finalcif 162__tar.gz → 164__tar.gz

{finalcif-162 → finalcif-164}/.gitignore

@@ -237,3 +237,7 @@ finalcif_keys_order.cif
 /tests/examples/work/report_cu_BruecknerJK_153F40_0m-finalcif.html
 /test-data/checkcif-DK_Zucker2_0m-finalcif.html
 /test-data/report_DK_Zucker2_0m-finalcif.html
+/work/dicts/cif_core.dic
+/work/dicts/cif_ms.dic
+/work/dicts/cif_pow.dic
+/work/dicts/ddl.dic

{finalcif-162 → finalcif-164}/AGENTS.md

@@ -33,7 +33,7 @@
   - SHELX parsing via the external `shelxfile` package (used in `report/templated_report.py`); in-tree `.lst` parser in `datafiles/shelx_lst.py`.
 - **CIF Parsing:** Standardized on `gemmi` (>=0.7.5); `gemmi.set_leak_warnings(False)` is set at startup.
 - **Key Third-Party Runtime Deps:** `qtpy` + `pyside6` / `pyside6-addons`, `gemmi`, `docxtpl[subdoc]`, `python-docx`, `shelxfile`, `fastmolwidget`, `crossrefapi`, `QtAwesome` (icon fonts), `pyenchant` (spell-check), `html2text`, `lxml`, `numpy<2.4`, `chardet` / `charset-normalizer`, `requests`/`urllib3`, `packaging`, `pefile` (see `pyproject.toml`).
-
+- Use gemmi for CIF parsinf if many files need to be processed, because it is much faster than CifContainer. CifContainer is a wrapper around gemmi.cif that provides a dict-like interface and additional features, but it is slower than using gemmi directly.
 ## Conventions
 - **UI Files:** Edit `.ui` files in Qt Designer (`scripts/designer.py`), then regenerate via `python scripts/compile_ui_files.py`. Never hand-edit generated `*_ui.py`.
 - **qtpy Imports:** `from qtpy import QtCore, QtGui, QtWebEngineWidgets, QtWidgets, compat` — `QtWebEngine` is used and requires `PySide6-Addons`.

{finalcif-162 → finalcif-164}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 162
+Version: 164
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues

finalcif-164/finalcif/__init__.py

@@ -0,0 +1,3 @@
+
+VERSION = 164
+__version__ = VERSION

{finalcif-162 → finalcif-164}/finalcif/appwindow.py

@@ -41,7 +41,7 @@ from gemmi import cif
 from finalcif import VERSION
 from finalcif.app_path import application_path
 from finalcif.cif.checkcif.checkcif import MyHTMLParser, AlertHelp, CheckCif
-from finalcif.cif.cif_file_io import CifContainer, GemmiError
+from finalcif.cif.cif_file_io import CifContainer, GemmiError, has_cif2_header
 from finalcif.cif.cod.deposit import CODdeposit
 from finalcif.cif.text import utf8_to_str, quote
 from finalcif.datafiles.bruker_data import BrukerData
@@ -160,7 +160,9 @@ class AppWindow(QMainWindow):
         # Inject the Author Editor tab (defined in the .ui file) into LoopsPage
         self.ui.loops_page.set_author_editor_tab(self.ui.author_editor_widget)
         self.fixfont = QtGui.QFontDatabase.systemFont(QtGui.QFontDatabase.SystemFont.FixedFont)
-        self.ui.shelx_TextEdit.setFont(self.fixfont)
+        shelx_font = QtGui.QFont(self.fixfont)
+        shelx_font.setPointSize(self.fixfont.pointSize() + 1)
+        self.ui.shelx_TextEdit.setFont(shelx_font)
         self.ui.shelx_warn_TextEdit.setFont(self.fixfont)
         self.ui.ckf_textedit.setFont(self.fixfont)
         self.settings = FinalCifSettings()
@@ -1248,17 +1250,18 @@ class AppWindow(QMainWindow):
                               log_widget=self.ui.CheckCifLogPlainTextEdit,
                               output_widget=self.ui.CheckcifPlaintextEdit,
                               cif_file=self.cif.fileobj)
-        if runner.platon_exe is not None and not Path(runner.platon_exe).exists():
+        if 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')
+            self.ui.CheckcifButton.setEnabled(True)
+            return None
         runner.tick.connect(self.append_to_ciflog_without_newline)
         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):
+    def add_moiety_furmula(self, formula_moiety: str) -> None:
         moiety = self.ui.cif_main_table.getTextFromKey(key='_chemical_formula_moiety', col=Column.CIF)
         if formula_moiety and moiety in ['', '?'] and not self.cif.is_multi_cif:
             self.ui.cif_main_table.setText(key='_chemical_formula_moiety', txt=formula_moiety, column=Column.EDIT)
@@ -1612,7 +1615,10 @@ class AppWindow(QMainWindow):
         """
         imp_cif: CifContainer
         if not filename:
-            filename = cif_file_open_dialog(parent=self, 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:
@@ -1859,6 +1865,12 @@ class AppWindow(QMainWindow):
             cif_file = self.get_file_from_dialog()
         if not cif_file:
             return
+        if has_cif2_header(cif_file):
+            show_general_warning(
+                self,
+                "This is a CIF2 file and cannot be opened directly.\n",
+            )
+            return
         cif2 = CifContainer(cif_file)
         if cif2.is_multi_cif:
             show_general_warning(self, 'Can add single data CIFs only!')
@@ -1919,6 +1931,12 @@ class AppWindow(QMainWindow):
         if filepath.stat().st_size == 0:
             show_general_warning(self, 'This file has zero byte size!')
             return False
+        if has_cif2_header(filepath):
+            show_general_warning(
+                self,
+                "This is a CIF2 file and cannot be opened directly.\n",
+            )
+            return False
         return True
 
