finalcif 141__tar.gz → 142__tar.gz

{finalcif-141 → finalcif-142}/.gitignore

@@ -220,3 +220,4 @@ test-data/report_1000007-multi-finalcif.docx
 test.html
 
 work/~$test.docx
+tests/examples/work/report_cu_BruecknerJK_153F40_0m-finalcif_pm.docx

{finalcif-141 → finalcif-142}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: finalcif
-Version: 141
+Version: 142
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues
@@ -12,7 +12,6 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: >=3.10
-Requires-Dist: altgraph
 Requires-Dist: certifi
 Requires-Dist: chardet
 Requires-Dist: crossrefapi

finalcif-142/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 142

{finalcif-141 → finalcif-142}/finalcif/appwindow.py

@@ -1103,7 +1103,10 @@ class AppWindow(QMainWindow):
         for index in range(self.ui.docxTemplatesListWidget.count()):
             item = self.ui.docxTemplatesListWidget.item(index)
             if item.checkState() == Qt.Checked:
-                return item.text()
+                if self.templates.report_from_default_template():
+                    return 'finalcif/template/report_default.docx'
+                else:
+                    return item.text()
 
     def make_report_tables(self) -> None:
         """
@@ -1122,36 +1125,32 @@ class AppWindow(QMainWindow):
         self.load_cif_file(self.cif.finalcif_file, block=current_block, load_changes=False)
         report_filename = self.cif.finalcif_file_prefixed(prefix='report_', suffix='-finalcif.docx')
         multi_table_document = self.cif.finalcif_file_prefixed(prefix='', suffix='-multitable.docx')
+        self.cif.picometer = self.options.use_picometers
         # The picture after the header:
         if self.report_picture_path:
             picfile = self.report_picture_path
         else:
             picfile = self.cif.finalcif_file.with_suffix('.gif')
         try:
-            if self.report_without_template():
-                print('Report without templates')
-                make_report_from(options=self.options, cif=self.cif,
-                                 output_filename=str(report_filename), picfile=picfile)
+            print('Report with templates')
+            template_path = Path(self.get_checked_templates_list_text())
+            ok = False
+            if template_path.suffix in ('.docx',):
+                t = TemplatedReport(format=ReportFormat.RICHTEXT, options=self.options, cif=self.cif)
+                ok = t.make_templated_docx_report(output_filename=str(report_filename),
+                                                  picfile=picfile,
+                                                  template_path=Path(self.get_checked_templates_list_text()))
                 if self.cif.is_multi_cif and self.cif.doc[0].name != 'global':
                     make_multi_tables(cif=self.cif, output_filename=str(multi_table_document))
-            else:
-                print('Report with templates')
-                template_path = Path(self.get_checked_templates_list_text())
-                ok = False
-                if template_path.suffix in ('.docx',):
-                    t = TemplatedReport(format=ReportFormat.RICHTEXT, options=self.options, cif=self.cif)
-                    ok = t.make_templated_docx_report(output_filename=str(report_filename),
-                                                      picfile=picfile,
-                                                      template_path=Path(self.get_checked_templates_list_text()))
-                elif template_path.suffix in ('.html', '.tmpl'):
-                    t = TemplatedReport(format=ReportFormat.HTML, options=self.options, cif=self.cif)
-                    report_filename = report_filename.with_suffix('.html')
-                    ok = t.make_templated_html_report(output_filename=str(report_filename),
-                                                      picfile=picfile,
-                                                      template_path=template_path.parent,
-                                                      template_file=template_path.name)
-                if not ok:
-                    return None
+            elif template_path.suffix in ('.html', '.tmpl'):
+                t = TemplatedReport(format=ReportFormat.HTML, options=self.options, cif=self.cif)
+                report_filename = report_filename.with_suffix('.html')
+                ok = t.make_templated_html_report(output_filename=str(report_filename),
+                                                  picfile=picfile,
+                                                  template_path=template_path.parent,
+                                                  template_file=template_path.name)
+            if not ok:
+                return None
         except FileNotFoundError as e:
             if DEBUG:
                 raise
@@ -1171,11 +1170,6 @@ class AppWindow(QMainWindow):
             # Save report and other files to a zip file:
             self.zip_report(report_filename)
 
