finalcif 158__tar.gz → 159__tar.gz

{finalcif-158 → finalcif-159}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: finalcif
-Version: 158
+Version: 159
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues
@@ -38,7 +38,7 @@ Requires-Dist: urllib3
 Requires-Dist: wheel
 Description-Content-Type: text/markdown
 
-![Lates Release](https://img.shields.io/github/v/tag/dkratzert/FinalCif?label=Release)
+![Latest Release](https://img.shields.io/github/v/tag/dkratzert/FinalCif?label=Release)
 [![Unit Tests](https://github.com/dkratzert/FinalCif/actions/workflows/python_tests.yml/badge.svg?branch=master)](https://github.com/dkratzert/FinalCif/actions/workflows/python_tests.yml)
 ![Contributions](https://img.shields.io/badge/contributions-welcome-blue)
 [![PyPI package](https://repology.org/badge/version-for-repo/pypi/python:finalcif.svg)](https://repology.org/project/python:finalcif/versions)
@@ -49,7 +49,7 @@ Description-Content-Type: text/markdown
 
 # FinalCif
 
-FinalCif helps you to get a complete [CIF](https://www.iucr.org/resources/cif) file from a single-xrystal X-ray diffraction experiment. See here [https://dkratzert.de/finalcif.html](https://dkratzert.de/finalcif.html) for details.
+FinalCif helps you to get a complete [CIF](https://www.iucr.org/resources/cif) file from a single-crystal X-ray diffraction experiment. See here [https://dkratzert.de/finalcif.html](https://dkratzert.de/finalcif.html) for details.
 
 For tables from multiple CIF files, you may want to use the program [multitable](https://github.com/dkratzert/multitable).
 

{finalcif-158 → finalcif-159}/README.md

@@ -1,4 +1,4 @@
-![Lates Release](https://img.shields.io/github/v/tag/dkratzert/FinalCif?label=Release)
+![Latest Release](https://img.shields.io/github/v/tag/dkratzert/FinalCif?label=Release)
 [![Unit Tests](https://github.com/dkratzert/FinalCif/actions/workflows/python_tests.yml/badge.svg?branch=master)](https://github.com/dkratzert/FinalCif/actions/workflows/python_tests.yml)
 ![Contributions](https://img.shields.io/badge/contributions-welcome-blue)
 [![PyPI package](https://repology.org/badge/version-for-repo/pypi/python:finalcif.svg)](https://repology.org/project/python:finalcif/versions)
@@ -9,7 +9,7 @@
 
 # FinalCif
 
-FinalCif helps you to get a complete [CIF](https://www.iucr.org/resources/cif) file from a single-xrystal X-ray diffraction experiment. See here [https://dkratzert.de/finalcif.html](https://dkratzert.de/finalcif.html) for details.
+FinalCif helps you to get a complete [CIF](https://www.iucr.org/resources/cif) file from a single-crystal X-ray diffraction experiment. See here [https://dkratzert.de/finalcif.html](https://dkratzert.de/finalcif.html) for details.
 
 For tables from multiple CIF files, you may want to use the program [multitable](https://github.com/dkratzert/multitable).
 

finalcif-159/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 159

{finalcif-158 → finalcif-159}/finalcif/appwindow.py

@@ -16,9 +16,10 @@ from contextlib import suppress
 from datetime import datetime
 from math import sin, radians
 from pathlib import Path, WindowsPath
-from typing import cast, Any
+from typing import cast
 
 from fastmolwidget.sdm import SDM
+
 from finalcif.gui.vzs_viewer import VZSImageViewer
 
 warnings.filterwarnings("ignore", category=RuntimeWarning, module="shibokensupport.signature.parser")
@@ -31,7 +32,7 @@ if hasattr(gemmi, 'set_leak_warnings'):
 import requests
 from qtpy import QtCore, QtGui, QtWebEngineWidgets, QtWidgets, compat
 from qtpy.QtCore import Qt, QEvent
-from qtpy.QtWidgets import (QMainWindow, QCheckBox, QListWidgetItem, QApplication,
+from qtpy.QtWidgets import (QMainWindow, QCheckBox, QApplication,
                             QPlainTextEdit, QMessageBox, QScrollBar)
 from gemmi import cif
 
