f'DBG> CIF file {filename} is empty.')
             return
         if not self.is_writable(filename):
             raise PermissionError(f'Failed to open {filename.resolve()} for writing: Operation not permitted')
@@ -714,18 +716,18 @@ class CifContainer:
         Atoms from the CIF where values are returned as string like in the CIF with esds.
         """
         labels = self.block.find_loop('_atom_site_label')
-        types = self.block.find_loop('_atom_site_type_symbol')
+        types = self.block.find_loop('_atom_site_type_symbol') or [atoms.get_atomlabel(x) for x in labels]
         x = self.block.find_loop('_atom_site_fract_x')
         y = self.block.find_loop('_atom_site_fract_y')
         z = self.block.find_loop('_atom_site_fract_z')
         part = self.block.find_loop('_atom_site_disorder_group') or ('0',) * len(labels)
         occ = self.block.find_loop('_atom_site_occupancy') or ('1.000000',) * len(labels)
-        u_eq = self.block.find_loop('_atom_site_U_iso_or_equiv')
+        u_eq = self.block.find_loop('_atom_site_U_iso_or_equiv') or ('.',) * len(labels)
         atom = namedtuple('atom', ('label', 'type', 'x', 'y', 'z', 'part', 'occ', 'u_eq'))
         for label, type, x, y, z, part, occ, u_eq in zip(labels, types, x, y, z,
                                                          part,
                                                          occ,
-                                                         u_eq, strict=True):
+                                                         u_eq, strict=False):
             if without_h and self.ishydrogen(label):
                 continue
             if self.picometer:
@@ -761,7 +763,7 @@ class CifContainer:
         u13 = self.block.find_loop('_atom_site_aniso_U_13')
         u12 = self.block.find_loop('_atom_site_aniso_U_12')
         adp = namedtuple('adp', ('label', 'U11', 'U22', 'U33', 'U23', 'U13', 'U12'))
-        for label, u11, u22, u33, u23, u13, u12 in zip(labels, u11, u22, u33, u23, u13, u12):
+        for label, u11, u22, u33, u23, u13, u12 in zip(labels, u11, u22, u33, u23, u13, u12, strict=True):
             if self.picometer:
                 u11 = _angstrom_to_x(u11, factor=100 ** 2)
                 u22 = _angstrom_to_x(u22, factor=100 ** 2)
@@ -817,7 +819,7 @@ class CifContainer:
         symm = self.block.find_loop('_geom_bond_site_symmetry_2')
         publ_loop = self.block.find_loop('_geom_bond_publ_flag') or len(label1) * ['?']
         bond = namedtuple('bond', ('label1', 'label2', 'dist', 'symm'))
-        for label1, label2, dist, symm, publ in zip(label1, label2, dist, symm, publ_loop):
+        for label1, label2, dist, symm, publ in zip(label1, label2, dist, symm, publ_loop, strict=False):
             if (without_h and (self.ishydrogen(label1) or self.ishydrogen(label2))) or self.yes_not_set(publ):
                 continue
             else:
@@ -855,17 +857,20 @@ class CifContainer:
         symm2 = self.block.find_loop('_geom_angle_site_symmetry_3')
         publ_loop = self.block.find_loop('_geom_angle_publ_flag') or len(label1) * ['?']
         angle = namedtuple('angle', ('label1', 'label2', 'label3', 'angle_val', 'symm1', 'symm2'))
-        for label1, label2, label3, angle_val, symm1, symm2, publ in \
-            zip(label1, label2, label3, angle_val, symm1, symm2, publ_loop, strict=True):
-            if ((without_H and (self.ishydrogen(label1) or self.ishydrogen(label2) or
-                                self.ishydrogen(label3))) or (self.yes_not_set(publ))):
+        for label1, label2, label3, angle_val, symm1, symm2, publ in (
+                zip(label1, label2, label3, angle_val, symm1, symm2, publ_loop, strict=False)):
+            if ((without_H and (self.ishydrogen(label1) or self.ishydrogen(label2) or self.ishydrogen(label3))) or
+                    self.yes_not_set(publ)):
                 continue
             else:
                 yield angle(label1=label1, label2=label2, label3=label3, angle_val=angle_val,
                             symm1=self.checksymm(symm1), symm2=self.checksymm(symm2))
 
