finalcif 153__tar.gz → 155__tar.gz

{finalcif-153 → finalcif-155}/.gitignore

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

{finalcif-153 → finalcif-155}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 153
+Version: 155
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues

finalcif-155/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 155

{finalcif-153 → finalcif-155}/finalcif/appwindow.py

@@ -127,6 +127,25 @@ class AppWindow(QMainWindow):
         if file:
             self.load_cif_file(file)
         self.load_recent_cifs_list()
+        self.ui.CheckcifPlaintextEdit.insertPlainText(
+            "\n"
+            "  Offline CheckCIF uses PLATON from Anthony L. Spek, Utrecht University, The Netherlands."
+            "\n"
+            "  https://platonsoft.nl\n"
+            "  \n"
+            "  Please cite PLATON in your publication if you use it.\n"
+            "  \n"
+            "  - PLATON References : \n"
+            "            Spek, A.L. (2003). J. Appl. Cryst. 36, 7-13.\n"
+            "            Spek, A.L. (2009). Acta Cryst. D65, 148-155.\n"
+            "            Spek, A.L. (2015). Acta Cryst. C71, 9-18.\n"
+            "            Spek, A.L. (2018). Inorg. Chim. Acta, 470, 232-237.\n"
+            "            Spek, A.L. (2020). Acta Cryst. E76, 1-11.\n"
+            "  \n"
+            "  \n"
+            "  - Recent versions of PLATON may be obtained from: https://platonsoft.nl/xraysoft\n"
+            "  "
+        )
         self.set_checkcif_output_font(self.ui.CheckcifPlaintextEdit)
         # To make file drag&drop working:
         self.setAcceptDrops(True)
@@ -902,7 +921,7 @@ class AppWindow(QMainWindow):
         url = QtCore.QUrl.fromLocalFile(str(self.htmlfile.resolve()))
         self.ui.MainStackedWidget.go_to_checkcif_page()
         self.ui.CheckCIFResultsTabWidget.setCurrentIndex(1)  # Index 1 is html page
-        self.checkcif_browser.load(url)
+        self.checkcif_browser.setHtml(self.htmlfile.resolve().read_text('utf-8', 'ignore'))
         self.ui.ResponsesTabWidget.setCurrentIndex(0)
         threading.Thread(target=self._display_structure_factor_report, args=(parser,)).start()
         # The picture file linked in the html file:
@@ -960,7 +979,8 @@ class AppWindow(QMainWindow):
         self.ckf = CheckCif(parent=self, cif=self.cif, outfile=self.htmlfile,
                             hkl_upload=(not self.ui.structfactCheckBox.isChecked()), pdf=False,
                             url=self.options.checkcif_url,
-                            full_iucr=self.ui.fullIucrCheckBox.isChecked())
+                            full_iucr=self.ui.fullIucrCheckBox.isChecked(),
+                            check_duplicates=self.ui.checkDuplicatesCheckBox.isChecked())
         self.ckf.progress.connect(self._ckf_progress)
         self.ckf.failed.connect(self._checkcif_failed)
         self.ckf.finished.connect(self._checkcif_finished)
@@ -1033,7 +1053,8 @@ class AppWindow(QMainWindow):
         self.ckf = CheckCif(parent=self, cif=self.cif, outfile=htmlfile,
                             hkl_upload=(not self.ui.structfactCheckBox.isChecked()),
                             pdf=True, url=self.options.checkcif_url,
-                            full_iucr=self.ui.fullIucrCheckBox.isChecked())
+                            full_iucr=self.ui.fullIucrCheckBox.isChecked(),
+                            check_duplicates=self.ui.checkDuplicatesCheckBox.isChecked())
         self.ckf.failed.connect(self._checkcif_failed)
         # noinspection PyUnresolvedReferences
         self.ckf.finished.connect(self._pdf_checkcif_finished)
@@ -1073,6 +1094,7 @@ class AppWindow(QMainWindow):
         runner.finished.connect(lambda: self.ui.CheckcifButton.setEnabled(True))
         runner.run_process()
         runner.formula.connect(self.add_moiety_furmula)
+        return None
 
     def add_moiety_furmula(self, formula_moiety):
         moiety = self.ui.cif_main_table.getTextFromKey(key='_chemical_formula_moiety', col=Column.CIF)

{finalcif-153 → finalcif-155}/finalcif/cif/atoms.py

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

{finalcif-153 → finalcif-155}/finalcif/cif/checkcif/checkcif.py

@@ -25,7 +25,7 @@ class CheckCif(QThread):
     failed = Signal(str)
 
     def __init__(self, parent, cif: CifContainer, outfile: Path, hkl_upload: bool = True,
-                 pdf: bool = False, url: str = '', full_iucr: bool = False):
+                 pdf: bool = False, url: str = '', full_iucr: bool = False, check_duplicates: bool = True):
         # hkl == False means no hkl upload
         super().__init__(parent=parent)
         self.hkl_upload = hkl_upload
@@ -34,6 +34,7 @@ class CheckCif(QThread):
         self.pdf = pdf
         self.checkcif_url = url
         self.full_iucr = full_iucr
+        self.check_duplicates = check_duplicates
 
     def _html_check(self) -> None:
         if self.hkl_upload:
@@ -63,11 +64,13 @@ class CheckCif(QThread):
             validation_type = 'checkcif_with_hkl'
         vrf = self.get_vrf()
         headers = {
+            "from_index": "from_index",
             "runtype"   : "symmonly",
             "referer"   : "checkcif_server",
             "outputtype": 'PDF' if self.pdf else 'HTML',
             "validtype" : validation_type,
             "valout"    : vrf,
+            "duplic"    : "duplicyes" if self.check_duplicates else "duplicno",
         }
         t1 = time.perf_counter()
         self.progress.emit('Report request sent. Please wait...')

{finalcif-153 → finalcif-155}/finalcif/cif/cif_file_io.py

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

{finalcif-153 → finalcif-155}/finalcif/equip_property/author_loop_templates.py

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

{finalcif-153 → finalcif-155}/finalcif/finalcif_start.py

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