@@ -57,15 +58,15 @@ from finalcif.gui.dialogs import show_update_warning, unable_to_open_message, sh
 from finalcif.gui.finalcif_gui_ui import Ui_FinalCifWindow
 from finalcif.gui.import_selector import ImportSelector
 from finalcif.gui.loop_creator import LoopCreator
-from finalcif.gui.loops import Loop, LoopTableModel, MyQTableView
 from finalcif.gui.plaintextedit import MyQPlainTextEdit
 from finalcif.gui.text_value_editor import MyTextTemplateEdit, TextEditItem
-from finalcif.gui.vrf_classes import MyVRFContainer, VREF
+from finalcif.cif.vrf_entry import VRFEntry
+from finalcif.gui.vrf_classes import MyVRFContainer
 from finalcif.report.templated_report import ReportFormat
 from finalcif.template.templates import ReportTemplates
 from finalcif.tools.download import MyDownloader
 from finalcif.tools.dsrmath import my_isnumeric
-from finalcif.tools.misc import (next_path, celltxt, to_float, cif_to_header_label, grouper, is_database_number,
+from finalcif.tools.misc import (next_path, celltxt, to_float, is_database_number,
                                  open_file, strip_finalcif_of_name, file_age_in_days)
 from finalcif.tools.options import Options
 from finalcif.tools.platon import PlatonRunner
@@ -101,7 +102,6 @@ class AppWindow(QMainWindow):
         self.sources: dict[str, tuple[str, str | None]] | None = None
         self.cif: CifContainer | None = None
         self.report_picture_path: Path | None = None
-        self.loopcreate: LoopCreator | None = None
         self.checkdef: list[str] = []
         self.changes_answer: int = 0
         self.validation_response_forms_list = []
@@ -113,6 +113,8 @@ class AppWindow(QMainWindow):
         self.ui = Ui_FinalCifWindow()
         self.ui.setupUi(self)
         self.ui.page_MainTable.setParent(self.ui.MainStackedWidget)
+        # 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)
         self.ui.shelx_warn_TextEdit.setFont(self.fixfont)
@@ -333,7 +335,6 @@ class AppWindow(QMainWindow):
         except Exception:
             self.ui.CCDCpushButton.setIcon(qta.icon('fa5s.cloud-upload-alt'))
         self.ui.CODpushButton.setIcon(qta.icon('mdi.upload'))
-        self.ui.SavePushButton.setIcon(qta.icon('mdi.content-save'))
         self.ui.revertLoopsPushButton.setIcon(qta.icon('mdi.backup-restore'))
         # Backbuttons:
         self.ui.BackpushButtonDetails.setIcon(qta.icon('mdi.keyboard-backspace'))
@@ -382,18 +383,17 @@ class AppWindow(QMainWindow):
         self.ui.ExploreDirButton.clicked.connect(self.explore_current_dir)
         self.ui.LoopsPushButton.clicked.connect(self._on_go_to_loops_page)
         self.ui.LoopsPushButton.clicked.connect(
-            lambda x: self.ui.LoopsTabWidget.setCurrentIndex(1) if self.ui.LoopsTabWidget.count() > 0 else None)
+            lambda x: self.ui.loops_page.tab_widget.setCurrentIndex(1) if self.ui.loops_page.tab_widget.count() > 0 else None)