     def _iselement(self, name: str) -> str:
-        return self._name2elements[name.upper()]
+        try:
+            return self._name2elements[name.upper()]
+        except KeyError:
+            return atoms.get_atomlabel(name)
 
     def natoms(self, without_h: bool = False) -> int:
         return len(tuple(self.atoms(without_h)))
@@ -902,12 +907,11 @@ class CifContainer:
         tors = namedtuple('Torsion',
                           ('label1', 'label2', 'label3', 'label4', 'torsang', 'symm1', 'symm2', 'symm3', 'symm4'))
         for label1, label2, label3, label4, torsang, symm1, symm2, symm3, symm4, publ in zip(label1, label2, label3,
-                                                                                             # noqa: B020
                                                                                              label4,
                                                                                              torsang, symm1, symm2,
                                                                                              symm3,
                                                                                              symm4, publ_loop,
-                                                                                             strict=True):
+                                                                                             strict=False):
             if ((without_h and (self.ishydrogen(label1) or self.ishydrogen(label2)
                                 or self.ishydrogen(label3) or self.ishydrogen(label3))) or self.yes_not_set(publ)):
                 continue
@@ -930,7 +934,7 @@ class CifContainer:
         hydr = namedtuple('HydrogenBond', ('label_d', 'label_h', 'label_a', 'dist_dh', 'dist_ha', 'dist_da',
                                            'angle_dha', 'symm'))
         for label_d, label_h, label_a, dist_dh, dist_ha, dist_da, angle_dha, symm, publ in (
-            zip(label_d, label_h, label_a, dist_dh, dist_ha, dist_da, angle_dha, symm, publ_loop)):
+                zip(label_d, label_h, label_a, dist_dh, dist_ha, dist_da, angle_dha, symm, publ_loop, strict=False)):
             if self.yes_not_set(publ):
                 continue
             if self.picometer:
@@ -947,7 +951,12 @@ class CifContainer:
         Returns the key/value pairs of a cif file sorted by priority.
         """
         keys_without_values, keys_with_values = self.keys_with_essentials()
-        return keys_without_values + [('These below are already in:', '---------------------')] + keys_with_values
+        return [*keys_without_values, ('These below are already in:', '---------------------'), *keys_with_values]
+
+    def pairs(self):
+        for item in self.block:
+            if item.pair is not None:
+                yield item.pair
 
     def _is_centrokey(self, key) -> bool:
         """
@@ -973,7 +982,7 @@ class CifContainer:
                 #    continue
                 if self._is_centrokey(key):
                     continue
-                if not value or value == '?' or value == "'?'":
+                if not value or value in {'?', "'?'"}:
                     questions.append((key, value))
                 else:
                     with_values.append((key, value))

