finalcif 152__tar.gz → 154__tar.gz

{finalcif-152 → finalcif-154}/.gitignore

@@ -225,3 +225,5 @@ tests/examples/multi-multitable.docx
 tests/examples/report_multi-finalcif.docx
 tests/examples/work/cu_BruecknerJK_153F40_0m.lxt
 finalcif_keys_order.cif
+!/.python-version
+/platon/*.mod

finalcif-154/.python-version

@@ -0,0 +1 @@
+cpython@3.12

{finalcif-152 → finalcif-154}/Finalcif_installer_win.spec

@@ -2,6 +2,7 @@
 
 import sys
 from os import path
+#pyinstaller myapp.py --noconfirm --onedir --hidden-import PySide6.QtWebEngineWidgets --exclude-module PySide6.QtMultimedia
 
 block_cipher = None
 site_packages = next(p for p in sys.path if 'site-packages' in p)

{finalcif-152 → finalcif-154}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 152
+Version: 154
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues
@@ -14,19 +14,20 @@ Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires-Python: >=3.10
 Requires-Dist: certifi
 Requires-Dist: chardet
+Requires-Dist: charset-normalizer
 Requires-Dist: crossrefapi
 Requires-Dist: docxtpl
 Requires-Dist: gemmi
-Requires-Dist: hatchling>=1.27.0
+Requires-Dist: hatchling
 Requires-Dist: html2text
 Requires-Dist: lxml
 Requires-Dist: numpy
+Requires-Dist: packaging
 Requires-Dist: pefile
 Requires-Dist: pybind11
 Requires-Dist: pyenchant
-Requires-Dist: pyqt5
-Requires-Dist: pyqt5-qt5==5.15.2
-Requires-Dist: pyside6<6.9
+Requires-Dist: pyside6
+Requires-Dist: pyside6-addons
 Requires-Dist: python-docx
 Requires-Dist: qtawesome
 Requires-Dist: qtpy

finalcif-154/finalcif/__init__.py

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

{finalcif-152 → finalcif-154}/finalcif/appwindow.py

@@ -14,12 +14,16 @@ from datetime import datetime
 from math import sin, radians
 from pathlib import Path, WindowsPath
 
-import gemmi.cif
+import gemmi
+
+if hasattr(gemmi, 'set_leak_warnings'):
+    gemmi.set_leak_warnings(False)
+
 import requests
-from PySide6 import QtCore, QtGui, QtWebEngineWidgets, QtWidgets
-from PySide6.QtCore import Qt, QEvent
-from PySide6.QtWidgets import (QMainWindow, QCheckBox, QListWidgetItem, QApplication,
-                               QPlainTextEdit, QFileDialog, QMessageBox, QScrollBar)
+from qtpy import QtCore, QtGui, QtWebEngineWidgets, QtWidgets, compat
+from qtpy.QtCore import Qt, QEvent
+from qtpy.QtWidgets import (QMainWindow, QCheckBox, QListWidgetItem, QApplication,
+                            QPlainTextEdit, QMessageBox, QScrollBar)
 from gemmi import cif
 