         self.ui.LoopsPushButton.clicked.connect(lambda x: self.ui.TemplatesStackedWidget.setCurrentIndex(1))
         self.ui.AuthorEditPushButton.clicked.connect(self._on_go_to_loops_page)
         self.ui.AuthorEditPushButton.clicked.connect(lambda x: self.ui.TemplatesStackedWidget.setCurrentIndex(1))
-        self.ui.AuthorEditPushButton.clicked.connect(lambda x: self.ui.LoopsTabWidget.setCurrentIndex(0))
+        self.ui.AuthorEditPushButton.clicked.connect(lambda x: self.ui.loops_page.tab_widget.setCurrentIndex(0))
         # checkcif
         self.ui.CheckcifStartButton.clicked.connect(self.open_checkcif_page)
         self.ui.CheckcifButton.clicked.connect(self.do_offline_checkcif)
         self.ui.CheckcifHTMLOnlineButton.clicked.connect(self.do_html_checkcif)
         self.ui.CheckcifPDFOnlineButton.clicked.connect(self.do_pdf_checkcif)
         self.ui.BackFromPlatonPushButton.clicked.connect(self.back_to_main_noload)
-        self.ui.SavePushButton.clicked.connect(self.save_responses)
         # open, import
         self.ui.SelectCif_PushButton.clicked.connect(self.load_cif_file)
         self.ui.SaveCifButton.clicked.connect(self.save_cif_and_display)
@@ -404,8 +404,10 @@ class AppWindow(QMainWindow):
         self.ui.cif_main_table.row_deleted.connect(self._deleted_row)
         self.ui.CODpushButton.clicked.connect(self.open_cod_page)
         self.ui.CCDCpushButton.clicked.connect(self._ccdc_deposit)
-        self.ui.newLoopPushButton.clicked.connect(self._go_to_new_loop_page)
-        self.ui.deleteLoopButton.clicked.connect(self._on_delete_current_loop)
+        self.ui.newLoopPushButton.clicked.connect(self.ui.loops_page.go_to_new_loop_page)
+        self.ui.loops_page.new_loop_requested.connect(self._on_new_loop_requested)
+        self.ui.deleteLoopButton.clicked.connect(self.ui.loops_page.on_delete_current_loop)
+        self.ui.revertLoopsPushButton.clicked.connect(self.ui.loops_page.revert_all_loops)
         save_shortcut = QtGui.QShortcut(QtGui.QKeySequence('Ctrl+S'), self)
         save_shortcut.activated.connect(self.save_current_cif_file)
         save_shortcut = QtGui.QShortcut(QtGui.QKeySequence('Ctrl+H'), self)
@@ -427,8 +429,6 @@ class AppWindow(QMainWindow):
         # help
         self.ui.HelpPushButton.clicked.connect(self.show_help)
         self.ui.ReportPicPushButton.clicked.connect(self.select_report_picture)
-        # brings the html checkcif in from in order to avoid confusion of an "empty" checkcif report page:
-        self.ui.CheckCIFResultsTabWidget.currentChanged.connect(lambda: self.ui.ResponsesTabWidget.setCurrentIndex(0))
         ##
         self.ui.SelectCif_LineEdit.returnPressed.connect(self.check_if_file_field_contains_database_number)
         self.ui.fullIucrCheckBox.clicked.connect(self.toggle_hkl_option)
@@ -473,9 +473,15 @@ class AppWindow(QMainWindow):
         return self.cif.finalcif_file_prefixed(prefix='', suffix='-finalcif_changes.cif', force_strip=True)
 