{finalcif-153 → finalcif-154}/finalcif/equip_property/author_loop_templates.py

@@ -171,34 +171,24 @@ class AuthorLoops:
     def save_author_to_loop(self) -> None:
         author = self.get_author_info()
         row = [author.name, author.address, author.email, author.phone, author.orcid, author.iucr_id, author.footnote]
-        if author.contact_author:
-            author_type = f'_{author.author_type}_contact_author_name'
-            del row[-1]  # contact author has no footnote
-        else:
-            author_type = f'_{author.author_type}_author_name'
-        if self.cif.block.find_loop(author_type):
-            gemmi_loop: Loop = self.cif.block.find_loop(author_type).get_loop()
-            if tuple(row) in list(grouper(gemmi_loop.values, len(row))):
-                self.app.status_bar.show_message('This author already exists.', 10)
+        author_loop_tags = self.get_author_loop(author)
+        table: gemmi.cif.Table = self.cif.block.find(author_loop_tags)
+        if table.width():
+            gemmi_loop: Loop = table.loop
+            if tuple(row) in list(grouper(gemmi_loop.values, gemmi_loop.width())):
+                self.app.status_bar.show_message('This author already exists.', 15)
                 print('dbg> Author already exists.')
                 return
         else:
-            author_loop = self.get_author_loop(author)
-            gemmi_loop = self.cif.init_loop(author_loop)
-        self.check_if_loop_and_row_size_fit_together(gemmi_loop, row)
+            gemmi_loop = self.cif.init_loop(author_loop_tags)
+        table = self.cif.block.find(author_loop_tags)
+        if gemmi_loop.width() < len(row):
+            row = row[:gemmi_loop.width()]
+        if row not in table:
+            table.append_row(row)
         self.app.make_loops_tables()
         self.show_authors_list()
 
-    def check_if_loop_and_row_size_fit_together(self, gemmi_loop: gemmi.cif.Loop, row: list[str]) -> None:
-        if gemmi_loop.width() < len(row):
-            cut_row = row[:gemmi_loop.width()]
-            if cut_row not in gemmi_loop.values:
-                gemmi_loop.add_row(cut_row)
-        elif gemmi_loop.width() > len(row):
-            show_general_warning(self, 'An author loop with larger size is already in the CIF. Can not proceed.')
-        elif row not in gemmi_loop.values:
-            gemmi_loop.add_row(row)
-
     def get_author_info(self) -> Author:
         if self.ui.authorEditTabWidget.currentWidget().objectName() == 'page_publication':
             name = quote(utf8_to_str(self.ui.FullNameLineEdit.text()))
@@ -445,4 +435,5 @@ if __name__ == '__main__':
     import pprint
 
     l = AuthorLoops(Ui_FinalCifWindow(), CifContainer('test-data/1000007.cif'), None)
-    pprint.pprint(l.export_raw_data())
+    data = l.export_raw_data()
+    pprint.pprint(data)

{finalcif-153 → finalcif-154}/finalcif/finalcif_start.py

@@ -53,7 +53,7 @@ def my_exception_hook(exctype: type[BaseException], value: BaseException, error_
 
     logfile = Path.home().joinpath(Path(r'finalcif-crash.txt'))
     try:
-        logfile.write_text(errortext)
+        logfile.write_text(errortext, encoding='utf-8', errors='ignore')
     except PermissionError:
         pass
     sys.__excepthook__(exctype, value, error_traceback)

{finalcif-153 → finalcif-154}/finalcif/report/templated_report.py

@@ -1,12 +1,12 @@
 from __future__ import annotations
 
+import abc
 import dataclasses
 import enum
 import itertools
 import pathlib
 import re
 import sys
-from abc import ABC
 from collections import namedtuple
 from collections.abc import Iterator
 from contextlib import suppress
@@ -499,7 +499,7 @@ class Disorder:
         return xml_to_html(self.rt)
 
 
-class Formatter(ABC):
+class Formatter(abc.ABC):
     def __init__(self, options: Options, cif: CifContainer) -> None:
         self.literature: dict[str, Reference] = {'finalcif'   : ref.FinalCifReference(),
                                                  'ccdc'       : ref.CCDCReference(),
@@ -513,17 +513,21 @@ class Formatter(ABC):
         self._torsions = TorsionAngles(cif, without_h=options.without_h)
         self._hydrogens = HydrogenBonds(cif)
 
+    @abc.abstractmethod
     def get_bonds(self):
-        raise NotImplementedError
+        ...
 
+    @abc.abstractmethod
     def get_angles(self):
-        raise NotImplementedError
+        ...
 
+    @abc.abstractmethod
     def get_torsion_angles(self) -> list[dict[str, RichText]] | list[Torsion]:
-        raise NotImplementedError
+        ...
 