 from finalcif import VERSION
@@ -123,6 +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)
@@ -417,11 +440,12 @@ class AppWindow(QMainWindow):
     def export_all_templates(self, filename: Path | None = None):
         import pickle
         if not filename:
-            filename, _ = QFileDialog.getSaveFileName(dir=str(Path(self.get_last_workdir()).joinpath(
-                f'finalcif_templates_{time.strftime("%Y-%m-%d")}.dat')),
-                selectedFilter="Template File (*.dat)",
-                filter="Template File (*.dat)",
-                caption='Save templates')
+            filename, _ = compat.getsavefilename(parent=self,
+                                                 basedir=str(Path(self.get_last_workdir()).joinpath(
+                                                     f'finalcif_templates_{time.strftime("%Y-%m-%d")}.dat')),
+                                                 selectedfilter="Template File (*.dat)",
+                                                 filters="Template File (*.dat)",
+                                                 caption='Save templates')
         if not filename:
             return
         templates = {'text'               : self.export_raw_text_templates(),
@@ -440,10 +464,11 @@ class AppWindow(QMainWindow):
     def import_all_templates(self, filename: Path | None = None):
         import pickle
         if not filename:
-            filename, _ = QFileDialog.getOpenFileName(dir=self.get_last_workdir(),
-                                                      selectedFilter="Template File (*.dat)",
-                                                      filter="Template File (*.dat)",
-                                                      caption='Save templates')
+            filename, _ = compat.getopenfilename(parent=self,
+                                                 basedir=self.get_last_workdir(),
+                                                 selectedfilter="Template File (*.dat)",
+                                                 filters="Template File (*.dat)",
+                                                 caption='Save templates')
         if not filename:
             return
         try:
@@ -495,7 +520,7 @@ class AppWindow(QMainWindow):
         """
         Imports a text template from a CIF file.
         """
-        filename = cif_file_open_dialog()
+        filename = cif_file_open_dialog(parent=self)
         if not filename:
             return
         try:
@@ -536,7 +561,8 @@ class AppWindow(QMainWindow):
         if not filename.strip():
             return
         try:
-            doc.write_file(filename, style=cif.Style.Indent35)
+            write_options = cif.WriteOptions(cif.Style.Indent35)
+            doc.write_file(filename, options=write_options)
             # Path(filename).write_text(doc.as_string(cif.Style.Indent35))
         except PermissionError:
             if Path(filename).is_dir():
@@ -1066,6 +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)
@@ -1103,9 +1130,10 @@ class AppWindow(QMainWindow):
         if file:
             self.report_picture_path = Path(file)
         else:
-            filename, _ = QFileDialog.getOpenFileName(filter="Image Files (*.png *.jpg *.jpeg *.bmp "
-                                                             "*.gif *.tif *.tiff *.eps *.emf *.wmf)",
-                                                      caption='Open a Report Picture')
+            filename, _ = compat.getopenfilename(parent=self,
+                                                 filters="Image Files (*.png *.jpg *.jpeg *.bmp "
+                                                         "*.gif *.tif *.tiff *.eps *.emf *.wmf)",
+                                                 caption='Open a Report Picture')
             self.set_report_picture_path(filename)
 
     def set_report_picture_path(self, filename: str):
@@ -1409,7 +1437,7 @@ class AppWindow(QMainWindow):
         """
         imp_cif: CifContainer | None = None
         if not filename:
-            filename = cif_file_open_dialog(filter="CIF file (*.cif *.pcf *.cif_od *.cfx *.sqf)")
+            filename = cif_file_open_dialog(parent=self, filter="CIF file (*.cif *.pcf *.cif_od *.cfx *.sqf)")
         if not filename:
             return
         try:
@@ -1460,7 +1488,7 @@ class AppWindow(QMainWindow):
         """
         self.ui.datanameComboBox.blockSignals(True)
         if not filepath:
-            filepath = Path(cif_file_open_dialog(last_dir=self.get_last_workdir()))
+            filepath = Path(cif_file_open_dialog(parent=self, last_dir=self.get_last_workdir()))
             if not filepath.is_file():
                 return
         self.set_path_display_in_file_selector(str(filepath))
@@ -1669,7 +1697,7 @@ class AppWindow(QMainWindow):
         self.load_cif_file(filepath=self.cif.fileobj, load_changes=False)
 
     def get_file_from_dialog(self) -> Path | None:
-        fp = cif_file_open_dialog(last_dir=self.get_last_workdir())
+        fp = cif_file_open_dialog(parent=self, last_dir=self.get_last_workdir())
         if not fp:
             return None
         filepath = Path(fp)

{finalcif-152 → 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-152 → finalcif-154}/finalcif/cif/checkcif/checkcif.py

