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dkratzert · Jan 20, 2025 · 8db2124 · 8db2124
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Showing 11 changed files with 97 additions and 34 deletions.
diff --git a/finalcif/appwindow.py b/finalcif/appwindow.py
@@ -62,6 +62,7 @@
 from finalcif.tools.settings import FinalCifSettings
 from finalcif.tools.shred import ShredCIF
 from finalcif.tools.space_groups import SpaceGroups
+from finalcif.tools.spgr_format import spgrps
 from finalcif.tools.statusbar import StatusBar
 from finalcif.tools.sumformula import formula_str_to_dict, sum_formula_to_html
 
@@ -1200,6 +1201,10 @@ def zip_report(self, report_filename: Path) -> None:
         with suppress(Exception):
             multitable = self.cif.finalcif_file_prefixed(prefix='', suffix='-multitable.docx')
             arc.zip.write(filename=multitable, arcname=multitable.name)
+        with suppress(Exception):
+            prp_list = self.cif.finalcif_file.parent.glob('*.prp')
+            sorted_prp = sorted(prp_list, key=lambda x: x.stat().st_mtime)
+            arc.zip.write(filename=sorted_prp[-1], arcname=sorted_prp[-1].name)
 
     def open_report_document(self, report_filename: Path, multi_table_document: Path) -> None:
         if self.cif.is_multi_cif:
@@ -1253,7 +1258,8 @@ def save_current_cif_file(self) -> Union[bool, None]:
         try:
             self.cif.save()
             self.status_bar.show_message(f'  File Saved:  {self.cif.finalcif_file}', 10)
-            print('File saved ...')
+            if DEBUG:
+                print('File saved ...')
             return True
         except Exception as e:
             print('Unable to save file:')
@@ -1617,8 +1623,9 @@ def fill_sum_formula_lineedit(self) -> None:
 
     def fill_space_group_lineedit(self) -> None:
         try:
-            self.ui.Spacegroup_top_LineEdit.setText(
-                SpaceGroups().to_html(self.cif.space_group))
+            txt = (f'<body style="">{SpaceGroups().to_html(self.cif.space_group)} '
+                   f'&thinsp;({spgrps[self.cif.space_group][1].get("itnumber")})</body>')
+            self.ui.Spacegroup_top_LineEdit.setText(txt)
         except Exception as e:
             print('Space group error:', str(e))
             self.ui.Spacegroup_top_LineEdit.setText(self.cif.space_group)

diff --git a/finalcif/cif/cif_order.py b/finalcif/cif/cif_order.py
@@ -212,6 +212,8 @@
     '_diffrn_radiation_monochromator',
     '_diffrn_radiation_polarisn_norm',
     '_diffrn_radiation_collimation',
+    '_bruker_diffrn_measurement_temperature_device',
+    '_bruker_diffrn_measurement_temperature_device_make',
     '_olex2_diffrn_ambient_temperature_device',
     '_diffrn_measurement_ambient_temperature_device_make',
     '_diffrn_radiation_probe',

diff --git a/finalcif/ciforder/order.py b/finalcif/ciforder/order.py
@@ -1,4 +1,5 @@
 from __future__ import annotations
+
 import enum
 import sys
 from pathlib import Path
@@ -23,7 +24,7 @@ class Column(enum.IntEnum):
 
 
 class CifOrder(QtWidgets.QGroupBox):
-    def __init__(self, parent, cif_file: Path = None):
+    def __init__(self, parent=None, cif_file: Path = None):
         super().__init__(parent)
         self.ui = Ui_CifOrderForm()
         self.ui.setupUi(self)
@@ -123,7 +124,7 @@ def set_keys(self, order_keys: List[str] = None):
             self.ui.cifOrderTableWidget.insertRow(row)
             self.set_row_text(key_text, row)
             row += 1
-        #self.ui.cifOrderTableWidget.resizeColumnsToContents()
+        # self.ui.cifOrderTableWidget.resizeColumnsToContents()
 
     def set_row_text(self, key_text: str, row: int) -> None:
         item1 = CifOrderItem(key_text)
@@ -189,8 +190,10 @@ def export_cif(self):
                 return
             show_general_warning(self, 'No permission to write file to {}'.format(Path(filename).resolve()))
 
+
 if __name__ == "__main__":
     from finalcif.tools.settings import FinalCifSettings
+
     app = QtWidgets.QApplication(sys.argv)
     # form = CifOrder(parent=None, cif_file=Path('test-data/1000007.cif').resolve())
     settings = FinalCifSettings()

diff --git a/finalcif/gui/combobox.py b/finalcif/gui/combobox.py
@@ -1,11 +1,14 @@
-from contextlib import suppress
 from textwrap import wrap
+from typing import TYPE_CHECKING
 