-    def report_without_template(self) -> bool:
-        """Check whether the report is generated from a template or hard-coded"""
-        return self.ui.docxTemplatesListWidget.item(0).checkState() == Qt.CheckState.Checked \
-            or not self.ui.docxTemplatesListWidget.currentItem()
-
     def zip_report(self, report_filename: Path) -> None:
         from finalcif.report.archive_report import ArchiveReport
         zipfile = self.cif.finalcif_file.with_suffix('.zip')
@@ -1196,7 +1190,7 @@ class AppWindow(QMainWindow):
             arc.zip.write(filename=multitable, arcname=multitable.name)
 
     def open_report_document(self, report_filename: Path, multi_table_document: Path) -> None:
-        if self.cif.is_multi_cif and self.report_without_template():
+        if self.cif.is_multi_cif:
             open_file(multi_table_document)
         open_file(report_filename)
 
@@ -1437,8 +1431,6 @@ class AppWindow(QMainWindow):
         Opens the cif file and fills information into the main table.
         """
         self.ui.datanameComboBox.blockSignals(True)
-        # Is also done in block load method
-        self._clear_state_before_block_load()
         if not filepath:
             filepath = Path(cif_file_open_dialog(last_dir=self.get_last_workdir()))
             if not filepath.is_file():
@@ -1464,7 +1456,11 @@ class AppWindow(QMainWindow):
             not_ok = e
         if not_ok:
             unable_to_open_message(self, filepath, not_ok)
-            return
+            return None
+        if not self.cif.is_valid_structure_cif:
+            show_general_warning(self, "The CIF file you are about to open contains no structure.\n\n"
+                                       "Use the Import button below to import metadata.")
+            return None
         if not self.cif.chars_ok:
             self.warn_about_bad_cif()
         # Do this only when sure we can load the file:
@@ -1476,6 +1472,16 @@ class AppWindow(QMainWindow):
         self.ui.datanameComboBox.blockSignals(False)
         if self.cif.is_multi_cif:
             self._flash_block_combobox()
+        # Enable to find widgets without parent:
+        # QtCore.QTimer(self).singleShot(1000, self.find_widgets_without_parent)
+
+    def find_widgets_without_parent(self) -> None:
+        print('Finding parents...')
+        all_widgets = app.allWidgets()
+        no_parent_widgets = [widget for widget in all_widgets if widget.parent is None]
+        print(f"Found {len(no_parent_widgets)} widget(s) out of {len(all_widgets)} without parent:")
+        for widget in no_parent_widgets:
+            print(widget, widget.objectName())
 
     def _flash_block_combobox(self):
         orig_pal = self.ui.datanameComboBox.palette()

{finalcif-141 → finalcif-142}/finalcif/cif/cif_file_io.py

@@ -20,7 +20,8 @@ from finalcif.cif.cif_order import order, special_keys
 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 essential_keys, non_centrosymm_keys, isnumeric, grouper, strip_finalcif_of_name
+from finalcif.tools.misc import essential_keys, non_centrosymm_keys, isnumeric, grouper, strip_finalcif_of_name, \
+    _angstrom_to_x
 
 
 class GemmiError(Exception):
@@ -40,6 +41,7 @@ class CifContainer():
             new_block: Create a new block (new file) if a name is given. Otherwise, just
                        the existing document is opened.
         """
+        self.picometer: bool = False
         self._hkl_file: str = ''
         self._abs_hkl_details: Dict[str, str] = {}
         if isinstance(file, str):
@@ -146,6 +148,13 @@ class CifContainer():
                 [x.upper() for x in self.block.find_loop('_atom_site_type_symbol')]))
         self.check_hkl_min_max()
 