@@ -14,7 +14,7 @@ from html.parser import HTMLParser
 from pathlib import Path
 
 import requests
-from PySide6.QtCore import QThread, Signal
+from qtpy.QtCore import QThread, Signal
 from requests.exceptions import MissingSchema
 
 from finalcif.cif.cif_file_io import CifContainer

{finalcif-152 → 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
@@ -12,6 +13,12 @@ from contextlib import suppress
 from pathlib import Path
 
 import gemmi
+
+from finalcif.cif import atoms
+
+if hasattr(gemmi, 'set_leak_warnings'):
+    gemmi.set_leak_warnings(False)
+
 from gemmi.cif import as_string, Document, Loop
 from packaging.version import Version
 from shelxfile import Shelxfile
@@ -20,8 +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):
@@ -41,6 +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):
@@ -68,6 +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)
 
@@ -119,7 +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
 
@@ -151,9 +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
@@ -207,18 +214,20 @@ class CifContainer:
         return doc
 
     def cif_as_string(self, without_hkl=False) -> str:
+        opt = gemmi.cif.WriteOptions()
+        opt.align_pairs = 33
         if without_hkl:
             # return a copy, do not delete hkl from original:
             doc = gemmi.cif.Document()
-            doc.parse_string(self.doc.as_string(style=gemmi.cif.Style.Indent35))
+            doc.parse_string(self.doc.as_string(options=opt))
             for block in doc:
                 if block.find_pair_item('_shelx_hkl_file'):
                     block.find_pair_item('_shelx_hkl_file').erase()
                 if block.find_pair_item('_shelx_fcf_file'):
                     block.find_pair_item('_shelx_fcf_file').erase()
-            return doc.as_string(style=gemmi.cif.Style.Indent35)
+            return doc.as_string(options=opt)
         else:
-            return self.doc.as_string(style=gemmi.cif.Style.Indent35)
+            return self.doc.as_string(options=opt)
 
     def __getitem__(self, item: str) -> str:
         """
@@ -251,7 +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):
@@ -272,13 +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')
@@ -708,18 +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')
-        occ = self.block.find_loop('_atom_site_occupancy')
-        u_eq = self.block.find_loop('_atom_site_U_iso_or_equiv')
+        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') 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 if part else ('0',) * len(labels),
-                                                         occ if occ else ('1.000000',) * len(labels),
-                                                         u_eq, strict=True):
+                                                         part,
+                                                         occ,
+                                                         u_eq, strict=False):
             if without_h and self.ishydrogen(label):
                 continue
             if self.picometer:
@@ -755,7 +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)
@@ -809,9 +817,9 @@ class CifContainer:
         label2 = self.block.find_loop('_geom_bond_atom_site_label_2')
         dist = self.block.find_loop('_geom_bond_distance')
         symm = self.block.find_loop('_geom_bond_site_symmetry_2')
-        publ_loop = self.block.find_loop('_geom_bond_publ_flag')
+        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:
@@ -847,19 +855,22 @@ class CifContainer:
         angle_val = self.block.find_loop('_geom_angle')
         symm1 = self.block.find_loop('_geom_angle_site_symmetry_1')
         symm2 = self.block.find_loop('_geom_angle_site_symmetry_3')
-        publ_loop = self.block.find_loop('_geom_angle_publ_flag')
+        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)))
@@ -892,14 +903,15 @@ class CifContainer:
         symm2 = self.block.find_loop('_geom_torsion_site_symmetry_2')
         symm3 = self.block.find_loop('_geom_torsion_site_symmetry_3')
         symm4 = self.block.find_loop('_geom_torsion_site_symmetry_4')
-        publ_loop = self.block.find_loop('_geom_torsion_publ_flag')
+        publ_loop = self.block.find_loop('_geom_torsion_publ_flag') or len(label1) * ['?']
         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
+        for label1, label2, label3, label4, torsang, symm1, symm2, symm3, symm4, publ in zip(label1, label2, label3,
                                                                                              label4,
                                                                                              torsang, symm1, symm2,
                                                                                              symm3,
-                                                                                             symm4, publ_loop, strict=True):
+                                                                                             symm4, publ_loop,
+                                                                                             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
@@ -918,11 +930,11 @@ class CifContainer:
         dist_da = self.block.find_loop('_geom_hbond_distance_DA')
         angle_dha = self.block.find_loop('_geom_hbond_angle_DHA')
         symm = self.block.find_loop('_geom_hbond_site_symmetry_A')
-        publ_loop = self.block.find_loop('_geom_hbond_publ_flag')
+        publ_loop = self.block.find_loop('_geom_hbond_publ_flag') or len(label_d) * ['?']
         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:
@@ -939,7 +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:
         """
@@ -965,7 +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-152 → finalcif-154}/finalcif/cif/cod/deposit.py