     def warn_about_bad_cif(self):
@@ -2077,7 +2095,10 @@ class AppWindow(QMainWindow):
             self.ui.zEstimateLabel.setText('?')
             self.ui.zEstimateLabel2.setText('?')
             return
-        confidence_icon = {'high': '✓', 'medium': '~', 'low': '?'}[result.confidence]
+        # Propagate moiety formula to the CIF table if not already filled.
+        if result.moiety_formula:
+            self.add_moiety_furmula(result.moiety_formula)
+        confidence_icon = {'high': '✓', 'medium': '~', 'formula': '≡', 'low': '?'}[result.confidence]
         self.ui.zEstimateLabel.setText(f"Z = {result.z}  Z′ = {result.z_prime:.3g}  {confidence_icon}")
         self.ui.zEstimateLabel2.setText(f"Z = {result.z}  Z′ = {result.z_prime:.3g}  {confidence_icon}")
         tip_lines = [
@@ -2092,6 +2113,11 @@ class AppWindow(QMainWindow):
             tip_lines.append("Confidence: MEDIUM — Z′ is a non-integer crystallographic")
             tip_lines.append("fraction (½, ⅓, ¼, or ⅙), suggesting the molecule sits")
             tip_lines.append("on a special position; the true Z may be higher.")
+        elif result.confidence == 'formula':
+            tip_lines.append("Confidence: FORMULA — Z was derived from the chemical formula.")
+            tip_lines.append("The bond-graph method is unreliable for this structure")
+            tip_lines.append("(typical for coordination polymers, metal–organic frameworks,")
+            tip_lines.append("or other extended inorganic networks).")
         else:
             tip_lines.append("Confidence: LOW — Z′ is not a multiple of ½.")
             tip_lines.append("The bond-graph estimate is likely incorrect")

{finalcif-162 → finalcif-164}/finalcif/cif/cif_file_io.py

@@ -23,17 +23,41 @@ from gemmi.cif import as_string, Document, Loop
 from packaging.version import Version
 from shelxfile import Shelxfile
 
+from finalcif.cif.cif_keyword_mapping import CIF2_TO_CIF11_KEYWORD_TABLE
+
+# CIF data names are case-insensitive per the CIF specification. Build a
+# case-folded lookup once at import time so the translator finds aliases
+# regardless of the source file's casing.
+_CIF2_TO_CIF11_LOWERCASE_LOOKUP = {
+    key.lower(): value for key, value in CIF2_TO_CIF11_KEYWORD_TABLE.items()
+}
 from finalcif.cif.cif_order import order, special_keys, essential_keys, non_centrosymm_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 isnumeric, grouper, strip_finalcif_of_name, _angstrom_to_x
 
+# Match CIF data names at line start (pairs or loop tags), allowing common
+# CIF2/mmCIF token characters (dot, hyphen, brackets, parentheses and slash variants).
+CIF_KEYWORD_PATTERN = re.compile(r'^(\s*)(_[a-zA-Z][a-zA-Z0-9_.\-\[\]()/]*)(?=\s|$)')
+
 
 class GemmiError(Exception):
     pass
 
 
+def has_cif2_header(path: Path) -> bool:
+    """
+    Detect CIF2 content by header marker independent of file suffix.
+    """
+    with suppress(OSError, UnicodeDecodeError):
+        with path.open('r', encoding='utf-8', errors='ignore') as file:
+            header = file.read(512)
+        header = header.lstrip('\ufeff \t\r\n')
+        return header.startswith('#\\#CIF_2.0')
+    return False
+
+
 class CifContainer:
     """
     This class holds the content of a cif file, independent of the file parser used.
@@ -164,7 +188,8 @@ class CifContainer:
         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')],
-                                       [y.upper() for y in self.block.find_loop('_atom_site_type_symbol')], strict=False))
+                                       [y.upper() for y in self.block.find_loop('_atom_site_type_symbol')],
+                                       strict=False))
         self.check_hkl_min_max()
 