+    @property
+    def is_valid_structure_cif(self):
+        """
+        Checkl wether this CIF contains a structure or just metadata.
+        """
+        return len(self.atomic_struct.sites) > 0 and self.cell.a
+
     @property
     def hkl_extra_info(self):
         if not self._abs_hkl_details:
@@ -665,10 +674,7 @@ class CifContainer():
             # Do not crash without symmops
             return False
         ops = gemmi.GroupOps([gemmi.Op(o) for o in self.symmops])
-        try:
-            return ops.is_centric()
-        except AttributeError:
-            return ops.is_centrosymmetric()
+        return ops.is_centrosymmetric()
 
     def atoms(self, without_h: bool = False) -> Generator:
         """
@@ -689,6 +695,8 @@ class CifContainer():
                                                          u_eq):
             if without_h and self.ishydrogen(label):
                 continue
+            if self.picometer:
+                u_eq = _angstrom_to_x(u_eq, factor=100 ** 2)
             #         0    1   2  3  4   5   6     7
             # yield label, type, x, y, z, part, occ, ueq
             yield atom(label=label, type=type, x=x, y=y, z=z, part=part, occ=occ, u_eq=u_eq)
@@ -721,6 +729,13 @@ class CifContainer():
         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):
+            if self.picometer:
+                u11 = _angstrom_to_x(u11, factor=100 ** 2)
+                u22 = _angstrom_to_x(u22, factor=100 ** 2)
+                u33 = _angstrom_to_x(u33, factor=100 ** 2)
+                u23 = _angstrom_to_x(u23, factor=100 ** 2)
+                u13 = _angstrom_to_x(u13, factor=100 ** 2)
+                u12 = _angstrom_to_x(u12, factor=100 ** 2)
             yield adp(label=label, U11=u11, U22=u22, U33=u33, U12=u12, U13=u13, U23=u23)
 
     @property
@@ -770,24 +785,29 @@ class CifContainer():
         publ_loop = self.block.find_loop('_geom_bond_publ_flag')
         bond = namedtuple('bond', ('label1', 'label2', 'dist', 'symm'))
         for label1, label2, dist, symm, publ in zip(label1, label2, dist, symm, publ_loop):
-            if (without_h and (self.ishydrogen(label1) or self.ishydrogen(label2)) or self.yes_not_set(publ)):
+            if without_h and (self.ishydrogen(label1) or self.ishydrogen(label2)) or self.yes_not_set(publ):
                 continue
             else:
+                if self.picometer:
+                    dist = _angstrom_to_x(dist)
                 yield bond(label1=label1, label2=label2, dist=dist, symm=self.checksymm(symm))
 
-    def bond_dist(self, pair: str) -> Union[float, None]:
+    def bond_dist(self, pair: str) -> Union[str, None]:
         for p in self.bonds():
             if f'{p.label1}-{p.label2}' == pair:
-                return p.dist
+                if self.picometer:
+                    return _angstrom_to_x(p.dist)
+                else:
+                    return p.dist
         return None
 
-    def angle(self, atoms: str) -> Union[float, None]:
+    def angle(self, atoms: str) -> Union[str, None]:
         for p in self.angles():
             if f'{p.label1}-{p.label2}-{p.label3}' == atoms:
                 return p.angle_val
         return None
 