@@ -10,7 +10,7 @@ from pathlib import Path
 from urllib.parse import urlparse
 
 import requests
-from PySide6.QtWidgets import QTableWidgetItem, QTextBrowser, QFrame
+from qtpy.QtWidgets import QTableWidgetItem, QTextBrowser, QFrame
 
 from finalcif.cif.cif_file_io import CifContainer
 from finalcif.cif.cod.deposition_list import CODFetcher
@@ -210,7 +210,7 @@ class CODdeposit:
             if f.authenticated:
                 self.token_valid = True
             else:
-                self.ui.statusBar.showMessage('Unable to login. Check username/password.', timeout=12000)
+                self.ui.statusBar.showMessage('Unable to login. Check username/password.', 12000)
         f.get_table_data_by_token(self._cod_token)
         parser = MyCODStructuresParser()
         parser.feed(f.table_html)
@@ -346,14 +346,14 @@ class CODdeposit:
         self.ui.depositionOptionsStackedWidget.setCurrentIndex(self.deposition_type_to_int(deposition_type))
 
     def reset_deposit_button_state_to_initial(self):
-        self.ui.depositCIFpushButton.disconnect()
+        self.ui.depositCIFpushButton.clicked.disconnect()
         self.ui.depositOutputTextBrowser.clear()
         self.ui.depositCIFpushButton.setText("Deposit CIF")
         self.ui.depositCIFpushButton.clicked.connect(self._init_deposit)
 
     def set_deposit_button_to_try_again(self):
         self.ui.depositCIFpushButton.setText("Try Again")
-        self.ui.depositCIFpushButton.disconnect()
+        self.ui.depositCIFpushButton.clicked.disconnect()
         self.ui.depositCIFpushButton.clicked.connect(lambda: self.switch_to_page(self.deposition_type))
 
     def log_response_text(self, resp: requests.Response, *args, **kwargs):
@@ -380,7 +380,7 @@ class CODdeposit:
         self.user_email = text
 
     def _set_external_hkl_file(self) -> None:
-        file = cif_file_open_dialog(filter="HKL file (*.hkl *.fcf)")
+        file = cif_file_open_dialog(parent=self, filter="HKL file (*.hkl *.fcf)")
         if file.endswith('.hkl'):
             if self.cif.res_file_data:
                 hklf = self.cif._hklf_number_from_shelxl_file()

{finalcif-152 → finalcif-154}/finalcif/ciforder/order.py

@@ -6,7 +6,7 @@ from pathlib import Path
 from typing import TYPE_CHECKING
 
 import gemmi
-from PySide6 import QtWidgets, QtCore
+from qtpy import QtWidgets, QtCore
 
 from finalcif.cif import cif_order
 from finalcif.ciforder.order_ui import Ui_CifOrderForm

{finalcif-152 → finalcif-154}/finalcif/ciforder/order_ui.py

@@ -6,14 +6,14 @@
 ##
 ################################################################################
 
-from PySide6.QtCore import (QCoreApplication, QDate, QDateTime, QLocale,
+from qtpy.QtCore import (QCoreApplication, QDate, QDateTime, QLocale,
     QMetaObject, QObject, QPoint, QRect,
     QSize, QTime, QUrl, Qt)
-from PySide6.QtGui import (QBrush, QColor, QConicalGradient, QCursor,
+from qtpy.QtGui import (QBrush, QColor, QConicalGradient, QCursor,
     QFont, QFontDatabase, QGradient, QIcon,
     QImage, QKeySequence, QLinearGradient, QPainter,
     QPalette, QPixmap, QRadialGradient, QTransform)
-from PySide6.QtWidgets import (QAbstractItemView, QApplication, QGridLayout, QHeaderView,
+from qtpy.QtWidgets import (QAbstractItemView, QApplication, QGridLayout, QHeaderView,
     QLabel, QPushButton, QSizePolicy, QSpacerItem,
     QTableWidget, QTableWidgetItem, QVBoxLayout, QWidget)
 