     @property
@@ -197,16 +222,92 @@ class CifContainer:
         Reads a cif file and returns a gemmi document object.
         """
         doc = gemmi.cif.Document()
+        suffix = path.suffix.lower()
+        has_cif2_header = self._has_cif2_header(path)
         # support for platon squeeze files:
-        if path.suffix == '.sqf':
+        if suffix == '.sqf':
             txt = path.read_text(encoding='ascii')
             txt = 'data_justrandomlkdsadflkmcn\n' + txt
             doc.parse_string(txt)
         else:
             doc.source = str(path.resolve())
             doc.parse_file(str(path.resolve()))
+        if suffix == '.mmcif' or has_cif2_header:
+            doc = self._convert_doc_to_cif11(doc)
         return doc
 
+    @staticmethod
+    def _has_cif2_header(path: Path) -> bool:
+        return has_cif2_header(path)
+
+    @staticmethod
+    def _convert_doc_to_cif11(doc: gemmi.cif.Document) -> gemmi.cif.Document:
+        """
+        Normalizes CIF2/mmCIF input to CIF 1.1 text representation.
+        This keeps downstream processing compatible with code paths that assume CIF 1.1 tokens.
+        Conversion is done as a round-trip serialization/parsing step with stable write options.
+        """
+        options = gemmi.cif.WriteOptions()
+        options.prefer_pairs = False
+        options.compact = False
+        # Keep alignment settings identical to the regular CifContainer text output.
+        options.align_pairs = 33
+        options.align_loops = 15
+        options.misuse_hash = False
+        normalized_text = doc.as_string(options=options)
+        translated_text = CifContainer._translate_keywords_to_cif11(normalized_text)
+        converted = gemmi.cif.Document()
+        converted.source = doc.source
+        converted.parse_string(translated_text)
+        return converted
+
+    @staticmethod
+    def _translate_keywords_to_cif11(cif_text: str) -> str:
+        """
+        Translate CIF2/mmCIF keyword notation to CIF 1.1-compatible names.
+        Uses the CIVET-style legacy conversion approach for data names:
+        modern dotted names are converted to underscore names.
+        """
+        translated_lines: list[str] = []
+        in_text_block = False
+        for line in cif_text.split('\n'):
+            stripped = line.strip()
+            if stripped == ';':
+                in_text_block = not in_text_block
+                translated_lines.append(line)
+                continue
+            if in_text_block or stripped.startswith('#') or not stripped:
+                translated_lines.append(line)
+                continue
+            field_match = CIF_KEYWORD_PATTERN.match(line)
+            if field_match:
+                indent, field_name = field_match.groups()
+                translated_field = CifContainer._translate_keyword_to_cif11(field_name)
+                if translated_field != field_name:
+                    remainder = line[field_match.end(2):]
+                    line = f'{indent}{translated_field}{remainder}'
+            translated_lines.append(line)
+        return '\n'.join(translated_lines)
+
+    @staticmethod
+    def _translate_keyword_to_cif11(keyword: str) -> str:
+        """
+        Translate one CIF2/mmCIF keyword to CIF 1.1 legacy naming.
+
+        The lookup is case-insensitive (CIF data names are case-insensitive
+        per the CIF specification). When no explicit alias is registered in
+        ``CIF2_TO_CIF11_KEYWORD_TABLE``, a trivial dot-to-underscore rewrite
+        is applied. The mapping table is regenerated by
+        ``scripts/generate_keyword_mapping.py`` from the upstream DDLm
+        dictionaries.
+        """
+        mapped = _CIF2_TO_CIF11_LOWERCASE_LOOKUP.get(keyword.lower())
+        if mapped is not None:
+            return mapped
+        if '.' not in keyword:
+            return keyword
+        return keyword.replace('.', '_')
+
     def read_string(self, cif_string: str) -> gemmi.cif.Document:
         """
         Reads a cif file from a string and returns a gemmi cif docment.
@@ -869,9 +970,9 @@ class CifContainer:
         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=False)):
+            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)):
+                self.yes_not_set(publ)):
                 continue
             else:
                 yield angle(label1=label1, label2=label2, label3=label3, angle_val=angle_val,
@@ -945,7 +1046,7 @@ 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, strict=False)):
+            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:

finalcif-164/finalcif/cif/cif_keyword_mapping.py

@@ -0,0 +1,232 @@
+#  ----------------------------------------------------------------------------
+#  "THE BEER-WARE LICENSE" (Revision 42):
+#  dkratzert@gmx.de> wrote this file.  As long as you retain
+#  this notice you can do whatever you want with this stuff. If we meet some day,
+#  and you think this stuff is worth it, you can buy me a beer in return.
+#  Dr. Daniel Kratzert
+#  ----------------------------------------------------------------------------
+
+# Auto-generated by scripts/generate_keyword_mapping.py -- DO NOT EDIT BY HAND.
+#
+# Mapping of CIF2/DDLm dotted data names to their preferred CIF 1.1 legacy
+# alias, restricted to entries where a plain ``replace('.', '_')`` would NOT
+# yield the correct legacy name. Trivial cases are handled at runtime in
+# CifContainer._translate_keyword_to_cif11.
+#
+# Source dictionaries (DDLm):
+#   * cif_core.dic  -- https://github.com/COMCIFS/cif_core
+#   * cif_pow.dic   -- https://github.com/COMCIFS/Powder_Dictionary
+#   * cif_ms.dic    -- https://github.com/COMCIFS/Modulated_Structures
+#   * ddl.dic       -- https://github.com/COMCIFS/DDLm
+#
+# When several legacy aliases are listed in a DDLm definition, the first
+# underscore-only (non-dotted) alias is selected as the most widely used form.
+# A small set of MANUAL_OVERRIDES (defined in the generator script) pins the
+# historically dominant CIF 1.1 names consumed by PLATON / SHELX / CheckCIF
+# / COD / CCDC even when the upstream dictionary no longer lists them as
+# aliases.
+
+CIF2_TO_CIF11_KEYWORD_TABLE = {
+    '_atom_scat_versus_stol.atom_type'           : '_atom_type_scat_versus_stol_list',
+    '_atom_site.refinement_flags_posn'           : '_atom_site_refinement_flags',
+    '_atom_site_U_Legendre.atom_site_label'      : '_jana_atom_site_U_Legendre_atom_site_label',
+    '_atom_site_U_Legendre.coeff'                : '_jana_atom_site_U_Legendre_param_coeff',
+    '_atom_site_U_Legendre.order'                : '_jana_atom_site_U_Legendre_param_order',
+    '_atom_site_U_Legendre.tens_elem'            : '_jana_atom_site_U_Legendre_tens_elem',
+    '_atom_site_U_ortho.coeff'                   : '_jana_atom_site_U_crenel_ortho_param_coeff',
+    '_atom_site_U_ortho.func_id'                 : '_jana_atom_site_U_crenel_ortho_id',
+    '_atom_site_U_ortho.tens_elem'               : '_jana_atom_site_U_crenel_ortho_tens_elem',
+    '_atom_site_U_xharm.atom_site_label'         : '_jana_atom_site_U_XHarm_atom_site_label',
+    '_atom_site_U_xharm.coeff'                   : '_jana_atom_site_U_XHarm_param_coeff',
+    '_atom_site_U_xharm.order'                   : '_jana_atom_site_U_XHarm_param_order',
+    '_atom_site_U_xharm.tens_elem'               : '_jana_atom_site_U_XHarm_tens_elem',
+    '_atom_site_displace_Legendre.axis'          : '_jana_atom_site_displace_Legendre_axis',
+    '_atom_site_displace_ortho.axis'             : '_jana_atom_site_displace_crenel_ortho_axis',
+    '_atom_site_displace_ortho.func_id'          : '_jana_atom_site_displace_crenel_ortho_id',
+    '_atom_site_displace_sawtooth.ax'            : '_atom_site_displace_special_func_sawtooth_ax',
+    '_atom_site_displace_sawtooth.ay'            : '_atom_site_displace_special_func_sawtooth_ay',
+    '_atom_site_displace_sawtooth.az'            : '_atom_site_displace_special_func_sawtooth_az',
+    '_atom_site_displace_sawtooth.c'             : '_atom_site_displace_special_func_sawtooth_c',
+    '_atom_site_displace_sawtooth.w'             : '_atom_site_displace_special_func_sawtooth_w',
+    '_atom_site_displace_xharm.atom_site_label'  : '_jana_atom_site_displace_XHarm_site_label',
+    '_atom_site_displace_xharm.axis'             : '_jana_atom_site_displace_XHarm_axis',
+    '_atom_site_displace_xharm.coeff'            : '_jana_atom_site_displace_XHarm_param_coeff',
+    '_atom_site_displace_xharm.order'            : '_jana_atom_site_displace_XHarm_param_order',