     def _on_go_to_loops_page(self) -> None:
-        self.make_loops_tables()
+        self.ui.loops_page.load(self.cif)
         self.ui.MainStackedWidget.go_to_loops_page()
 
+    def _on_new_loop_requested(self) -> None:
+        """Hide loop-management buttons when the LoopCreator tab is active."""
+        self.ui.revertLoopsPushButton.hide()
+        self.ui.newLoopPushButton.hide()
+        self.ui.deleteLoopButton.hide()
+
     def export_all_templates(self, filename: Path | None = None) -> None:
         from finalcif.tools.settings import _custom_encoder
         if not filename:
@@ -660,7 +666,15 @@ class AppWindow(QMainWindow):
         text = self.textedit.ui.plainTextEdit.toPlainText()
         if text:
             TextEditItem._num = 1
-            self.ui.cif_main_table.setText(key=self.textedit.cif_key, column=Column.EDIT, txt=text)
+            cif_key = self.textedit.cif_key
+            # If the template was opened from a VRF widget, write the text into
+            # that widget's response field directly (the table cell is spanned).
+            if cif_key and cif_key.startswith('_vrf_'):
+                vrf_widget = self.ui.cif_main_table.get_vrf_widget(cif_key)
+                if vrf_widget is not None:
+                    vrf_widget.response_text_edit.setPlainText(text)
+            else:
+                self.ui.cif_main_table.setText(key=cif_key, column=Column.EDIT, txt=text)
             self.ui.MainStackedWidget.got_to_main_page()
             self.textedit.clear_fields()
         else:
@@ -959,7 +973,7 @@ class AppWindow(QMainWindow):
             self.ui.CheckCifLogPlainTextEdit.appendHtml('<b>CheckCIF failed to finish. '
                                                         'Please try it at https://checkcif.iucr.org/ instead.</b>')
             return
-        self.checkcif_browser = QtWebEngineWidgets.QWebEngineView(self.ui.htmlTabwidgetPage)
+        self.checkcif_browser = QtWebEngineWidgets.QWebEngineView(parent=self)
         self.ui.htmlCHeckCifGridLayout.addWidget(self.checkcif_browser)
         url = QtCore.QUrl.fromLocalFile(str(self.htmlfile.resolve()))
         self.ui.MainStackedWidget.go_to_checkcif_page()
@@ -968,30 +982,65 @@ class AppWindow(QMainWindow):
             self.checkcif_browser.setHtml(self.htmlfile.resolve().read_text('utf-8', 'ignore'))
         except FileNotFoundError:
             print(f'{self.htmlfile} not found')
-        self.ui.ResponsesTabWidget.setCurrentIndex(0)
         threading.Thread(target=self._display_structure_factor_report, args=(parser,), daemon=True).start()
         # The picture file linked in the html file:
         threading.Thread(target=parser.save_image, args=(self.cif.finalcif_file.with_suffix('.gif'),),
                          daemon=True).start()
         self.ui.CheckCifLogPlainTextEdit.appendPlainText('CheckCIF Report finished.')
-        forms = parser.response_forms
-        # makes all gray:
-        # self.ui.responseFormsListWidget.setStyleSheet("background: 'gray';")
+        html_entries = parser.response_forms
+        # Merge HTML-parsed entries into the main table:
+        # - Entries already shown in the main table (source='cif') get their source badge
+        #   updated to 'checkcif' to indicate they were returned by this run.  The existing
+        #   response text is preserved.
+        # - New entries (not yet in the CIF or table) are added as new rows at the top of
+        #   the main table, marked 'checkcif'.
         a = AlertHelp(self.checkdef)
-        self.validation_response_forms_list = []
-        self.ui.responseFormsListWidget.clear()
-        for form in forms:
-            vrf = MyVRFContainer(form, a.get_help(form['alert_num']), parent=self, is_multi_cif=self.cif.is_multi_cif)
-            self.validation_response_forms_list.append(vrf)
-            item = QListWidgetItem()
-            item.setSizeHint(vrf.sizeHint())
-            self.ui.responseFormsListWidget.addItem(item)
-            self.ui.responseFormsListWidget.setItemWidget(item, vrf)
-        if not forms:
-            iteme = QListWidgetItem(' ')
-            item = QListWidgetItem(' No level A, B or C alerts to explain.')
-            self.ui.responseFormsListWidget.addItem(iteme)
-            self.ui.responseFormsListWidget.addItem(item)
+        table = self.ui.cif_main_table
+        # Build a lookup of already-saved CIF VRF entries once, outside the loop.
+        existing_by_key = {e.key: e for e in self.cif.get_vrf_entries()}
+        for entry in html_entries:
+            existing_widget = table.get_vrf_widget(entry.key)
+            if existing_widget is not None:
+                # Row already in table (loaded from CIF): update badge to "From CheckCIF"
+                # but keep the user's existing response text.
+                existing_widget.update_source('checkcif')
+            else:
+                # New entry not yet in the CIF: add a row at the top of the table.
+                # Preserve any existing CIF response if the key happens to be in the CIF
+                # block even though it didn't appear in the table (edge-case safety).
+                if entry.key in existing_by_key:
+                    entry.response = existing_by_key[entry.key].response
+                insert_pos = self._vrf_insert_position()
+                table.add_row(key=entry.key, position=insert_pos)
+                if entry.key not in self.cif.order:
+                    self.cif.order.insert(insert_pos, entry.key)
+                vrf = MyVRFContainer(entry, a.get_help(entry.alert_num), parent=self,
+                                     is_multi_cif=self.cif.is_multi_cif)
+                vrf.deleted.connect(self._on_vrf_deleted)
+                vrf.template_requested.connect(self._on_vrf_template_requested)
+                self.validation_response_forms_list.append(vrf)
+                table.place_vrf_widget(insert_pos, vrf)
+        if html_entries:
+            n = len(html_entries)
+            form_noun = 'form' if n == 1 else 'forms'
+            self.ui.CheckCifLogPlainTextEdit.appendHtml(
+                f'<br><b>{n} validation response forms {form_noun} added to the main table.</b>')
+        else:
+            self.ui.CheckCifLogPlainTextEdit.appendHtml(
+                '<br><b>No level A, B or C alerts require a response.</b>')
+
+    def _vrf_insert_position(self) -> int:
+        """Return the row index just after the last existing ``_vrf_*`` row in the main table.
+
+        New VRF rows added during a CheckCIF run are inserted here so that all
+        VRF entries remain grouped at the top of the table.
+        """
+        keys = self.ui.cif_main_table.vheaderitems
+        pos = 0
+        for i, k in enumerate(keys):
+            if k.startswith('_vrf_'):
+                pos = i + 1
+        return pos
 
