finalcif 136__tar.gz → 138__tar.gz

{finalcif-136 → finalcif-138}/.gitignore

@@ -219,3 +219,4 @@ test-data/1000007-multi-multitable.docx
 test-data/report_1000007-multi-finalcif.docx
 test.html
 
+work/~$test.docx

{finalcif-136 → finalcif-138}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: finalcif
-Version: 136
+Version: 138
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues
@@ -11,7 +11,7 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Requires-Dist: altgraph
 Requires-Dist: certifi
 Requires-Dist: chardet

finalcif-138/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 138

{finalcif-136 → finalcif-138}/finalcif/appwindow.py

@@ -13,18 +13,20 @@ from contextlib import suppress
 from datetime import datetime
 from math import sin, radians
 from pathlib import Path, WindowsPath
-from shutil import which
 from typing import Union, Dict, Tuple, List, Optional
 
 import gemmi.cif
-import requests  # type: ignore
-from PyQt5 import QtCore, QtGui, QtWebEngineWidgets
+import requests
+from PyQt5 import QtCore, QtGui, QtWebEngineWidgets, QtWidgets
 from PyQt5.QtCore import Qt, QEvent
-from PyQt5.QtWidgets import QMainWindow, QShortcut, QCheckBox, QListWidgetItem, QApplication, \
-    QPlainTextEdit, QFileDialog, QMessageBox, QScrollBar
+from PyQt5.QtWidgets import (QMainWindow, QShortcut, QCheckBox, QListWidgetItem, QApplication,
+                             QPlainTextEdit, QFileDialog, QMessageBox, QScrollBar)
 from gemmi import cif
 
 from finalcif import VERSION
+# QtCore.QCoreApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling)
+# QtCore.QCoreApplication.setAttribute(QtCore.Qt.AA_ShareOpenGLContexts)
+from finalcif.cif.checkcif.checkcif import MyHTMLParser, AlertHelp, CheckCif
 from finalcif.cif.cif_file_io import CifContainer, GemmiError
 from finalcif.cif.cod.deposit import CODdeposit
 from finalcif.cif.text import utf8_to_str, quote
@@ -67,7 +69,6 @@ if app is None:
     app = QApplication([])
 with suppress(ImportError):
     import qtawesome as qta
-from finalcif.cif.checkcif.checkcif import MyHTMLParser, AlertHelp, CheckCif
 
 
 class AppWindow(QMainWindow):
@@ -633,10 +634,9 @@ class AppWindow(QMainWindow):
 
     def setTextEditSizes(self):
         for ui in [self.ui.Spacegroup_top_LineEdit, self.ui.CCDCNumLineEdit, self.ui.SumFormMainLineEdit]:
-            ui.setFixedHeight(self.ui.appendCifPushButton.height() + 6)
-            ui.setFixedHeight(self.ui.appendCifPushButton.height() + 6)
-            ui.setFixedHeight(self.ui.appendCifPushButton.height() + 6)
+            ui.setFixedHeight(self.ui.appendCifPushButton.height())
             vScrollBar = ui.verticalScrollBar()
+            # Scroll down a bit, or text will not be in the vertical center:
             vScrollBar.triggerAction(QScrollBar.SliderSingleStepAdd)
 
     def moveEvent(self, a0: QtGui.QMoveEvent) -> None:
@@ -1035,7 +1035,7 @@ class AppWindow(QMainWindow):
                               log_widget=self.ui.CheckCifLogPlainTextEdit,
                               output_widget=self.ui.CheckcifPlaintextEdit,
                               cif_file=self.cif.fileobj)
-        if not Path(which(runner.platon_exe)).exists():
+        if runner.platon_exe is not None and not Path(runner.platon_exe).exists():
             self.ui.CheckCifLogPlainTextEdit.setPlainText('\nPlaton executable not found!')
             self.ui.CheckCifLogPlainTextEdit.appendPlainText(
                 'You can download Platon at http://www.platonsoft.nl/platon/\n')
@@ -1135,12 +1135,20 @@ class AppWindow(QMainWindow):
                     make_multi_tables(cif=self.cif, output_filename=str(multi_table_document))
             else:
                 print('Report with templates')
-                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()))
-                # t = TemplatedReport(format=ReportFormat.HTML, options=self.options, cif=self.cif)
-                # t.make_templated_html_report(options=self.options, picfile=picfile)
+                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
         except FileNotFoundError as e:
@@ -1308,7 +1316,7 @@ class AppWindow(QMainWindow):
                 previous_values.append(loop2.values)
             for loop in self.cif.loops:
                 if loop.values not in previous_values:
-                    changes_cif.add_loop_to_cif(loop_tags=loop.tags, loop_values=loop.values)
+                    changes_cif.add_loop_to_cif(loop_tags=loop.tags, row_values=loop.values)
             changes_cif.save(filename=self.finalcif_changes_filename)
 