+    '_atom_site_occ_Legendre.atom_site_label'    : '_jana_atom_site_occ_Legendre_atom_site_label',
+    '_atom_site_occ_Legendre.coeff'              : '_jana_atom_site_occ_Legendre_param_coeff',
+    '_atom_site_occ_Legendre.order'              : '_jana_atom_site_occ_Legendre_param_order',
+    '_atom_site_occ_crenel.atom_site_label'      : '_atom_site_occ_special_func_atom_site_label',
+    '_atom_site_occ_crenel.c'                    : '_atom_site_occ_special_func_crenel_c',
+    '_atom_site_occ_crenel.ortho_eps'            : '_jana_atom_site_crenel_ortho_func_eps',
+    '_atom_site_occ_crenel.w'                    : '_atom_site_occ_special_func_crenel_w',
+    '_atom_site_occ_ortho.coeff'                 : '_jana_atom_site_occ_crenel_ortho_param_coeff',
+    '_atom_site_occ_ortho.func_id'               : '_jana_atom_site_occ_crenel_ortho_id',
+    '_atom_site_occ_xharm.atom_site_label'       : '_jana_atom_site_occ_XHarm_atom_site_label',
+    '_atom_site_occ_xharm.coeff'                 : '_jana_atom_site_occ_XHarm_param_coeff',
+    '_atom_site_occ_xharm.order'                 : '_jana_atom_site_occ_XHarm_param_order',
+    '_atom_site_rot_sawtooth.atom_site_label'    : '_atom_site_rot_special_func_atom_site_label',
+    '_atom_site_rot_sawtooth.ax'                 : '_atom_site_rot_special_func_sawtooth_ax',
+    '_atom_site_rot_sawtooth.ay'                 : '_atom_site_rot_special_func_sawtooth_ay',
+    '_atom_site_rot_sawtooth.az'                 : '_atom_site_rot_special_func_sawtooth_az',
+    '_atom_site_rot_sawtooth.c'                  : '_atom_site_rot_special_func_sawtooth_c',
+    '_atom_site_rot_sawtooth.w'                  : '_atom_site_rot_special_func_sawtooth_w',
+    '_atom_sites_Cartn_transform.mat_11'         : '_atom_sites_Cartn_tran_matrix_11',
+    '_atom_sites_Cartn_transform.mat_12'         : '_atom_sites_Cartn_tran_matrix_12',
+    '_atom_sites_Cartn_transform.mat_13'         : '_atom_sites_Cartn_tran_matrix_13',
+    '_atom_sites_Cartn_transform.mat_21'         : '_atom_sites_Cartn_tran_matrix_21',
+    '_atom_sites_Cartn_transform.mat_22'         : '_atom_sites_Cartn_tran_matrix_22',
+    '_atom_sites_Cartn_transform.mat_23'         : '_atom_sites_Cartn_tran_matrix_23',
+    '_atom_sites_Cartn_transform.mat_31'         : '_atom_sites_Cartn_tran_matrix_31',
+    '_atom_sites_Cartn_transform.mat_32'         : '_atom_sites_Cartn_tran_matrix_32',
+    '_atom_sites_Cartn_transform.mat_33'         : '_atom_sites_Cartn_tran_matrix_33',
+    '_atom_sites_Cartn_transform.vec_1'          : '_atom_sites_Cartn_tran_vector_1',
+    '_atom_sites_Cartn_transform.vec_2'          : '_atom_sites_Cartn_tran_vector_2',
+    '_atom_sites_Cartn_transform.vec_3'          : '_atom_sites_Cartn_tran_vector_3',
+    '_atom_sites_cartn_transform.mat_11'         : '_atom_sites_Cartn_tran_matrix_11',
+    '_atom_sites_cartn_transform.mat_12'         : '_atom_sites_Cartn_tran_matrix_12',
+    '_atom_sites_cartn_transform.mat_13'         : '_atom_sites_Cartn_tran_matrix_13',
+    '_atom_sites_cartn_transform.mat_21'         : '_atom_sites_Cartn_tran_matrix_21',
+    '_atom_sites_cartn_transform.mat_22'         : '_atom_sites_Cartn_tran_matrix_22',
+    '_atom_sites_cartn_transform.mat_23'         : '_atom_sites_Cartn_tran_matrix_23',
+    '_atom_sites_cartn_transform.mat_31'         : '_atom_sites_Cartn_tran_matrix_31',
+    '_atom_sites_cartn_transform.mat_32'         : '_atom_sites_Cartn_tran_matrix_32',
+    '_atom_sites_cartn_transform.mat_33'         : '_atom_sites_Cartn_tran_matrix_33',
+    '_atom_sites_cartn_transform.vec_1'          : '_atom_sites_Cartn_tran_vector_1',
+    '_atom_sites_cartn_transform.vec_2'          : '_atom_sites_Cartn_tran_vector_2',
+    '_atom_sites_cartn_transform.vec_3'          : '_atom_sites_Cartn_tran_vector_3',
+    '_atom_sites_fract_transform.mat_11'         : '_atom_sites_fract_tran_matrix_11',