+    @abc.abstractmethod
     def get_hydrogen_bonds(self) -> list[dict[str, RichText]] | list[HydrogenBond]:
-        raise NotImplementedError
+        ...
 
     def get_bonds_angles_symminfo(self) -> str:
         return self._bonds_angles.symminfo
@@ -537,8 +541,9 @@ class Formatter(ABC):
     def get_crystallization_method(self, cif: CifContainer) -> str:
         return string_to_utf8(gstr(cif['_exptl_crystal_recrystallization_method']))
 
+    @abc.abstractmethod
     def get_radiation(self, cif: CifContainer) -> str | RichText:
-        raise NotImplementedError
+        ...
 
     def get_wavelength(self, cif: CifContainer) -> str:
         try:
@@ -547,8 +552,9 @@ class Formatter(ABC):
         except ValueError:
             return ''
 
+    @abc.abstractmethod
     def hkl_index_limits(self, cif: CifContainer) -> str:
-        raise NotImplementedError
+        ...
 
     def make_3d(self, cif: CifContainer, options: Options) -> str:
         raise NotImplementedError
@@ -559,8 +565,9 @@ class Formatter(ABC):
     def make_picture(self, options: Options, picfile: Path, tpl_doc: DocxTemplate):
         raise NotImplementedError
 
+    @abc.abstractmethod
     def format_sum_formula(self, sum_formula: str) -> str:
-        raise NotImplementedError
+        ...
 
     def hydrogen_atoms_refinement(self, cif: CifContainer) -> RichText | str:
         """
@@ -729,34 +736,45 @@ class Formatter(ABC):
             self.literature['solution'] = ref.SHELXDReference()
         return string_to_utf8(solution_prog.split('(')[0]).strip()
 
-    def _tvalue(self, tval: str) -> str:
+    def t_minvalue(self, cif: CifContainer) -> str:
+        t_min = cif['_exptl_absorpt_correction_T_min']
+        with suppress(ValueError):
+            return f'{float(t_min):.4f}'
+        return '?'
+
+    def t_maxvalue(self, cif: CifContainer) -> str:
+        t_max = cif['_exptl_absorpt_correction_T_max']
         with suppress(ValueError):
-            return f'{float(tval):.4f}'
-        return tval
+            return f'{float(t_max) :.4f}'
+        return '?'
 
-    def get_atomic_coordinates(self, cif: CifContainer) -> Iterator[dict[str, str]]:
+    def get_atomic_coordinates(self, cif: CifContainer) -> tuple[dict[str, str], ...]:
+        coords = []
         for at in cif.atoms(without_h=False):
-            yield {'label': at.label,
-                   'type' : at.type,
-                   'x'    : at.x.replace('-', minus_sign),
-                   'y'    : at.y.replace('-', minus_sign),
-                   'z'    : at.z.replace('-', minus_sign),
-                   'part' : at.part.replace('-', minus_sign),
-                   'occ'  : at.occ.replace('-', minus_sign),
-                   'u_eq' : at.u_eq.replace('-', minus_sign)}
-
-    def get_displacement_parameters(self, cif: CifContainer) -> Iterator[AdpWithMinus]:
+            coords.append({
+                'label': at.label,
+                'type' : at.type,
+                'x'    : at.x.replace('-', minus_sign),
+                'y'    : at.y.replace('-', minus_sign),
+                'z'    : at.z.replace('-', minus_sign),
+                'part' : at.part.replace('-', minus_sign),
+                'occ'  : at.occ.replace('-', minus_sign),
+                'u_eq' : at.u_eq.replace('-', minus_sign)
+            })
+        return tuple(coords)
+
+    def get_displacement_parameters(self, cif: CifContainer) -> tuple[AdpWithMinus, ...]:
         """
-        Yields the anisotropic displacement parameters. With hypehens replaced to minus signs.
+        Returns anisotropic displacement parameters with hyphens replaced by minus signs.
         """
-        for label, u11, u22, u33, u23, u13, u12 in cif.displacement_parameters():
-            yield AdpWithMinus(label=label,
-                               U11=u11.replace('-', minus_sign),
-                               U22=u22.replace('-', minus_sign),
-                               U33=u33.replace('-', minus_sign),
-                               U12=u12.replace('-', minus_sign),
-                               U13=u13.replace('-', minus_sign),
-                               U23=u23.replace('-', minus_sign))
+        return tuple(AdpWithMinus(label=label,
+                                  U11=u11.replace('-', minus_sign),
+                                  U22=u22.replace('-', minus_sign),
+                                  U33=u33.replace('-', minus_sign),
+                                  U12=u12.replace('-', minus_sign),
+                                  U13=u13.replace('-', minus_sign),
+                                  U23=u23.replace('-', minus_sign))
+                     for label, u11, u22, u33, u23, u13, u12 in cif.displacement_parameters())
 