-    def torsion(self, atoms: str) -> Union[float, None]:
+    def torsion(self, atoms: str) -> Union[str, None]:
         for p in self.torsion_angles():
             if f'{p.label1}-{p.label2}-{p.label3}-{p.label4}' == atoms:
                 return p.torsang
@@ -803,9 +823,9 @@ class CifContainer():
         publ_loop = self.block.find_loop('_geom_angle_publ_flag')
         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):
+            zip(label1, label2, label3, angle_val, symm1, symm2, publ_loop):
             if (without_H and (self.ishydrogen(label1) or self.ishydrogen(label2) or
-                              self.ishydrogen(label3)) or (self.yes_not_set(publ))):
+                               self.ishydrogen(label3)) or (self.yes_not_set(publ))):
                 continue
             else:
                 yield angle(label1=label1, label2=label2, label3=label3, angle_val=angle_val,
@@ -854,7 +874,7 @@ class CifContainer():
                                                                                              symm3,
                                                                                              symm4, publ_loop):
             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)):
+                               or self.ishydrogen(label3) or self.ishydrogen(label3)) or self.yes_not_set(publ)):
                 continue
             yield tors(label1=label1, label2=label2, label3=label3, label4=label4, torsang=torsang,
                        symm1=self.checksymm(symm1),
@@ -875,9 +895,13 @@ 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)):
             if self.yes_not_set(publ):
                 continue
+            if self.picometer:
+                dist_dh = _angstrom_to_x(dist_dh)
+                dist_ha = _angstrom_to_x(dist_ha)
+                dist_da = _angstrom_to_x(dist_da)
             yield hydr(label_d, label_h, label_a, dist_dh, dist_ha, dist_da, angle_dha, self.checksymm(symm))
 
     def yes_not_set(self, publ: str):