     def get_changes_cif(self, finalcif_changes_filename: Path) -> CifContainer:
@@ -1336,7 +1344,7 @@ class AppWindow(QMainWindow):
                 self.add_row(key=key, value=value)
                 self.ui.cif_main_table.setText(key=key, column=Column.EDIT, color=None, txt=value)
         for loop in changes.loops:
-            self.cif.add_loop_to_cif(loop_tags=loop.tags, loop_values=loop.values)
+            self.cif.add_loop_to_cif(loop_tags=loop.tags, row_values=loop.values)
         return True
 
     def is_row_a_cif_item(self, vhead: str) -> bool:
@@ -1513,6 +1521,7 @@ class AppWindow(QMainWindow):
             raise
             # unable_to_open_message(Path(self.cif.filename), not_ok)
         self.load_recent_cifs_list()
+        self.set_vertical_header_width()
         if self.options.track_changes and load_changes:
             changes_exist = False
             if self.changes_cif_has_zero_size():
@@ -1557,6 +1566,16 @@ class AppWindow(QMainWindow):
             t = QtCore.QTimer(self)
             t.singleShot(1000, self.check_cecksums)
 
+    def set_vertical_header_width(self):
+        """
+        Sets the width of the vertical header to the length of the longest string in the list.
+        """
+        vheader: QtWidgets.QHeaderView = self.ui.cif_main_table.verticalHeader()
+        fm = QtGui.QFontMetrics(vheader.font(), self)
+        # noinspection PyTypeChecker
+        longest_string: str = max(self.ui.cif_main_table.vheaderitems, key=len)
+        vheader.setMaximumWidth(fm.width(longest_string + 'O'))
+
     def changes_cif_has_values(self) -> bool:
         try:
             return not self.get_changes_cif(self.finalcif_changes_filename).is_empty()

{finalcif-136 → finalcif-138}/finalcif/cif/cif_dict_foo.py

@@ -21,6 +21,15 @@ def format_definition(definition: str):
     return newdef
 
 
+formats = {
+    'char' : 'string',
+    'uchar': 'case-insensitive string',
+    'numb' : 'number (int or float)',
+    'null' : '? (unknown)' or '. (not applicable)',
+    ''     : '--'
+}
+
+
 def process_cif_dict(cdic):
     """
     Creates a dictionary with cif keywords as key and help text as value.
@@ -36,6 +45,7 @@ def process_cif_dict(cdic):
                 example_detail = item.get('_example_detail', '')
                 enumeration = item.get('_enumeration', '')
                 enumeration_detail = item.get('_enumeration_detail', '')
+                default = item.get('_enumeration_default', '')
                 if example:
                     if isinstance(example, list) and not enumeration_detail:
                         example = '\n'.join([str(x) for x in example])
@@ -52,15 +62,29 @@ def process_cif_dict(cdic):
                             ["{}\n\t{}\n".format(str(x), str(y)) for x, y in zip(enumeration, enumeration_detail)])
                     enumeration = format_definition(escape(str(enumeration)))
                     definition = '{}\n\n<h3>Example:</h3>\n{}'.format(definition, enumeration)
+                type_format = item.get("_type", "")
+                enum_range = item.get('_enumeration_range', '')
                 if isinstance(name, list):
                     for n in name:
                         # For keys like 'atom_site_aniso_b_[]' where the name has several subnames:
-                        alldic[n] = '<pre><h2>{}</h2>{}</pre>'.format(n, format_definition(definition))
+                        alldic[n] = help_text(definition, n, type_format, enum_range, default)
                 else:
-                    alldic[name] = '<pre><h2>{}</h2>{}</pre>'.format(name, format_definition(definition))
+                    alldic[name] = help_text(definition, name, type_format, enum_range, default)
     return alldic
 