+    '_atom_sites_fract_transform.mat_12'         : '_atom_sites_fract_tran_matrix_12',
+    '_atom_sites_fract_transform.mat_13'         : '_atom_sites_fract_tran_matrix_13',
+    '_atom_sites_fract_transform.mat_21'         : '_atom_sites_fract_tran_matrix_21',
+    '_atom_sites_fract_transform.mat_22'         : '_atom_sites_fract_tran_matrix_22',
+    '_atom_sites_fract_transform.mat_23'         : '_atom_sites_fract_tran_matrix_23',
+    '_atom_sites_fract_transform.mat_31'         : '_atom_sites_fract_tran_matrix_31',
+    '_atom_sites_fract_transform.mat_32'         : '_atom_sites_fract_tran_matrix_32',
+    '_atom_sites_fract_transform.mat_33'         : '_atom_sites_fract_tran_matrix_33',
+    '_atom_sites_fract_transform.vec_1'          : '_atom_sites_fract_tran_vector_1',
+    '_atom_sites_fract_transform.vec_2'          : '_atom_sites_fract_tran_vector_2',
+    '_atom_sites_fract_transform.vec_3'          : '_atom_sites_fract_tran_vector_3',
+    '_atom_sites_ortho.func_id'                  : '_jana_atom_site_crenel_ortho_func_id',
+    '_atom_type.analytical_mass_percent'         : '_atom_type_analytical_mass_%',
+    '_cell.commen_supercell_matrix_1_1'          : '_jana_cell_commen_supercell_matrix_1_1',
+    '_cell.commen_supercell_matrix_1_2'          : '_jana_cell_commen_supercell_matrix_1_2',
+    '_cell.commen_supercell_matrix_1_3'          : '_jana_cell_commen_supercell_matrix_1_3',
+    '_cell.commen_supercell_matrix_2_1'          : '_jana_cell_commen_supercell_matrix_2_1',
+    '_cell.commen_supercell_matrix_2_2'          : '_jana_cell_commen_supercell_matrix_2_2',
+    '_cell.commen_supercell_matrix_2_3'          : '_jana_cell_commen_supercell_matrix_2_3',
+    '_cell.commen_supercell_matrix_3_1'          : '_jana_cell_commen_supercell_matrix_3_1',
+    '_cell.commen_supercell_matrix_3_2'          : '_jana_cell_commen_supercell_matrix_3_2',
+    '_cell.commen_supercell_matrix_3_3'          : '_jana_cell_commen_supercell_matrix_3_3',
+    '_cell_measurement.temperature_su'           : '_cell_measurement_temp_su',
+    '_citation_editor.name'                      : '_citation_editor',
+    '_computing.diffrn_collection'               : '_computing_data_collection',
+    '_computing.diffrn_reduction'                : '_computing_data_reduction',
+    '_diffrn.ambient_temperature'                : '_cell_measurement_temperature',
+    '_diffrn.ambient_temperature_details'        : '_diffrn_ambient_temp_details',
+    '_diffrn.ambient_temperature_gt'             : '_diffrn_ambient_temp_gt',
+    '_diffrn.ambient_temperature_lt'             : '_diffrn_ambient_temp_lt',
+    '_diffrn_detector.description'               : '_diffrn_radiation_detector',
+    '_diffrn_detector.make'                      : '_diffrn_detector_type',
+    '_diffrn_measurement.device_class'           : '_diffrn_measurement_device',
+    '_diffrn_measurement.device_make'            : '_diffrn_measurement_device_type',
+    '_diffrn_radiation_wavelength.value'         : '_cell_measurement_wavelength',
+    '_diffrn_radiation_wavelength.value_su'      : '_diffrn_radiation_wavelength_su',
+    '_diffrn_refln.intensity_net_su'             : '_diffrn_refln_intensity_u',
+    '_diffrn_refln.sin_theta_over_lambda'        : '_diffrn_refln_sint/lambda',
+    '_diffrn_reflns.av_sunetI_over_netI'         : '_diffrn_reflns_av_sigmaI/netI',
+    '_diffrn_reflns_class.av_suI_over_I'         : '_diffrn_reflns_class_av_uI_over_I',
+    '_diffrn_source.description'                 : '_diffrn_source',
+    '_diffrn_source.take_off_angle'              : '_diffrn_source_take-off_angle',
+    '_diffrn_standards.decay_percent'            : '_diffrn_standards_decay_%',
+    '_diffrn_standards.scale_su_average'         : '_diffrn_standards_scale_sigma',
+    '_exptl_crystal_appearance.general'          : '_exptl_crystal_colour_lustre',
+    '_exptl_crystal_appearance.hue'              : '_exptl_crystal_colour_primary',