{finalcif-141 → finalcif-142}/finalcif/gui/finalcif_gui_ui.py

@@ -13,7 +13,7 @@ from PyQt5 import QtCore, QtGui, QtWidgets
 class Ui_FinalCifWindow(object):
     def setupUi(self, FinalCifWindow):
         FinalCifWindow.setObjectName("FinalCifWindow")
-        FinalCifWindow.resize(1596, 812)
+        FinalCifWindow.resize(1596, 860)
         self.Mainwidget = QtWidgets.QWidget(FinalCifWindow)
         self.Mainwidget.setObjectName("Mainwidget")
         self.horizontalLayout_4 = QtWidgets.QHBoxLayout(self.Mainwidget)
@@ -242,6 +242,9 @@ class Ui_FinalCifWindow(object):
         self.HAtomsCheckBox = QtWidgets.QCheckBox(self.groupBox_5)
         self.HAtomsCheckBox.setObjectName("HAtomsCheckBox")
         self.gridLayout_26.addWidget(self.HAtomsCheckBox, 1, 0, 1, 2)
+        self.UsePicometersCheckBox = QtWidgets.QCheckBox(self.groupBox_5)
+        self.UsePicometersCheckBox.setObjectName("UsePicometersCheckBox")
+        self.gridLayout_26.addWidget(self.UsePicometersCheckBox, 2, 1, 1, 1)
         self.verticalLayout_35.addLayout(self.gridLayout_26)
         self.groupBox_6 = QtWidgets.QGroupBox(self.groupBox_5)
         sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Preferred)
@@ -551,7 +554,6 @@ class Ui_FinalCifWindow(object):
         font.setFamily("Courier New")
         font.setPointSize(11)
         font.setBold(True)
-        font.setWeight(75)
         self.shelx_warn_TextEdit.setFont(font)
         self.shelx_warn_TextEdit.setUndoRedoEnabled(False)
         self.shelx_warn_TextEdit.setLineWrapMode(QtWidgets.QPlainTextEdit.NoWrap)
@@ -589,7 +591,6 @@ class Ui_FinalCifWindow(object):
         font = QtGui.QFont()
         font.setBold(False)
         font.setItalic(False)
-        font.setWeight(50)
         self.wR2Label.setFont(font)
         self.wR2Label.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.wR2Label.setObjectName("wR2Label")
@@ -602,7 +603,6 @@ class Ui_FinalCifWindow(object):
         font = QtGui.QFont()
         font.setBold(False)
         font.setItalic(False)
-        font.setWeight(50)
         self.r1Label.setFont(font)
         self.r1Label.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.r1Label.setObjectName("r1Label")
@@ -630,7 +630,6 @@ class Ui_FinalCifWindow(object):
         self.completeLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
-        font.setWeight(50)
         self.completeLabel.setFont(font)
         self.completeLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.completeLabel.setObjectName("completeLabel")
@@ -678,7 +677,6 @@ class Ui_FinalCifWindow(object):
         self.dataReflnsLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
-        font.setWeight(50)
         self.dataReflnsLabel.setFont(font)
         self.dataReflnsLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.dataReflnsLabel.setObjectName("dataReflnsLabel")
@@ -745,7 +743,6 @@ class Ui_FinalCifWindow(object):
         self.rintLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
-        font.setWeight(50)
         self.rintLabel.setFont(font)
         self.rintLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.rintLabel.setObjectName("rintLabel")
@@ -757,7 +754,6 @@ class Ui_FinalCifWindow(object):
         self.rsigmaLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
-        font.setWeight(50)
         self.rsigmaLabel.setFont(font)
         self.rsigmaLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.rsigmaLabel.setObjectName("rsigmaLabel")
@@ -793,7 +789,6 @@ class Ui_FinalCifWindow(object):
         self.dLabel = QtWidgets.QLabel(self.groupBox_3)
         font = QtGui.QFont()
         font.setBold(False)
-        font.setWeight(50)
         self.dLabel.setFont(font)
         self.dLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
         self.dLabel.setObjectName("dLabel")
@@ -1971,7 +1966,7 @@ class Ui_FinalCifWindow(object):
         self.EquipmentTemplatesListWidget.setToolTip(_translate("FinalCifWindow", "<html><head/><body><p>Each entry can have a list of key/value pairs. For example a Diffractometer model can have a list of features.</p></body></html>"))
         self.NewEquipmentTemplateButton.setText(_translate("FinalCifWindow", "New Template"))
         self.EditEquipmentTemplateButton.setText(_translate("FinalCifWindow", "Edit Template"))
-        self.ImportEquipmentTemplateButton.setText(_translate("FinalCifWindow", "Import"))
+        self.ImportEquipmentTemplateButton.setText(_translate("FinalCifWindow", "Import Template"))
         self.EquipmentEditTableWidget.setSortingEnabled(True)
         item = self.EquipmentEditTableWidget.horizontalHeaderItem(0)
         item.setText(_translate("FinalCifWindow", "key"))
@@ -1987,6 +1982,7 @@ class Ui_FinalCifWindow(object):
         self.ReportTextCheckBox.setText(_translate("FinalCifWindow", "No report text in structure report"))
         self.PictureWidthLabel.setText(_translate("FinalCifWindow", "Picture width [cm]"))
         self.HAtomsCheckBox.setText(_translate("FinalCifWindow", "No bonds and angles to hydrogen atoms"))
+        self.UsePicometersCheckBox.setText(_translate("FinalCifWindow", "Use picometers"))
         self.groupBox_6.setTitle(_translate("FinalCifWindow", "Report Templates:"))
         __sortingEnabled = self.docxTemplatesListWidget.isSortingEnabled()
         self.docxTemplatesListWidget.setSortingEnabled(False)