     def _display_structure_factor_report(self, parser: MyHTMLParser) -> None:
         self.ui.ckf_textedit.setPlainText(parser.get_ckf())
@@ -1041,43 +1090,65 @@ class AppWindow(QMainWindow):
         else:
             self.get_checkdef_for_response_forms()
 
-    def save_responses(self) -> None:
-        """
-        Saves the validation response form text to _vrf_ CIF entries.
-        :return: None
+    def _write_vrf_data_to_cif(self) -> int:
+        """Flush inline VRF response text and pending deletions into the CIF document.
+
+        Returns the number of non-empty responses written.  This must be called
+        **before** ``self.cif.save()`` so that the CIF file on disk is up-to-date.
         """
-        current_block = self.ui.datanameComboBox.currentIndex()
-        if not self.validation_response_forms_list:
-            return
         n = 0
         for response_row in self.validation_response_forms_list:
             response_txt = response_row.response_text_edit.toPlainText()
             if not response_txt:
-                # No response was written
                 continue
             n += 1
-            v = VREF()
-            v.key = response_row.form['name']
-            v.problem = response_row.form['problem']
-            v.response = response_txt
-            v.data_name = response_row.form['data_name']
-            for block in self.cif.doc:
-                if block.name == v.data_name:
-                    block.set_pair(v.key, quote(utf8_to_str(v.value)))
-        self.save_current_cif_file()
-        self.load_cif_file(self.cif.finalcif_file, current_block, load_changes=False)
-        if n:
-            self.ui.CheckCifLogPlainTextEdit.appendPlainText('Forms saved')
-        else:
-            self.ui.CheckCifLogPlainTextEdit.appendPlainText('No forms were filled in.')
-
-    def _switch_to_report(self) -> None:
-        self.ui.ResponsesTabWidget.setCurrentIndex(0)
+            vrf_entry = response_row.vrf_entry
+            vrf_entry.response = response_txt
+            self.cif.block.set_pair(vrf_entry.key, quote(utf8_to_str(vrf_entry.value)))
+        return n
 
     def _pdf_checkcif_finished(self) -> None:
         self.ui.CheckcifPDFOnlineButton.setEnabled(True)
         self.ui.CheckcifHTMLOnlineButton.setEnabled(True)
 