+    '_exptl_crystal_appearance.intensity'        : '_exptl_crystal_colour_modifier',
+    '_geom_angle.value'                          : '_geom_angle',
+    '_geom_angle.value_av'                       : '_geom_angle_av',
+    '_geom_angle.value_max'                      : '_geom_angle_max',
+    '_geom_angle.value_min'                      : '_geom_angle_min',
+    '_geom_angle.value_su'                       : '_geom_angle_su',
+    '_geom_hbond.distance_HA_max'                : '_geom_hbond_distance_max_av',
+    '_geom_hbond.distance_HA_min'                : '_geom_hbond_distance_min_av',
+    '_geom_torsion.angle'                        : '_geom_torsion',
+    '_geom_torsion.angle_av'                     : '_geom_torsion_av',
+    '_geom_torsion.angle_max'                    : '_geom_torsion_max',
+    '_geom_torsion.angle_min'                    : '_geom_torsion_min',
+    '_geom_torsion.angle_su'                     : '_geom_torsion_su',
+    '_journal.validation_number'                 : '_journal_data_validation_number',
+    '_pd_instr.dist_anal_detc'                   : '_pd_instr_dist_anal/detc',
+    '_pd_instr.dist_mono_spec'                   : '_pd_instr_dist_mono/spec',
+    '_pd_instr.dist_spec_anal'                   : '_pd_instr_dist_spec/anal',
+    '_pd_instr.dist_spec_detc'                   : '_pd_instr_dist_spec/detc',
+    '_pd_instr.dist_src_mono'                    : '_pd_instr_dist_src/mono',
+    '_pd_instr.dist_src_spec'                    : '_pd_instr_dist_src/spec',
+    '_pd_instr.divg_ax_anal_detc'                : '_pd_instr_divg_ax_anal/detc',
+    '_pd_instr.divg_ax_mono_spec'                : '_pd_instr_divg_ax_mono/spec',
+    '_pd_instr.divg_ax_spec_anal'                : '_pd_instr_divg_ax_spec/anal',
+    '_pd_instr.divg_ax_spec_detc'                : '_pd_instr_divg_ax_spec/detc',
+    '_pd_instr.divg_ax_src_mono'                 : '_pd_instr_divg_ax_src/mono',
+    '_pd_instr.divg_ax_src_spec'                 : '_pd_instr_divg_ax_src/spec',
+    '_pd_instr.divg_eq_anal_detc'                : '_pd_instr_divg_eq_anal/detc',
+    '_pd_instr.divg_eq_mono_spec'                : '_pd_instr_divg_eq_mono/spec',
+    '_pd_instr.divg_eq_spec_anal'                : '_pd_instr_divg_eq_spec/anal',
+    '_pd_instr.divg_eq_spec_detc'                : '_pd_instr_divg_eq_spec/detc',
+    '_pd_instr.divg_eq_src_mono'                 : '_pd_instr_divg_eq_src/mono',
+    '_pd_instr.divg_eq_src_spec'                 : '_pd_instr_divg_eq_src/spec',
+    '_pd_instr.slit_ax_anal_detc'                : '_pd_instr_slit_ax_anal/detc',
+    '_pd_instr.slit_ax_mono_spec'                : '_pd_instr_slit_ax_mono/spec',
+    '_pd_instr.slit_ax_spec_anal'                : '_pd_instr_slit_ax_spec/anal',
+    '_pd_instr.slit_ax_spec_detc'                : '_pd_instr_slit_ax_spec/detc',
+    '_pd_instr.slit_ax_src_mono'                 : '_pd_instr_slit_ax_src/mono',
+    '_pd_instr.slit_ax_src_spec'                 : '_pd_instr_slit_ax_src/spec',
+    '_pd_instr.slit_eq_anal_detc'                : '_pd_instr_slit_eq_anal/detc',
+    '_pd_instr.slit_eq_mono_spec'                : '_pd_instr_slit_eq_mono/spec',
+    '_pd_instr.slit_eq_spec_anal'                : '_pd_instr_slit_eq_spec/anal',
+    '_pd_instr.slit_eq_spec_detc'                : '_pd_instr_slit_eq_spec/detc',
+    '_pd_instr.slit_eq_src_mono'                 : '_pd_instr_slit_eq_src/mono',
+    '_pd_instr.slit_eq_src_spec'                 : '_pd_instr_slit_eq_src/spec',
+    '_pd_instr.soller_ax_anal_detc'              : '_pd_instr_soller_ax_anal/detc',
+    '_pd_instr.soller_ax_mono_spec'              : '_pd_instr_soller_ax_mono/spec',
+    '_pd_instr.soller_ax_spec_anal'              : '_pd_instr_soller_ax_spec/anal',
+    '_pd_instr.soller_ax_spec_detc'              : '_pd_instr_soller_ax_spec/detc',
+    '_pd_instr.soller_ax_src_mono'               : '_pd_instr_soller_ax_src/mono',