{finalcif-141 → finalcif-142}/finalcif/gui/finalcif_gui_ui.ui

@@ -8,7 +8,7 @@
     <x>0</x>
     <y>0</y>
     <width>1596</width>
-    <height>812</height>
+    <height>860</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -282,7 +282,7 @@
                      <item>
                       <widget class="QPushButton" name="ImportEquipmentTemplateButton">
                        <property name="text">
-                        <string>Import</string>
+                        <string>Import Template</string>
                        </property>
                       </widget>
                      </item>
@@ -554,6 +554,13 @@
                    </property>
                   </widget>
                  </item>
+                 <item row="2" column="1">
+                  <widget class="QCheckBox" name="UsePicometersCheckBox">
+                   <property name="text">
+                    <string>Use picometers</string>
+                   </property>
+                  </widget>
+                 </item>
                 </layout>
                </item>
                <item>
@@ -1357,7 +1364,6 @@
                   <font>
                    <family>Courier New</family>
                    <pointsize>11</pointsize>
-                   <weight>75</weight>
                    <bold>true</bold>
                   </font>
                  </property>
@@ -1424,7 +1430,6 @@
                   <widget class="QLabel" name="wR2Label">
                    <property name="font">
                     <font>
-                     <weight>50</weight>
                      <italic>false</italic>
                      <bold>false</bold>
                     </font>
@@ -1448,7 +1453,6 @@
                   <widget class="QLabel" name="r1Label">
                    <property name="font">
                     <font>
-                     <weight>50</weight>
                      <italic>false</italic>
                      <bold>false</bold>
                     </font>
@@ -1506,7 +1510,6 @@
                   <widget class="QLabel" name="completeLabel">
                    <property name="font">
                     <font>
-                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -1622,7 +1625,6 @@
                   <widget class="QLabel" name="dataReflnsLabel">
                    <property name="font">
                     <font>
-                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -1770,7 +1772,6 @@
                   <widget class="QLabel" name="rintLabel">
                    <property name="font">
                     <font>
-                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -1793,7 +1794,6 @@
                   <widget class="QLabel" name="rsigmaLabel">
                    <property name="font">
                     <font>
-                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -1867,7 +1867,6 @@
                   <widget class="QLabel" name="dLabel">
                    <property name="font">
                     <font>
-                     <weight>50</weight>
                      <bold>false</bold>
                     </font>
                    </property>
@@ -4294,7 +4293,7 @@ please add a publication author:</string>
    <extends>QPlainTextEdit</extends>
    <header>finalcif.gui.file_editor.h</header>
   </customwidget>
- <customwidget>
+  <customwidget>
    <class>ComboBoxWithContextMenu</class>
    <extends>QComboBox</extends>
    <header>finalcif.gui.block_combobox.h</header>

{finalcif-141 → finalcif-142}/finalcif/report/references.py

@@ -121,7 +121,6 @@ class ReferenceList():
             paragraph_reflist = document.add_paragraph('', template)
             paragraph_reflist.add_run(f'[{str(num)}] \t')
             ref.add_reference(paragraph_reflist)
-            # paragraph_reflist.add_run('\n')
 
     def __repr__(self):
         return '\n'.join([f'[{num}] {x}' for num, x in enumerate(self._references)])

