73 make attributes of multi cif accessible in report templates

.gitignore

@@ -215,3 +215,5 @@ test-data/DK_Zucker2_0m-finalcif_changes.cif
 olex2
 .vs
 x64
+test-data/1000007-multi-multitable.docx
+test-data/report_1000007-multi-finalcif.docx

.run/make documentation Windows.run.xml

@@ -1,8 +1,8 @@
 <component name="ProjectRunConfigurationManager">
   <configuration default="false" name="make documentation Windows" type="ShConfigurationType">
     <option name="SCRIPT_TEXT" value="" />
-    <option name="INDEPENDENT_SCRIPT_PATH" value="true" />
-    <option name="SCRIPT_PATH" value="docs/make.bat" />
+    <option name="INDEPENDENT_SCRIPT_PATH" value="false" />
+    <option name="SCRIPT_PATH" value="$PROJECT_DIR$/docs/make.bat" />
     <option name="SCRIPT_OPTIONS" value="singlehtml" />
     <option name="INDEPENDENT_SCRIPT_WORKING_DIRECTORY" value="true" />
     <option name="SCRIPT_WORKING_DIRECTORY" value="$PROJECT_DIR$" />

docs/report.rst

@@ -106,6 +106,9 @@ Data Available for the Report
 
     'cif'                   : Gives you access to the full CIF information, use it like
                               {{ cif._exptl_crystal_density_diffrn }} or the variables in the next table.
+    'name'                  : Name of the current CIF block.
+    'block'                 : The context of all CIF blocks of a multi-CIF usable as attribute, e.g. block.name.foo
+    'blocklist'             : A list of all CIF blocks of a multi-CIF usable for iteration over blocks.
     'atomic_coordinates'    : The atomic coordinates as ('label', 'x', 'y', 'z', 'u_eq') for each atom.
     'displacement_parameters': The atomic displacement parameters as ('label', 'U11', 'U22', 'U33',
                                'U23', 'U13', 'U12') for each atom.
@@ -150,6 +153,8 @@ Data Available for the Report
     'restraints'            : The value of '_refine_ls_number_restraints'.
     'parameters'            : The value of '_refine_ls_number_parameters'.
     'goof'                  : The value of '_refine_ls_goodness_of_fit_ref'.
+    't_min'                 : The value of '_exptl_absorpt_correction_T_min'.
+    't_max'                 : The value of '_exptl_absorpt_correction_T_max'.
     'ls_R_factor_gt'        : The value of '_refine_ls_R_factor_gt'.
     'ls_wR_factor_gt'       : The value of '_refine_ls_wR_factor_gt'.
     'ls_R_factor_all'       : The value of '_refine_ls_R_factor_all'.
@@ -181,6 +186,9 @@ no real minus sign in front. The former values hav hyphens replaced with minus s
    'cif.disorder_present'       : Is true if atoms in parts are present in the structure.
    'cif.cell'                   : The unit cell as 'a', 'b', 'c', 'alpha', 'beta', 'gamma', 'volume'.
    'cif.bonds'                  : The list of bonds as 'label1', 'label2', 'dist', 'symm'.
+   'cif.bond_dist("atom1-atom2")'    : The bond distance between two atoms.
+   'cif.angle("atom1-atom2-atom3")'  : The angle between three atoms.
+   'cif.torsion("atom1-atom2-atom3-atom4")'  : The torsion angle between four atoms.
    'angles'                     : The list of angles as 'label1', 'label2', 'label3', 'angle_val',
                                   'symm1', 'symm2'.
    'torsion_angles'             : The list of torsion angles as 'label1', 'label2', 'label3', 'label4',
@@ -195,6 +203,41 @@ no real minus sign in front. The former values hav hyphens replaced with minus s
 The above is not limited to the templates of FinalCif. It is also possible to insert template tags
 into any other Word document and replace them with values from a CIF file. There are no limits to
 the imagination.
+Sine version 130, it is possible to address the values of individual blocks of a multi-CIF. For example,
+
+.. code-block:: jinja
+
+   {% for block in blocklist %}
+      {{ block.name }}
+   {% enfor %}
+
+prints all block names of a multi-CIF.
+
+Another way is to use the 'block' variable in the template. It contains the respective block data.
+To access the values of the block, you have to use the block name in square brackets. This prevents
+conflicts with the Jinja2 syntax.
+For example, the chemical formula of the block 'compound1' of a multi-CIF is:
+
+.. code-block:: jinja
+
+    {{ block['compound1']._chemical_formula_sum }}
+
+Special methods allow you to access the values of the atoms, bonds, angles, torsion angles of single- and
+multi-CIF files:
+
+.. code-block:: jinja
+
+    {{ block['p-1'].cif.bond_dist('C1-C2') }}
+    {{ block['p-1'].cif.angle('C1-C2-C3') }}
+
+Prints out the distance between C1 and C2 as well as the angle between C1, C2 and C3.
+This can be used to render specific bond distances of a multi-CIF
+file to a publication without the need to change the values by hand every time a refinement changes.
+Be aware that the atom labels must be given in the order they have in the respective CIF loop. When a
+an atom combination is not present in a CIF loop, the value 'None' will appear.
+
+For a single-CIF, leave out the "block['block name']." part.
+
 