+    def _on_vrf_deleted(self, vrf_widget) -> None:
+        """
+        Handles the ``deleted`` signal emitted by a ``MyVRFContainer`` widget.
+
+        Removes the widget from ``validation_response_forms_list`` and from the
+        main CIF table row.  The table's ``row_deleted`` signal then calls
+        ``_deleted_row`` which removes the key from the in-memory CIF block; the
+        deletion is written to disk on the next save.
+        """
+        if vrf_widget in self.validation_response_forms_list:
+            self.validation_response_forms_list.remove(vrf_widget)
+        # Remove the row from the main table (this also emits row_deleted → _deleted_row
+        # which removes the key from the CIF block in memory).
+        table = self.ui.cif_main_table
+        row = table.row_from_key(vrf_widget.vrf_entry.key)
+        table.delete_row(row)
+
+    def _on_vrf_template_requested(self, key: str) -> None:
+        """
+        Opens the text-snippet template editor for the given VRF *key*.
+
+        The editor is keyed on the alert code portion of the key
+        (e.g. ``_vrf_PLAT307`` regardless of the data-block suffix), so all
+        structures sharing the same alert code share their templates.
+        The current response text from the VRF widget is pre-filled in the
+        editor's preview field so the user can combine it with a snippet.
+        """
+        alert_code = self.get_vrf_errortype(key)
+        self.textedit.cif_key = key
+        self.textedit.ui.cifKeyLineEdit.setText(alert_code)
+        self.textedit.add_textfields(self.settings.load_settings_list('text_templates', alert_code))
+        # Pre-fill the editor preview with the current response text from the VRF widget.
+        vrf_widget = self.ui.cif_main_table.get_vrf_widget(key)
+        if vrf_widget is not None:
+            current_response = vrf_widget.response_text_edit.toPlainText()
+            self.textedit.ui.plainTextEdit.setPlainText(current_response)
+        self.ui.MainStackedWidget.go_to_text_template_page()
+
     def do_pdf_checkcif(self) -> None:
         """
         Performs an online checkcif and shows the result as pdf.
@@ -1339,6 +1410,9 @@ class AppWindow(QMainWindow):
         if not self.cif:
             # No file is opened
             return None
+        # Flush VRF response text *before* rename_data_name, because the
+        # rename replaces VRF keys with new names derived from the block name.
+        self._write_vrf_data_to_cif()
         if not self.cif.is_multi_cif:
             self.cif.rename_data_name(''.join(self.ui.datanameComboBox.currentText().split(' ')))
         self.store_data_from_table_rows()
@@ -1475,7 +1549,9 @@ class AppWindow(QMainWindow):
         # increases the pont size every time a bit more :)
         # size = font.pointSize()
         # font.setPointSize(14)
-        doc.setDefaultFont(self.fixfont)
+        fixfont = QtGui.QFontDatabase.systemFont(QtGui.QFontDatabase.SystemFont.FixedFont)
+        fixfont.setPointSize(fixfont.pointSize() + 2)
+        doc.setDefaultFont(fixfont)
         final_textedit.setLineWrapMode(QPlainTextEdit.LineWrapMode.NoWrap)
         final_textedit.setPlainText(self.cif.finalcif_file.read_text(encoding='utf-8', errors='ignore'))
         QtCore.QTimer().singleShot(0, lambda: final_textedit.highlighter.setDocument(doc))
@@ -1484,7 +1560,7 @@ class AppWindow(QMainWindow):
         """
         Import an additional cif file to the main table.
         """
-        imp_cif: CifContainer | None = None
+        imp_cif: CifContainer
         if not filename:
             filename = cif_file_open_dialog(parent=self, filter="CIF file (*.cif *.pcf *.cif_od *.cfx *.sqf)")
         if not filename:
@@ -1569,8 +1645,8 @@ class AppWindow(QMainWindow):
         self._load_block(block, load_changes=load_changes)
         self.add_data_names_to_combobox()
         self.ui.datanameComboBox.setCurrentIndex(block)
-        QtCore.QTimer.singleShot(0, self.ui.cif_main_table.resizeRowsToContents)
         self.ui.datanameComboBox.blockSignals(False)
+        QtCore.QTimer.singleShot(500, self.ui.cif_main_table.resizeRowsToContents)
         if self.cif.is_multi_cif:
             self._flash_block_combobox()
         self.cif.set_order_keys(self.ui.cifOrderWidget.order_keys)
@@ -1613,8 +1689,10 @@ class AppWindow(QMainWindow):
         self.ui.ckf_textedit.clear()
         # Set to empty state before loading:
         self.missing_data = set()
-        # clean table and vheader before loading:
+        # clean table (including any inline VRF widgets) before loading:
         self.ui.cif_main_table.delete_content()
+        # reset VRF tracking lists; fill_cif_table repopulates them via inline widgets
+        self.validation_response_forms_list = []
 