     def get_completeness(self, cif: CifContainer) -> str:
         try:
@@ -897,9 +915,13 @@ class HtmlFormatter(Formatter):
             # spgrxml = s.to_mathml(cif.space_group)
         except KeyError:
             spgrxml = '<math xmlns="http://www.w3.org/1998/Math/MathML">?</math>'
-        return f'{spgrxml} ({cif.spgr_number})'
+        try:
+            number = cif.spgr_number
+        except AttributeError:
+            return '?'
+        return f'{spgrxml} ({number})'
 
-    def make_picture(self, options: Options, picfile: Path, _: None):
+    def make_picture(self, options: Options, picfile: Path, _: None) -> str:
         picture_path = ''
         if options.report_text and picfile and picfile.exists():
             picture_path = str(picfile.resolve())
@@ -1043,7 +1065,7 @@ class RichTextFormatter(Formatter):
         radiation.add(radline, italic=True, subscript=True)
         return radiation
 
-    def make_picture(self, options: Options, picfile: Path, tpl_doc: DocxTemplate):
+    def make_picture(self, options: Options, picfile: Path, tpl_doc: DocxTemplate) -> InlineImage | None:
         if options.report_text and picfile and picfile.exists():
             return InlineImage(tpl_doc, str(picfile.resolve()), width=Cm(options.picture_width))
         return None
@@ -1138,6 +1160,7 @@ class TemplatedReport:
             show_general_warning(parent=None, window_title='Warning', warn_text='Document generation failed',
                                  info_text=str(e))
             print(e)
+            raise
             return False
 
     def make_templated_html_report(self,
@@ -1173,6 +1196,7 @@ class TemplatedReport:
         except Exception as e:
             show_general_warning(parent=None, window_title='Warning', warn_text='Document generation failed',
                                  info_text=str(e))
+            raise
             return False
         return True
 
@@ -1245,10 +1269,8 @@ class TemplatedReport:
                    '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']),
-                   't_min'                  : self.text_formatter._tvalue(
-                       this_or_quest(cif['_exptl_absorpt_correction_T_min'])),
-                   't_max'                  : self.text_formatter._tvalue(
-                       this_or_quest(cif['_exptl_absorpt_correction_T_max'])),
+                   't_min'                  : self.text_formatter.t_minvalue(cif),
+                   't_max'                  : self.text_formatter.t_maxvalue(cif),
                    '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']),
@@ -1316,6 +1338,7 @@ if __name__ == '__main__':
     data = Path('tests')
     testcif = Path(data / 'examples/1979688.cif').absolute()
     testcif = Path(r'test-data/p31c.cif').absolute()
+    testcif = Path(r"D:\Downloads\9008564.cif").absolute()
     cif = CifContainer(testcif)
 
     pic = pathlib.Path("screenshots/finalcif_checkcif.png")