-from PyQt5 import QtCore
+from PyQt5 import QtCore, QtGui
 from PyQt5.QtCore import Qt, QObject, QEvent
 from PyQt5.QtWidgets import QComboBox, QSizePolicy, QAction
 
-from typing import TYPE_CHECKING
+from finalcif.gui.validators import validators
+
+light_red = QtGui.QColor(254, 191, 189)
+white = QtGui.QColor(255, 255, 255)
 
 if TYPE_CHECKING:
     from finalcif.gui.custom_classes import MyCifTable
@@ -21,6 +24,7 @@ def __init__(self, parent: 'MyCifTable' = None):
         super().__init__(parent)
         self.parent: 'MyCifTable' = parent
         self.cif_key = ''
+        self.color = white
         self.setFocusPolicy(Qt.StrongFocus)
         self.setSizeAdjustPolicy(QComboBox.AdjustToMinimumContentsLength)
         self.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Expanding)
@@ -56,6 +60,29 @@ def eventFilter(self, widget: QObject, event: QEvent):
             return True
         return QObject.eventFilter(self, widget, event)
 
+    def keyPressEvent(self, event: QtGui.QKeyEvent):
+        super().keyPressEvent(event)
+        self.validate_text(self.currentText())
+
+    def validate_text(self, text: str):
+        validator = validators.get(self.cif_key, None)
+        if validator and not validator.valid(text):
+            self.setBadStyle()
+            self.setToolTip(validator.help_text)
+        else:
+            self.setToolTip('')
+            self.setRegularStyle()
+
+    def setBadStyle(self) -> None:
+        self.setStyleSheet(f"""
+        QComboBox {{
+            border: 3px solid {light_red};
+        }}
+        """)
+
+    def setRegularStyle(self) -> None:
+        self.setStyleSheet('')
+
     def setUneditable(self):
         # noinspection PyUnresolvedReferences
         self.setFlags(self.flags() ^ Qt.ItemIsEditable)

diff --git a/finalcif/gui/custom_classes.py b/finalcif/gui/custom_classes.py
@@ -19,6 +19,7 @@
 light_blue = QColor(244, 244, 249)
 blue = QColor(102, 150, 179)
 yellow = QColor(250, 247, 150)  # #faf796
+light_red = QColor(254, 191, 189)
 
 
 class Column(IntEnum):

diff --git a/finalcif/gui/import_selector.py b/finalcif/gui/import_selector.py
@@ -66,7 +66,7 @@ def _save_selection(self):
         self.settings.save_key_value('do_not_import_keys', self.get_keys(include=False))
         self.settings.save_key_value('do_not_import_loops', self.get_loops(include=False))
 
-    def _empty_saved_selection(self):
+    def _empty_saved_selection(self) -> None:
         self.settings.save_key_value('do_not_import_keys', [])
         self.settings.save_key_value('do_not_import_loops', [])
 
@@ -82,7 +82,8 @@ def _get_excluded_items(self) -> Tuple[List[str], List[List[str]]]:
         return excluded_kv, excluded_loops
 
     def _set_label(self) -> None:
-        self.ui.importInfoLabel.setText(f"The CIF to import contains {self.keys_to_import} keys "
+        self.ui.importInfoLabel.setText(f"Importing\n{self.import_cif.fileobj}\n\n"
+                                        f"The CIF to import contains {self.keys_to_import} keys "
                                         f"and {self.loops_to_import} loops from which "
                                         f"{len(self.get_keys(include=True)) + len(self.get_loops(include=True))} "
                                         f"are selected for import.")
@@ -126,6 +127,10 @@ def do_not_import_this_key(self, key: str) -> bool:
         return False
 
     def _select_only_new(self) -> None:
+        self.select_pairs()
+        self.select_loops()
+
+    def select_pairs(self):
         rows = self.ui.importTable_keys.rowCount()
         for row in range(rows):
             widget: QtWidgets.QCheckBox = self.ui.importTable_keys.cellWidget(row, 0)
@@ -135,6 +140,8 @@ def _select_only_new(self) -> None:
                 widget.setChecked(False)
                 continue
             widget.setChecked(True)
+
+    def select_loops(self):
         rows = self.ui.importTable_loops.rowCount()
         for row in range(rows):
             widget: QtWidgets.QCheckBox = self.ui.importTable_loops.cellWidget(row, 0)

diff --git a/finalcif/gui/loops.py b/finalcif/gui/loops.py
@@ -11,7 +11,7 @@
 
 import gemmi
 
-from finalcif.gui.custom_classes import light_blue
+from finalcif.gui.custom_classes import light_blue, light_red
 from finalcif.gui.plaintextedit import MyQPlainTextEdit
 from finalcif.gui.validators import validators
 