     def _load_block(self, index: int, load_changes: bool = True) -> None:
         if not self.cif:
@@ -2098,11 +2176,21 @@ class AppWindow(QMainWindow):
         # Phase 3 – create widgets (with view repaints suspended)
         # ------------------------------------------------------------------
         table.setUpdatesEnabled(False)
+        alert_help = AlertHelp(self.checkdef)
         try:
             for row_num, row_data in enumerate(model_rows):
                 if row_data.is_separator:
                     table.add_separation_line(row_num)
                     self.complete_data_row = row_num
+                elif row_data.key.startswith('_vrf_'):
+                    # Show a VRF response-form widget spanning all 3 columns inline.
+                    entry = VRFEntry.from_cif_pair(row_data.key, row_data.raw_value)
+                    vrf = MyVRFContainer(entry, alert_help.get_help(entry.alert_num),
+                                         parent=self, is_multi_cif=self.cif.is_multi_cif)
+                    vrf.deleted.connect(self._on_vrf_deleted)
+                    vrf.template_requested.connect(self._on_vrf_template_requested)
+                    self.validation_response_forms_list.append(vrf)
+                    table.place_vrf_widget(row_num, vrf)
                 else:
                     table.setText(row=row_num, key=row_data.key, column=Column.CIF,
                                   txt=row_data.strval)
@@ -2140,78 +2228,6 @@ class AppWindow(QMainWindow):
         self.ui.cif_main_table.setText(key=key, column=Column.DATA, txt=strval)
         self.ui.cif_main_table.setText(key=key, column=Column.EDIT, txt=strval)
 
-    def make_loops_tables(self) -> None:
-        for _ in range(self.ui.LoopsTabWidget.count()):
-            # I use this, so that always the first tab stays.
-            self.ui.LoopsTabWidget.removeTab(1)
-        if self.cif and self.cif.loops:
-            self.add_loops_tables()
-
-    def add_loops_tables(self) -> None:
-        """
-        Generates a list of tables containing the cif loops.
-        """
-        # do_not_display = ('_diffrn_refln_index_h')
-        for num, loop in enumerate(self.cif.loops):
-            tags = loop.tags
-            if not tags or len(tags) < 1:
-                continue
-            # if tags[0] in do_not_display:
-            #    continue
-            self.new_loop_tab(loop, num, tags)
-        if self.cif.res_file_data:
-            self.add_res_file_to_loops()
-
-    def new_loop_tab(self, loop: gemmi.cif.Loop, num: int, tags: list[str]):
-        loop = Loop(tags, values=grouper(loop.values, loop.width()),
-                    parent=self.ui.LoopsTabWidget, block=self.cif.block)
-        self.add_loop_widget(loop, first_tag=tags[0])
-        self.ui.LoopsTabWidget.setTabToolTip(num + 1, tags[0])
-        self.ui.revertLoopsPushButton.clicked.connect(loop.model.revert)
-
-    def add_loop_widget(self, loop: Loop, first_tag: str) -> None:
-        self.ui.LoopsTabWidget.addTab(loop.tableview, cif_to_header_label.get(first_tag) or first_tag)
-
-    def add_res_file_to_loops(self) -> None:
-        textedit = QPlainTextEdit()
-        self.ui.LoopsTabWidget.addTab(textedit, 'SHELX res file')
-        textedit.setPlainText(self.cif.res_file_data[1:-1])
-        doc = textedit.document()
-        doc.setDefaultFont(self.fixfont)
-        textedit.setLineWrapMode(QPlainTextEdit.LineWrapMode.NoWrap)
-        textedit.setReadOnly(True)
-
-    def _go_to_new_loop_page(self) -> None:
-        self.loopcreate = LoopCreator(parent=self, cif=self.cif)
-        self.ui.LoopsTabWidget.addTab(self.loopcreate, 'Create Loops')
-        self.ui.LoopsTabWidget.setCurrentIndex(self.ui.LoopsTabWidget.count() - 1)
-        self.ui.revertLoopsPushButton.hide()
-        self.ui.newLoopPushButton.hide()
-        self.ui.deleteLoopButton.hide()
-        self.loopcreate.saveLoopPushButton.clicked.connect(self.save_new_loop_to_cif)
-
-    def _on_delete_current_loop(self) -> None:
-        current_tab_index = self.ui.LoopsTabWidget.currentIndex()
-        current_table_view: MyQTableView = self.ui.LoopsTabWidget.widget(current_tab_index)
-        try:
-            header_model: LoopTableModel | QtCore.QAbstractItemModel = current_table_view.horizontalHeader().model()
-        except AttributeError:
-            # Not a QTableView
-            return
-        header_item = header_model._header[0]
-        loop: gemmi.cif.Loop = self.cif.block.find_loop(header_item).get_loop()
-        table: gemmi.cif.Table = self.cif.block.find(loop.tags)
-        table.erase()
-        self.ui.LoopsTabWidget.removeTab(current_tab_index)
-
-    def save_new_loop_to_cif(self):
-        if self.loopcreate:
-            loop = self.loopcreate.save_new_loop_to_cif()
-            self.new_loop_tab(loop=loop, num=self.ui.LoopsTabWidget.count(), tags=self.loopcreate.tags)
-            self.ui.LoopsTabWidget.removeTab(self.ui.LoopsTabWidget.count() - 2)
-            self.loopcreate.deleteLater()
-            self.ui.LoopsTabWidget.setCurrentIndex(self.ui.LoopsTabWidget.count() - 1)
-
     def add_row(self, key: str, value: str, at_start=False, position: int | None = None) -> None:
         """
         Create a empty row at bottom of cif_main_table. This method only fills cif data in the