 
+def help_text(definition: str, name: str, type_format: str, enum_range: str, enum_default) -> str:
+    if enum_range.endswith(':'):
+        enum_range = enum_range + '∞'
+    limits = f'\n<br><p><h4>Limits:</h4> {enum_range} </p>'
+    default = f'\n<br><p><h4>Default:</h4> {enum_default} </p>'
+    return (f'<pre><h2>{name}</h2>{format_definition(definition)}</pre>'
+            f'\n<br><p><h4>Type:</h4> {formats.get(type_format, "")}</p>'
+            f'{limits if enum_range else ""}'
+            f'{default if enum_default else ""}'
+            )
+
+
 def load_cif_as_dictionary(link, path_to_cif):
     if not path_to_cif.exists():
         get_dictionary_cif(link, path_to_cif)

{finalcif-136 → finalcif-138}/finalcif/cif/cif_file_io.py

@@ -13,6 +13,7 @@ from typing import Dict, List, Tuple, Union, Generator
 
 import gemmi
 from gemmi.cif import as_string, Document, Loop
+from packaging.version import Version
 from shelxfile import Shelxfile
 
 from finalcif.cif.cif_order import order, special_keys
@@ -39,6 +40,8 @@ class CifContainer():
             new_block: Create a new block (new file) if a name is given. Otherwise, just
                        the existing document is opened.
         """
+        self._hkl_file: str = ''
+        self._abs_hkl_details: Dict[str, str] = {}
         if isinstance(file, str):
             self.fileobj = Path(file)
         elif isinstance(file, Path):
@@ -94,7 +97,7 @@ class CifContainer():
         The suffix needs '-finalcif' in order to contain the finalcif ending.
         "foo/bar/baz-finalcif.cif"
 
-        :param forece_strip: Forces to strip the filename also after the '-finalcif' string.
+        :param force_strip: Forces to strip the filename also after the '-finalcif' string.
         """
         file_witout_finalcif = strip_finalcif_of_name(Path(self.filename).stem, till_name_ends=force_strip)
         filename = self.path_base.joinpath(Path(prefix + file_witout_finalcif + suffix))
@@ -141,7 +144,9 @@ class CifContainer():
 
     @property
     def hkl_extra_info(self):
-        return self._abs_hkl_details()
+        if not self._abs_hkl_details:
+            self._abs_hkl_details = self._sadabs_hkl_details()
+        return self._abs_hkl_details
 
     def check_hkl_min_max(self) -> None:
         if not all([self['_diffrn_reflns_limit_h_min'], self['_diffrn_reflns_limit_h_max'],
@@ -198,8 +203,8 @@ class CifContainer():
         """
         This method returns an empty string when the item value is '?'
         """
-        if self.block.find_value(item):
-            return as_string(self.block.find_value(item))
+        if value := self.block.find_value(item):
+            return as_string(value)
         else:
             return ''
 
@@ -255,15 +260,17 @@ class CifContainer():
             print(f'File {filename} is empty.')
             return
         self.order_cif_keys()
-        print('Saving to', Path(filename).resolve())
-        """
-        # For later gemmi versions:
-        options = gemmi.cif.WriteOptions()
-        options.prefer_pairs = True
-        options.compact = False
-        options.align_pairs = 33
-        options.align_loops = 30"""
-        self.doc.write_file(str(filename), gemmi.cif.Style.Indent35)
+        print('Saving CIF to', Path(filename).resolve())
+        if Version(gemmi.__version__) > Version('0.6.3'):
+            options = gemmi.cif.WriteOptions()
+            options.prefer_pairs = False
+            options.compact = False
+            options.align_pairs = 33
+            options.align_loops = 15
+            options.misuse_hash = False
+            self.doc.write_file(str(filename), options=options)
+        else:
+            self.doc.write_file(str(filename), gemmi.cif.Style.Indent35)
 