 
 Further information for programmers:

finalcif/appwindow.py

@@ -1113,14 +1113,16 @@ def make_report_tables(self) -> None:
                 print('Report without templates')
                 make_report_from(options=self.options, cif=self.cif,
                                  output_filename=str(report_filename), picfile=picfile)
+                if self.cif.is_multi_cif and self.cif.doc[0].name != 'global':
+                    make_multi_tables(cif=self.cif, output_filename=str(multi_table_document))
             else:
                 print('Report with templates')
                 t = TemplatedReport()
-                t.make_templated_report(options=self.options, cif=self.cif,
-                                        output_filename=str(report_filename), picfile=picfile,
-                                        template_path=Path(self.get_checked_templates_list_text()))
-            if self.cif.is_multi_cif and self.cif.doc[0].name != 'global':
-                make_multi_tables(cif=self.cif, output_filename=str(multi_table_document))
+                ok = t.make_templated_report(options=self.options, cif=self.cif,
+                                             output_filename=str(report_filename), picfile=picfile,
+                                             template_path=Path(self.get_checked_templates_list_text()))
+                if not ok:
+                    return None
         except FileNotFoundError as e:
             if DEBUG:
                 raise
@@ -1137,8 +1139,9 @@ def make_report_tables(self) -> None:
             return
         if not self.running_inside_unit_test:
             self.open_report_document(report_filename, multi_table_document)
+            print('dbg> disabled temporarily!')
             # Save report and other files to a zip file:
-            self.zip_report(report_filename)
+            # self.zip_report(report_filename)
 
     def report_without_template(self) -> bool:
         """Check whether the report is generated from a template or hard-coded"""
@@ -1165,7 +1168,7 @@ def zip_report(self, report_filename: Path) -> None:
             arc.zip.write(filename=multitable, arcname=multitable.name)
 
     def open_report_document(self, report_filename: Path, multi_table_document: Path) -> None:
-        if self.cif.is_multi_cif:
+        if self.cif.is_multi_cif and self.report_without_template():
             open_file(multi_table_document)
         open_file(report_filename)
 
@@ -1444,8 +1447,16 @@ def load_cif_file(self, filepath: Path, block=0, load_changes: bool = True) -> N
         self.ui.cif_main_table.resizeRowsToContents()
         self.ui.datanameComboBox.blockSignals(False)
         if self.cif.is_multi_cif:
-            # short after start, because window size is not finished
-            QtCore.QTimer(self).singleShot(1000, self.ui.datanameComboBox.showPopup)
+            self._flash_block_combobox()
+
+    def _flash_block_combobox(self):
+        orig_pal = self.ui.datanameComboBox.palette()
+        pal = QtGui.QPalette()
+        pal.setColor(QtGui.QPalette.Base, light_blue)
+        self.ui.datanameComboBox.setAutoFillBackground(True)
+        # short after start, because window size is not finished before:
+        QtCore.QTimer(self).singleShot(1500, lambda: self.ui.datanameComboBox.setPalette(pal))
+        QtCore.QTimer(self).singleShot(2600, lambda: self.ui.datanameComboBox.setPalette(orig_pal))
 