{finalcif-158 → finalcif-159}/finalcif/cif/checkcif/checkcif.py

@@ -19,6 +19,7 @@ from requests import Response
 from requests.exceptions import MissingSchema
 
 from finalcif.cif.cif_file_io import CifContainer
+from finalcif.cif.vrf_entry import VRFEntry
 
 
 class CheckCif(QThread):
@@ -198,37 +199,39 @@ class MyHTMLParser(HTMLParser):
             return ''
 
     @property
-    def response_forms(self) -> list[dict[str, str]]:
+    def response_forms(self) -> list[VRFEntry]:
         """
-        :returns
-        [
-        {'level'     : 'PLAT035_ALERT_1_B',
-         'name'      : '_vrf_PLAT035_DK_zucker2_0m',
-         'problem'   : '_chemical_absolute_configuration Info  Not Given     Please Do '
-                       '!  ',
-         'alert_num': 'PLAT035'},
-         {...},
-         ]
+        :returns a list of VRFEntry instances, one per alert with a validation response form.
         """
-        forms = []
-        single_form = {}
+        entries = []
+        current_key = ''
+        current_plat = ''
+        current_data = ''
+        current_level = ''
         for line in self.vrf.split('\n'):
             if line.startswith('_vrf'):
-                single_form = {'level': ''}
-                plat = line.split('_')[2]
-                data = line.split('_', 3)[3]
-                single_form.update({'name': line, 'alert_num': plat, 'data_name': data})
+                parts = line.split('_')
+                current_key = line
+                current_plat = parts[2] if len(parts) > 2 else ''
+                current_data = line.split('_', 3)[3] if len(parts) > 3 else ''
+                current_level = ''
             if line.startswith(';'):
                 continue
             if line.startswith('PROBLEM'):
                 problem = line[9:]
-                single_form.update({'problem': problem})
                 for x in self.alert_levels:
-                    if single_form['alert_num'] == x[:7]:
-                        single_form.update({'level': x})
+                    if current_plat == x[:7]:
+                        current_level = x
                         break
-                forms.append(single_form)
-        return forms
+                entries.append(VRFEntry(
+                    key=current_key,
+                    data_name=current_data,
+                    problem=problem,
+                    response='?',
+                    alert_num=current_plat,
+                    level=current_level,
+                ))
+        return entries
 
 
 class AlertHelp:
@@ -238,7 +241,7 @@ class AlertHelp:
     def get_help(self, alert: str) -> str:
         checkdef_help = self._parse_checkdef(alert)
         if not checkdef_help or 'PLAT' not in alert:
-            return 'No help available.'
+            return ''
         return checkdef_help
 
     def _parse_checkdef(self, alert: str) -> str:

{finalcif-158 → finalcif-159}/finalcif/cif/cif_file_io.py

@@ -965,6 +965,22 @@ class CifContainer:
             if item.pair is not None:
                 yield item.pair
 
+    def get_vrf_entries(self) -> list:
+        """
+        Returns a list of VRFEntry instances for every ``_vrf_*`` key/value pair
+        found in the current block.  The VRFEntry objects are constructed by
+        parsing the semicolon-delimited text value that stores PROBLEM and
+        RESPONSE lines.
+        """
+        from finalcif.cif.vrf_entry import VRFEntry
+        entries = []
+        for item in self.block:
+            if item.pair is not None:
+                key, raw_value = item.pair
+                if key.startswith('_vrf_'):
+                    entries.append(VRFEntry.from_cif_pair(key, raw_value))
+        return entries
+
     def _is_centrokey(self, key) -> bool:
         """
         Is True if the kurrent key is only valid