@@ -249,7 +249,7 @@ def data(self, index: QModelIndex, role: int = None):
             (row, col) in [(x['row'], x['column']) for x in self.modified] and self.validate_text(value, col)):
             return QVariant(light_blue)
         elif role == Qt.BackgroundColorRole and not self.validate_text(value, col):
-            return QVariant(QColor(254, 191, 189))
+            return QVariant(light_red)
         else:
             QVariant(QColor(255, 255, 255))
         if role == Qt.EditRole:

diff --git a/finalcif/gui/plaintextedit.py b/finalcif/gui/plaintextedit.py
@@ -12,7 +12,7 @@
 from finalcif.gui.validators import validators
 
 if TYPE_CHECKING:
-    from finalcif.gui.custom_classes import MyCifTable
+    from finalcif.gui.custom_classes import MyCifTable, light_red
 
 
 class Column(IntEnum):
@@ -157,7 +157,7 @@ def keyPressEvent(self, event: QtGui.QKeyEvent):
     def validate_text(self, text: str):
         validator = validators.get(self.cif_key, None)
         if validator and not validator.valid(text):
-            self.setBackground(QColor(254, 191, 189))
+            self.setBackground(light_red)
             self.setToolTip(validator.help_text)
         else:
             self.setToolTip('')

diff --git a/finalcif/report/templated_report.py b/finalcif/report/templated_report.py
@@ -15,6 +15,7 @@
 
 from PyQt5.QtWidgets import QApplication
 
+from finalcif.cif.text import string_to_utf8
 from finalcif.template.xsl.convert import xml_to_html
 
 # This is necessary, because if jinja crashes, we show an error dialog:
@@ -527,8 +528,8 @@ def get_torsion_symminfo(self) -> str:
     def get_hydrogen_symminfo(self) -> str:
         return self._hydrogens.symminfo
 
-    def get_crystallization_method(self, cif) -> str:
-        return gstr(cif['_exptl_crystal_recrystallization_method'])
+    def get_crystallization_method(self, cif: CifContainer) -> str:
+        return string_to_utf8(gstr(cif['_exptl_crystal_recrystallization_method']))
 
     def get_radiation(self, cif: CifContainer) -> str | RichText:
         raise NotImplementedError
@@ -546,7 +547,7 @@ def hkl_index_limits(self, cif: CifContainer) -> str:
     def make_3d(self, cif: CifContainer, options: Options) -> str:
         raise NotImplementedError
 
-    def space_group_subdoc(self, cif: CifContainer, tpl_doc: DocxTemplate):
+    def space_group_formatted(self, cif: CifContainer, tpl_doc: DocxTemplate):
         raise NotImplementedError
 
     def make_picture(self, options: Options, picfile: Path, tpl_doc: DocxTemplate):
@@ -661,7 +662,7 @@ def get_refinement_gui(self, cif: CifContainer) -> str:
         else:
             refinement_gui = '[Unknown program in _computing_structure_refinement]'
         self.literature['gui'] = gui_reference
-        return refinement_gui
+        return string_to_utf8(refinement_gui)
 
     def _get_scaling_program(self, absdetails: str) -> tuple[str, str]:
         scale_prog = ''
@@ -695,11 +696,11 @@ def get_absortion_correction_program(self, cif: CifContainer) -> str:
             scale_prog = 'STOE X-RED'
             self.literature['absorption'] = ref.XRedReference('X-RED', 'unknown version')
         scale_prog += " " + version
-        return scale_prog
+        return string_to_utf8(scale_prog)
 
     def solution_method(self, cif: CifContainer) -> str:
         solution_method = gstr(cif['_atom_sites_solution_primary']) or '??'
-        return solution_method.strip('\n\r')
+        return solution_method.strip('\n\r').strip()
 
     def refinement_prog(self, cif: CifContainer) -> Reference | str:
         refined = gstr(cif['_computing_structure_refinement']) or '??'
@@ -768,7 +769,10 @@ def get_angstrom_resolution(self, cif: CifContainer):
         return f'{d:.2f}'
 
     def get_redundancy(self, cif):
-        n_refl = cif['_diffrn_reflns_number']
+        if twinabs := cif['_diffrn_reflns_bruker_twinabs_number']:
+            n_refl = twinabs
+        else:
+            n_refl = cif['_diffrn_reflns_number']
         n_all = cif['_reflns_number_total']
         try:
             redundancy = float(n_refl) / float(n_all)
@@ -785,6 +789,10 @@ def get_data_to_param(self, cif):
             return ''
         return f'{redundancy:.2f}'
 