     def order_cif_keys(self) -> None:
         """
@@ -304,10 +311,14 @@ class CifContainer():
     def hkl_file(self) -> str:
         hkl_loop: Loop = self.get_loop('_diffrn_refln_index_h')
         if hkl_loop and hkl_loop.width() > 4:
-            return self._hkl_from_cif_format(hkl_loop)
+            if not self._hkl_file:
+                self._hkl_file = self._hkl_from_cif_format(hkl_loop)
+            return self._hkl_file
         else:
             # returns an empty string if no cif hkl was found:
-            return self._hkl_from_shelx()
+            if not self._hkl_file:
+                self._hkl_file = self._hkl_from_shelx()
+            return self._hkl_file
 
     def _hkl_from_cif_format(self, hkl_loop: Loop) -> str:
         hkl_list = []
@@ -333,7 +344,7 @@ class CifContainer():
             return ''
 
     @property
-    def hkl_as_cif(self):
+    def hkl_as_cif(self) -> str:
         return HKL(self.hkl_file, self.block.name, hklf_type=self.hklf_number).hkl_as_cif
 
     @property
@@ -362,7 +373,7 @@ class CifContainer():
             return self.hkl_file
 
     @staticmethod
-    def _find_line_of_000(lines: str):
+    def _find_line_of_000(lines: str) -> int:
         pattern = re.compile(r'^\s+0\s+0\s+0\s+0.*')
         for num, line in enumerate(lines.splitlines(keepends=False)):
             found = pattern.match(line)
@@ -370,7 +381,7 @@ class CifContainer():
                 return num
         return 0
 
-    def _abs_hkl_details(self) -> Dict[str, str]:
+    def _sadabs_hkl_details(self) -> Dict[str, str]:
         """
         This method tries to determine the information witten at the end of a cif hkl file by sadabs.
         """
@@ -411,7 +422,7 @@ class CifContainer():
                 all_sadabs_items[key] = gemmi.cif.as_string(val).strip()
         return all_sadabs_items
 
-    def normal_search(self, hkl):
+    def normal_search(self, hkl) -> int:
         pattern = re.compile(r'\s+0\s+0\s+0\s+0')
         found = pattern.search(hkl)
         if found:
@@ -420,7 +431,7 @@ class CifContainer():
             zero_reflection_position = 0
         return zero_reflection_position
 
-    def reversed_search(self, hkl_splitted: List):
+    def reversed_search(self, hkl_splitted: List[str]) -> int:
         pattern = re.compile(r'\s+0\s+0\s+0\s+0')
         zero_reflection_position = 0
         for num, line in enumerate(reversed(hkl_splitted)):
@@ -463,14 +474,20 @@ class CifContainer():
                 loops.append(b.loop)
         return loops
 
-    def add_loop_to_cif(self, loop_tags: List[str], loop_values: Union[list, tuple]) -> gemmi.cif.Loop:
+    def add_loop_to_cif(self, loop_tags: List[str], row_values: Union[List[str], Tuple[str]]) -> gemmi.cif.Loop:
         gemmi_loop = self.init_loop(loop_tags)
-        for row in list(grouper(loop_values, len(loop_tags))):
+        for row in list(grouper(row_values, len(loop_tags))):
             gemmi_loop.add_row(row)
         return gemmi_loop
 
+    def add_loop_from_columns(self, loop_tags: List[str],
+                              column_values: Union[List[List[str]], Tuple[Tuple[str]]]) -> gemmi.cif.Loop:
+        gemmi_loop = self.init_loop(loop_tags)
+        gemmi_loop.set_all_values(column_values)
+        return gemmi_loop
+
     @property
-    def n_loops(self):
+    def n_loops(self) -> int:
         return len(self.loops)
 
     def get_loop(self, key_in_loop: str) -> gemmi.cif.Loop:
@@ -483,7 +500,7 @@ class CifContainer():
         return self.block.init_loop('', loop_keywords)
 
     @property
-    def z_value(self):
+    def z_value(self) -> float:
         return self.atomic_struct.cell.volume / self.atomic_struct.cell.volume_per_image()
 