     def add_data_names_to_combobox(self) -> None:
         self.ui.datanameComboBox.clear()
@@ -1489,7 +1500,7 @@ def _load_block(self, index: int, load_changes: bool = True) -> None:
                 self.finalcif_changes_filename.unlink(missing_ok=True)
             elif self.finalcif_changes_filename.exists() and self.changes_cif_has_values():
                 changes_exist = True
-            if changes_exist and not self.running_inside_unit_test and self.changes_answer == 0:
+            if changes_exist and not self.running_inside_unit_test and self.changes_answer == 0 and not self.cif.is_multi_cif:
                 self.changes_answer = QMessageBox.question(self, 'Previous changes found',
                                                            f'Previous changes from a former FinalCif session '
                                                            f'were found in\n{self.finalcif_changes_filename.name}.\n\n'

finalcif/cif/cif_file_io.py

@@ -8,9 +8,8 @@
 import re
 from collections import namedtuple
 from contextlib import suppress
-from functools import cache
 from pathlib import Path
-from typing import Dict, List, Tuple, Union, Generator, Type
+from typing import Dict, List, Tuple, Union, Generator
 
 import gemmi
 from gemmi.cif import as_string, Document, Loop
@@ -141,7 +140,6 @@ def _on_load(self) -> None:
         self.check_hkl_min_max()
 
     @property
-    @cache
     def hkl_extra_info(self):
         return self._abs_hkl_details()
 
@@ -595,10 +593,10 @@ def calc_checksum(input_str: str) -> int:
         """
         crc_sum = 0
         try:
-            input_str = input_str.encode('cp1250', 'ignore')
+            bytes_str = input_str.encode('cp1250', 'ignore')
         except Exception:
-            input_str = input_str.encode('ascii', 'ignore')
-        for char in input_str:
+            bytes_str = input_str.encode('ascii', 'ignore')
+        for char in bytes_str:
             # print(char)
             if char > 32:  # ascii 32 is space character
                 crc_sum += char
@@ -663,7 +661,7 @@ def atoms(self, without_h: bool = False) -> Generator:
         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')
-        atom = namedtuple('Atom', ('label', 'type', 'x', 'y', 'z', 'part', 'occ', 'u_eq'))
+        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),
@@ -682,7 +680,7 @@ def atoms_fract(self) -> Generator:
 
     @property
     def atoms_orth(self) -> Generator:
-        atom = namedtuple('Atom', ('label', 'type', 'x', 'y', 'z', 'part', 'occ', 'u_eq'))
+        atom = namedtuple('atom', ('label', 'type', 'x', 'y', 'z', 'part', 'occ', 'u_eq'))
         cell = self.atomic_struct.cell
         for at in self.atomic_struct.sites:
             x, y, z = at.orth(cell)
@@ -719,10 +717,10 @@ def disorder_present(self) -> bool:
         return False
 
     @property
-    def cell(self) -> Type['cell']:
+    def cell(self):
         c = self.atomic_struct.cell
-        nt = namedtuple('cell', 'a, b, c, alpha, beta, gamma, volume')
-        return nt(c.a, c.b, c.c, c.alpha, c.beta, c.gamma, c.volume)
+        cell = namedtuple('cell', 'a, b, c, alpha, beta, gamma, volume')
+        return cell(c.a, c.b, c.c, c.alpha, c.beta, c.gamma, c.volume)
 
     def ishydrogen(self, label: str) -> bool:
         """
@@ -749,14 +747,32 @@ def bonds(self, without_h: bool = False) -> Generator:
         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')
-        bond = namedtuple('Bond', ('label1', 'label2', 'dist', 'symm'))
+        bond = namedtuple('bond', ('label1', 'label2', 'dist', 'symm'))
         for label1, label2, dist, symm, publ in zip(label1, label2, dist, symm, publ_loop):
             if without_h and (self.ishydrogen(label1) or self.ishydrogen(label2)) or \
                     self.yes_not_set(publ, self._has_publ_flag_set(publ_loop)):
                 continue
             else:
                 yield bond(label1=label1, label2=label2, dist=dist, symm=self.checksymm(symm))
 