+    '_pd_instr.soller_ax_src_spec'               : '_pd_instr_soller_ax_src/spec',
+    '_pd_instr.soller_eq_anal_detc'              : '_pd_instr_soller_eq_anal/detc',
+    '_pd_instr.soller_eq_mono_spec'              : '_pd_instr_soller_eq_mono/spec',
+    '_pd_instr.soller_eq_spec_anal'              : '_pd_instr_soller_eq_spec/anal',
+    '_pd_instr.soller_eq_spec_detc'              : '_pd_instr_soller_eq_spec/detc',
+    '_pd_instr.soller_eq_src_mono'               : '_pd_instr_soller_eq_src/mono',
+    '_pd_instr.soller_eq_src_spec'               : '_pd_instr_soller_eq_src/spec',
+    '_pd_phase_mass.percent'                     : '_pd_phase_mass_%',
+    '_pd_qpa_internal_std.mass_percent'          : '_pd_calib_std_internal_mass_%',
+    '_publ_contact_author.contact_details'       : '_publ_contact_author',
+    '_publ_contact_author.name'                  : '_publ_contact_author',
+    '_refine_ls.R_factor_gt'                     : '_refine_ls_R_factor_obs',
+    '_refine_ls.restrained_S_gt'                 : '_refine_ls_restrained_S_obs',
+    '_refine_ls.shift_over_su_max_lt'            : '_refine_ls_shift/su_max_lt',
+    '_refine_ls.shift_over_su_mean_lt'           : '_refine_ls_shift/su_mean_lt',
+    '_refine_ls.wR_factor_gt'                    : '_refine_ls_wR_factor_obs',
+    '_refln.F_meas_su'                           : '_refln_F_sigma',
+    '_refln.F_squared_meas_su'                   : '_refln_F_squared_sigma',
+    '_refln.sin_theta_over_lambda'               : '_refln_sint/lambda',
+    '_reflns_class.number_gt'                    : '_reflns_class_number_observed',
+    '_reflns_shell.Rmerge_F_gt'                  : '_reflns_shell_Rmerge_F_obs',
+    '_reflns_shell.Rmerge_I_gt'                  : '_reflns_shell_Rmerge_I_obs',
+    '_reflns_shell.meanI_over_suI_all'           : '_reflns_shell_meanI_over_uI_all',
+    '_reflns_shell.meanI_over_suI_gt'            : '_reflns_shell_meanI_over_sigI_obs',
+    '_reflns_shell.number_measured_gt'           : '_reflns_shell_number_measured_obs',
+    '_space_group.IT_number'                     : '_symmetry_Int_Tables_number',
+    '_space_group.crystal_system'                : '_symmetry_cell_setting',
+    '_space_group.name_H-M_alt'                  : '_symmetry_space_group_name_H-M',
+    '_space_group.name_H-M_full'                 : '_symmetry_space_group_name_H-M',
+    '_space_group.name_Hall'                     : '_symmetry_space_group_name_Hall',
+    '_space_group_symop.id'                      : '_symmetry_equiv_pos_site_id',
+    '_space_group_symop.operation_xyz'           : '_symmetry_equiv_pos_as_xyz',
+    '_superspace_group.IT_number'                : '_space_group_ssg_IT_number',
+    '_superspace_group.WJJ_code'                 : '_space_group_ssg_WJJ_code',
+    '_superspace_group.name'                     : '_space_group_ssg_name',
+    '_superspace_group.name_IT'                  : '_space_group_ssg_name_IT',
+    '_superspace_group.name_WJJ'                 : '_space_group_ssg_name_WJJ',
+    '_superspace_group_symop.id'                 : '_space_group_symop_ssg_id',
+    '_superspace_group_symop.operation_algebraic': '_space_group_symop_ssg_operation_algebraic',
+}

{finalcif-162 → finalcif-164}/finalcif/ciforder/order_ui.py

@@ -108,6 +108,7 @@ class Ui_CifOrderForm(object):
 
         self.helpTextLabel = QLabel(CifOrderForm)
         self.helpTextLabel.setObjectName(u"helpTextLabel")
+        self.helpTextLabel.setWordWrap(True)
 
         self.gridLayout.addWidget(self.helpTextLabel, 1, 0, 1, 2)
 

{finalcif-162 → finalcif-164}/finalcif/ciforder/order_ui.ui

@@ -183,6 +183,9 @@
      <property name="text">
       <string>Order of CIF keys in the output file. Enabled means they will be forced to remain in the output CIF.</string>
      </property>
+     <property name="wordWrap">
+      <bool>true</bool>
+     </property>
     </widget>
    </item>
   </layout>