finalcif-142/finalcif/report/report_text.py

@@ -0,0 +1,150 @@
+import os
+from builtins import str
+from typing import Union, List, Tuple
+
+import gemmi
+from docx import Document
+from docx.oxml.xmlchemy import BaseOxmlElement
+from docx.text.paragraph import Paragraph
+from docx.text.run import Run
+from lxml import etree
+from lxml.etree import XSLTAccessControl
+from shelxfile.atoms.atoms import Atom as SHXAtom
+
+from finalcif.app_path import application_path
+from finalcif.cif.cif_file_io import CifContainer
+from finalcif.cif.text import retranslate_delimiter, string_to_utf8
+from finalcif.report import references
+from finalcif.tools.misc import (protected_space, angstrom, zero_width_space, remove_line_endings,
+                                 flatten)
+
+
+def math_to_word(eq: str) -> BaseOxmlElement:
+    """Transform a sympy equation to be printed in word document."""
+    tree = etree.fromstring(eq)
+    xslt = etree.parse(os.path.join(application_path, 'template/mathml2omml.xsl'))
+    acess_control = XSLTAccessControl(read_network=False, write_network=False)
+    transform = etree.XSLT(xslt, access_control=acess_control)
+    new_dom = transform(tree)
+    return new_dom.getroot()
+
+
+def clean_string(string: str) -> str:
+    """
+    Removes control characters from a string.
+    """
+    repl = string.replace('\t', ' ') \
+        .replace('\f', ' ') \
+        .replace('\0', ' ') \
+        .strip(' ') \
+        .strip('.')
+    return remove_line_endings(repl)
+
+
+def gstr(string: str) -> str:
+    """
+    Turn a string into a gemmi string and remove control characters.
+    """
+    return clean_string(gemmi.cif.as_string(string))
+
+
+def _get_cooling_device(cif: CifContainer) -> str:
+    olx = gstr(cif['_olex2_diffrn_ambient_temperature_device'])
+    iucr = gstr(cif['_diffrn_measurement_ambient_temperature_device_make'])
+    if olx and iucr:
+        return iucr
+    if olx:
+        return olx
+    elif iucr:
+        return iucr
+    else:
+        return ''
+
+
+class FormatMixin():
+
+    def bold(self, run: Run):
+        r = run.bold = True
+        return r
+
+
+
+class SpaceChar():
+    def __init__(self, paragraph: Paragraph):
+        self.p = paragraph
+
+    def regular(self) -> None:
+        self.p.add_run(' ')
+
+    def protected(self):
+        self.p.add_run(protected_space)
+
+
+class RefinementDetails():
+    def __init__(self, cif: CifContainer, document: Document):
+        ph = document.add_paragraph(style='Heading 2')
+        ph.add_run(text=fr"Refinement details for {cif.block.name}")
+        p = document.add_paragraph()
+        try:
+            p.style = document.styles['fliesstext']
+        except KeyError:
+            print('DBG> Text style not found')
+        text = ' '.join(cif['_refine_special_details'].splitlines(keepends=False))
+        if cif['_olex2_refine_details']:
+            text += ' '.join(cif['_olex2_refine_details'].splitlines(keepends=False))
+        # Replacing semicolon, because it can damage the CIF:
+        text = text.replace(';', '.')
+        p.add_run(string_to_utf8(text).strip())
+
+
+def get_inf_article(next_word: str) -> str:
+    if not next_word:
+        return 'a'
+    voc = 'aeiou'
+    return 'an' if next_word[0].lower() in voc else 'a'
+
+
+def get_distance_unit(picometers: bool) -> str:
+    if picometers:
+        return 'pm'
+    else:
+        return angstrom
+
+
+def get_volume_unit(picometers: bool) -> str:
+    if picometers:
+        return 'nm'
+    else:
+        return angstrom
+
+
+def format_float_with_decimal_places(number: float, places=2) -> str:
+    try:
+        fnum = float(number)
+        return f'{fnum:.{places}f}'
+    except ValueError:
+        return f'{number}'
+
+
+def utf8(text: str) -> str:
+    """A Jinja2 filter for CIF to utf8"""
+    return string_to_utf8(text)
+
+
+def format_radiation(radiation_type: str) -> list:
+    radtype = list(radiation_type.partition("K"))
+    if len(radtype) > 2:
+        radtype[2] = retranslate_delimiter(radtype[2])
+        return radtype
+    else:
+        return radtype
+
+
+def make_report_text(cif, document: Document) -> references.ReferenceList:
+    paragr = document.add_paragraph()
+    try:
+        paragr.style = document.styles['fliesstext']
+    except KeyError:
+        print('DBG> Text style not found')
+    ref = references.ReferenceList(paragr)
+    return ref

{finalcif-141 → finalcif-142}/finalcif/report/tables.py

@@ -628,8 +628,6 @@ def add_sum_formula(formula_paragraph: Paragraph, sum_formula: str) -> None:
 def add_decimal_tab(num_string: str) -> str:
     """
     Adds a tab character in front of the decimal point in order to get proper alignment of the tabstops.
-    >>> add_decimal_tab('-0.123')
-    '-0\\t.123'
     """
     return '\t.'.join(num_string.split('.'))