{finalcif-152 → finalcif-154}/finalcif/datafiles/shelx_lst.py

@@ -19,7 +19,7 @@ class SHELXTlistfile(ParserMixin):
             self.solutions = {}
             self.parse_file()
 
-    def parse_file(self):
+    def parse_file(self) -> None:
         """
          +  SHELXT  -  CRYSTAL STRUCTURE SOLUTION - VERSION 2018/2            +
         """
@@ -29,11 +29,15 @@ class SHELXTlistfile(ParserMixin):
                 if 'SHELXTL' in line:
                     self.version = 'SHELXT ' + line.split()[-1]
             if line.strip().startswith('R1  Rweak Alpha'):
-                for n in range(100):
-                    if not self._text[num + 1 + n]:
-                        break
-                    if self._text[num + 1]:
-                        self.solutions[self._text[num + 1 + n][58:76].strip()] = self._text[num + 1 + n][37:51].strip()
+                try:
+                    for n in range(100):
+                        if not self._text[num + 1 + n]:
+                            break
+                        if self._text[num + 1]:
+                            self.solutions[self._text[num + 1 + n][58:76].strip()] = self._text[num + 1 + n][37:51].strip()
+                except IndexError:
+                    return None
+        return None
 
 
 class SolutionProgram:
@@ -58,17 +62,22 @@ class SolutionProgram:
         except (TypeError, AttributeError):
             res = ''
         byxt = res.find('REM SHELXT solution in')
-        for x in xt_files:
-            shelxt = SHELXTlistfile(x.as_posix())
-            if shelxt.version and byxt:
-                self.method = 'direct'
-                self.solution_listfile = 'foo'  # x.name
-                return shelxt
         if byxt > 0:
+            for x in xt_files:
+                shelxt = SHELXTlistfile(x.as_posix())
+                if shelxt.version and byxt:
+                    self.method = 'direct'
+                    self.solution_listfile = 'foo'  # x.name
+                    return shelxt
             xt = SHELXTlistfile('')
             xt.version = "SHELXT (G. Sheldrick)"
             self.method = 'direct'
             return xt
+        if res.find('Best SHELXD solution'):
+            xt = SHELXTlistfile('')
+            xt.version = "SHELXD (G. Sheldrick)"
+            self.method = 'dual space'
+            return xt
         xt = SHELXTlistfile('')
         xt.version = "SHELXS (G. Sheldrick)"
         self.method = 'direct'

{finalcif-152 → finalcif-154}/finalcif/displaymol/molecule2D.py

@@ -5,9 +5,9 @@ from math import sqrt, cos, sin, dist
 from pathlib import Path
 
 import numpy as np
-from PySide6 import QtWidgets, QtCore, QtGui
-from PySide6.QtCore import Qt
-from PySide6.QtGui import QPainter, QPen, QBrush, QColor, QMouseEvent, QPalette, QImage, QResizeEvent, QWheelEvent
+from qtpy import QtWidgets, QtCore, QtGui
+from qtpy.QtCore import Qt
+from qtpy.QtGui import QPainter, QPen, QBrush, QColor, QMouseEvent, QPalette, QImage, QResizeEvent, QWheelEvent
 
 from finalcif.cif.atoms import get_radius_from_element, element2color
 from finalcif.cif.cif_file_io import CifContainer

{finalcif-152 → finalcif-154}/finalcif/displaymol/vtk_molecule.py

@@ -1,8 +1,8 @@
 import sys
 
 import vtk
-from PySide6 import QtWidgets, QtCore
-from PySide6.QtGui import QSurfaceFormat
+from qtpy import QtWidgets, QtCore
+from qtpy.QtGui import QSurfaceFormat
 from vtkmodules.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
 from vtkmodules.vtkCommonCore import vtkLookupTable
 from vtkmodules.vtkDomainsChemistry import vtkPeriodicTable