     @property
@@ -638,7 +655,7 @@ class CifContainer():
     @property
     def is_centrosymm(self) -> bool:
         """
-        Whether a structuere is centro symmetric or not.
+        Whether a structure is centrosymmetric or not.
         """
         if not self.symmops or self.symmops == ['']:
             # Do not crash without symmops
@@ -749,8 +766,7 @@ 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, self._has_publ_flag_set(publ_loop)):
+            if (without_h and (self.ishydrogen(label1) or self.ishydrogen(label2)) or self.yes_not_set(publ)):
                 continue
             else:
                 yield bond(label1=label1, label2=label2, dist=dist, symm=self.checksymm(symm))
@@ -773,9 +789,6 @@ class CifContainer():
                 return p.torsang
         return None
 
-    def _has_publ_flag_set(self, publ_loop: gemmi.cif.Column) -> bool:
-        return any([x[0].lower() == 'y' for x in list(publ_loop) if x])
-
     def angles(self, without_H: bool = False) -> Generator:
         label1 = self.block.find_loop('_geom_angle_atom_site_label_1')
         label2 = self.block.find_loop('_geom_angle_atom_site_label_2')
@@ -787,9 +800,8 @@ class CifContainer():
         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):
-            if without_H and (
-                    self.ishydrogen(label1) or self.ishydrogen(label2) or self.ishydrogen(label3)) or \
-                    self.yes_not_set(publ, self._has_publ_flag_set(publ_loop)):
+            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,
@@ -837,9 +849,8 @@ class CifContainer():
                                                                                              torsang, symm1, symm2,
                                                                                              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, self._has_publ_flag_set(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)):
                 continue
             yield tors(label1=label1, label2=label2, label3=label3, label4=label4, torsang=torsang,
                        symm1=self.checksymm(symm1),
@@ -859,14 +870,14 @@ class CifContainer():
         publ_loop = self.block.find_loop('_geom_hbond_publ_flag')
         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):
-            if self.yes_not_set(publ, self._has_publ_flag_set(publ_loop)):
+        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)):
+            if self.yes_not_set(publ):
                 continue
             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, publ_flag):
-        return publ_flag and publ not in {'y', 'yes'} or publ in {'n', 'no'}
+    def yes_not_set(self, publ: str):
+        return publ not in {'y', 'yes', '?', '.'} or publ in {'n', 'no'}
 
     def key_value_pairs(self) -> List[Tuple[str, str]]:
         """
@@ -957,7 +968,6 @@ class CifContainer():
 if __name__ == '__main__':
     # c = CifContainer('../41467_2015.cif')
     # c = CifContainer('test-data/p21c.cif')
-    from pprint import pp
 
     c = CifContainer('test-data/DK_Zucker2_0m.cif')
     c.load_this_block(len(c.doc) - 1)

{finalcif-136 → finalcif-138}/finalcif/cif/cif_order.py

@@ -17,6 +17,13 @@ special_keys = ['_iucr_refine_instructions_details',
                 ]
 
 order = [
+    '_audit_update_record',
+    '_audit_contact_author',
+    '_audit_contact_author_name',
+    '_audit_contact_author_phone',
+    '_audit_contact_author_email',
+    '_audit_contact_author_fax',
+    '_audit_contact_author_address',
     '_audit_author_id',
     '_audit_author_id_audit',
     '_audit_author_name',
@@ -128,7 +135,6 @@ order = [
     '_publ_contact_author_id_orcid',
     '_publ_contact_author_footnote',
 
-
     '_shelx_SHELXL_version_number',
     '_chemical_name_systematic',
     '_chemical_name_common',
@@ -341,4 +347,17 @@ order = [
     '_geom_details',
     '_geom_special_details',
 
+    '_bruker_diffrn_runs_wavelength',
+    '_bruker_diffrn_runs_temperature',
+    '_bruker_diffrn_runs_current',
+    '_bruker_diffrn_runs_voltage',
+    '_bruker_diffrn_runs_images',
+    '_bruker_diffrn_runs_time',
+    '_bruker_diffrn_runs_width',
+    '_bruker_diffrn_runs_axis',
+    '_bruker_diffrn_runs_chi',
+    '_bruker_diffrn_runs_phi',
+    '_bruker_diffrn_runs_omega',
+    '_bruker_diffrn_runs_theta',
+    '_bruker_diffrn_runs_distance',
 ]