+    def refinement_details(self, cif):
+        details = ' '.join(cif['_refine_special_details'].splitlines(keepends=False)).strip()
+        return string_to_utf8(details)
+
 
 class HtmlFormatter(Formatter):
 
@@ -812,19 +820,21 @@ def _format_symminfo(self, txt):
     def get_bonds_angles_symminfo(self) -> str:
         return self._format_symminfo(self._bonds_angles.symminfo)
 
-    def get_torsion_symminfo(self):
+    def get_torsion_symminfo(self) -> str:
         return self._format_symminfo(self._torsions.symminfo)
 
-    def get_hydrogen_symminfo(self):
+    def get_hydrogen_symminfo(self) -> str:
         return self._format_symminfo(self._hydrogens.symminfo)
 
     def make_3d(self, cif: CifContainer, options: Options) -> str:
         return '[3D representation of the structure in html/javascript not implemented]'
 
-    def space_group_subdoc(self, cif: CifContainer, _: None) -> str:
+    def space_group_formatted(self, cif: CifContainer, _: None) -> str:
         s = SpaceGroups()
         try:
-            spgrxml = s.to_mathml(cif.space_group)
+            spgrxml = s.to_html(cif.space_group)
+            # Mathml doesn't work well in pyQt
+            # 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})'
@@ -945,7 +955,7 @@ def disorder_description(self, cif: CifContainer) -> RichText:
         self.literature['dsr'] = ref.DSRReference2018()
         return Disorder(cif).richtext()
 
-    def space_group_subdoc(self, cif: CifContainer, tpl_doc: DocxTemplate) -> Subdoc:
+    def space_group_formatted(self, cif: CifContainer, tpl_doc: DocxTemplate) -> Subdoc:
         """
         Generates a Subdoc subdocument with the xml code for a math element in MSWord.
         """
@@ -1056,6 +1066,12 @@ def make_templated_docx_report(self,
             tpl_doc.render(context, jinja_env=jinja_env, autoescape=True)
             tpl_doc.save(output_filename)
             return True
+        except PermissionError:
+            #raise
+            show_general_warning(parent=None, window_title='Warning',
+                                 warn_text=f'The document {output_filename} could not be opened to write the report.\n'
+                                           f'Is the file already opened?')
+            return False
         except Exception as e:
             show_general_warning(parent=None, window_title='Warning', warn_text='Document generation failed',
                                  info_text=str(e))
@@ -1124,7 +1140,7 @@ def get_context(self, cif: CifContainer, options: Options, picfile: Path, tpl_do
         context = {'options'                : options,
                    'cif'                    : cif,
                    'name'                   : cif.block.name,
-                   'space_group'            : self.text_formatter.space_group_subdoc(cif, tpl_doc),
+                   'space_group'            : self.text_formatter.space_group_formatted(cif, tpl_doc),
                    'structure_figure'       : self.text_formatter.make_picture(options, picfile, tpl_doc),
                    '3d_structure'           : self.text_formatter.make_3d(cif, options),
                    'crystallization_method' : self.text_formatter.get_crystallization_method(cif),

diff --git a/finalcif/tools/space_groups.py b/finalcif/tools/space_groups.py
@@ -66,7 +66,7 @@ def to_html(self, space_group: str) -> str:
         if not space_group:
             return ''
         txt = self.to_html_without_body(space_group)
-        return f'<body style="">{txt} &thinsp;({self.spgrps[space_group][1].get("itnumber")})</body>'
+        return txt
 
     def to_plain_text(self, space_group: str) -> str:
         """

diff --git a/finalcif/tools/sumformula.py b/finalcif/tools/sumformula.py
@@ -14,7 +14,7 @@ def sum_formula_to_html(sumform: Dict[str, float | int], break_after: int = 99)
     """
     if not sumform:
         return ''
-    l = ['<html><body>']
+    formula_list = ['<html><body>']
     num = 0
     for el in sumform:
         if sumform[el] == 0 or sumform[el] is None:
@@ -24,12 +24,12 @@ def sum_formula_to_html(sumform: Dict[str, float | int], break_after: int = 99)
         except (TypeError, ValueError):
             times = 1
         if num > 3 and num % break_after == 0:
-            l.append("<br>")
+            formula_list.append("<br>")
         if times == 1:
-            l.append('{}'.format(el))
+            formula_list.append('{}'.format(el))
         else:
-            l.append("{}<sub>{:g}</sub>".format(el, times))
+            formula_list.append("{}<sub>{:g}</sub>".format(el, times))
         num += 1
-    l.append('</body></html>')
-    formula = "".join(l)
+    formula_list.append('</body></html>')
+    formula = "".join(formula_list)
     return formula