{finalcif-153 → finalcif-154}/finalcif/template/report.tmpl

@@ -76,7 +76,13 @@
                 used {{ radiation }} radiation {% if wavelength %}(λ = {{ wavelength }} Å){% endif %}.
                 All data were integrated with {{ integration_progr }} yielding {{ cif._diffrn_reflns_number }}
                 reflections of which {{ cif._reflns_number_total }} where independent and
-                {{ '%0.1f'| format((cif._reflns_number_gt|float() / cif._reflns_number_total|float()) * 100) }} %
+                {% set gt = cif._reflns_number_gt | float %}
+                {% set total = cif._reflns_number_total | float %}
+                {% if total > 0 %}
+                    {{ (gt / total * 100) | round(1) }} %
+                {% else %}
+                    n/a
+                {% endif %}
                 were greater than 2σ(<i>F</i><sup>2</sup>).<sup>[{{ literature.integration|ref_num }}]</sup> A
                 {{ abstype }} absorption correction using {{ abs_details }} was applied.<sup>[{{ literature.absorption|ref_num }}]</sup>
                 The structure was solved by

{finalcif-153 → finalcif-154}/finalcif/tools/platon.py

@@ -43,7 +43,7 @@ class PlatonRunner(QtCore.QObject):
         self.cif_file.with_suffix('.chk').unlink(missing_ok=True)
         self.process.start(self.platon_exe, ["-U", str(self.cif_file.name)])
 
-    def _onfinished(self):
+    def _onfinished(self) -> None:
         self._on_ready_read()
         # os.chdir(self._origdir)
         self._parse_chk_file()
@@ -51,11 +51,11 @@ class PlatonRunner(QtCore.QObject):
         self.finished.emit(True)
         self.delete_orphaned_files()
 
-    def _on_ready_read(self):
+    def _on_ready_read(self) -> None:
         output = self.process.readAllStandardOutput().data().decode()
         self.log_widget.appendPlainText(output)
 
-    def _monitor_output_log(self):
+    def _monitor_output_log(self) -> None:
         while not self.is_stopped:
             self.tick.emit('#')
             time.sleep(0.3)
@@ -68,13 +68,13 @@ class PlatonRunner(QtCore.QObject):
             except FileNotFoundError:
                 break
 
-    def _stop_program(self):
+    def _stop_program(self) -> None:
         self.is_stopped = True
         # if self.process and self.process.state() == QProcess.Running:
         self.process.terminate()
         self.finished.emit(True)
 
-    def _parse_chk_file(self):
+    def _parse_chk_file(self) -> None:
         try:
             self.chk_file_text = self.cif_file.with_suffix('.chk').read_text(encoding='latin1', errors='ignore')
         except FileNotFoundError as e:
@@ -89,6 +89,9 @@ class PlatonRunner(QtCore.QObject):
 
     @property
     def platon_exe(self) -> str:
+        special_platon = Path(__file__).resolve().parent.parent.parent.joinpath('platon/platon_special.exe')
+        if special_platon.exists():
+            return str(special_platon)
         if sys.platform.startswith('win'):
             in_pwt = r'C:\pwt\platon.exe'
         else:
@@ -103,10 +106,10 @@ class PlatonRunner(QtCore.QObject):
     def kill(self):
         if sys.platform.startswith('win'):
             with suppress(FileNotFoundError):
-                subprocess.run(["taskkill", "/f", "/im", "platon.exe"], shell=False)
+                subprocess.run(["taskkill", "/f", "/im", "platon.exe"], check=False, shell=False)
         if sys.platform[:5] in ('linux', 'darwi'):
             with suppress(FileNotFoundError):
-                subprocess.run(["killall", "platon"], shell=False)
+                subprocess.run(["killall", "platon"], check=False, shell=False)
 
     def delete_orphaned_files(self):
         # delete orphaned files:

{finalcif-153 → finalcif-154}/finalcif/tools/sumformula.py

@@ -1,5 +1,3 @@
-from typing import Union, Dict
-
 from finalcif.tools import chemparse