+    def bond_dist(self, pair: str) -> Union[float, None]:
+        for p in self.bonds():
+            if f'{p.label1}-{p.label2}' == pair:
+                return p.dist
+        return None
+
+    def angle(self, atoms: str) -> Union[float, None]:
+        for p in self.angles():
+            if f'{p.label1}-{p.label2}-{p.label3}' == atoms:
+                return p.angle_val
+        return None
+
+    def torsion(self, atoms: str) -> Union[float, None]:
+        for p in self.torsion_angles():
+            if f'{p.label1}-{p.label2}-{p.label3}-{p.label4}' == atoms:
+                return p.torsang
+        return None
+
     def _has_publ_flag_set(self, publ_loop: gemmi.cif.Column) -> bool:
         return any([x[0].lower() == 'y' for x in list(publ_loop) if x])
 
@@ -768,7 +784,7 @@ def angles(self, without_H: bool = False) -> Generator:
         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')
-        angle = namedtuple('Angle', ('label1', 'label2', 'label3', 'angle_val', 'symm1', 'symm2'))
+        angle = namedtuple('angle', ('label1', 'label2', 'label3', 'angle_val', 'symm1', 'symm2'))
         for label1, label2, label3, angle_val, symm1, symm2, publ in \
                 zip(label1, label2, label3, angle_val, symm1, symm2, publ_loop):
             if without_H and (
@@ -876,10 +892,10 @@ def keys_with_essentials(self) -> Tuple[List[Tuple[str, str]], List[Tuple[str, s
         for item in self.block:
             if item.pair is not None:
                 key, value = item.pair
-                #if key.startswith('_shelx'):
+                # if key.startswith('_shelx'):
                 #    # No-one should edit shelx values:
                 #    continue
-                #if key == '_iucr_refine_instructions_details':
+                # if key == '_iucr_refine_instructions_details':
                 #    continue
                 if self._is_centrokey(key):
                     continue
@@ -945,7 +961,8 @@ def test_hkl_checksum(self) -> bool:
 
     c = CifContainer('test-data/DK_Zucker2_0m.cif')
     c.load_this_block(len(c.doc) - 1)
-    pp(list(c.torsion_angles()))
+    # pp(list(c.torsion_angles()))
+    print(c.bond_dist('C1-C2'))
     # pp(c.hkl_extra_info)
     # print(c.hkl_file)
     # print(c.hkl_as_cif)

finalcif/gui/dialogs.py

@@ -82,6 +82,9 @@ def show_general_warning(parent, warn_text: str = '', info_text: str = '', windo
     """
     if not warn_text:
         return None
+    if "PYTEST_CURRENT_TEST" in os.environ:
+        print(f'DBG> Running inside a pytest -> not showing error message:\n{warn_text}\n{info_text}')
+        return None
     box = QMessageBox(parent=parent)
     box.setTextFormat(Qt.AutoText)
     box.setWindowTitle(window_title)

finalcif/report/report_text.py

@@ -4,9 +4,11 @@
 
 import gemmi
 from docx import Document
+from docx.oxml.xmlchemy import BaseOxmlElement
 from docx.text.paragraph import Paragraph
 from docx.text.run import Run
 from lxml import etree
+from lxml.etree import XSLTAccessControl
 from shelxfile.atoms.atoms import Atom as SHXAtom
 
 from finalcif.app_path import application_path
@@ -19,11 +21,12 @@
 from finalcif.tools.misc import protected_space, angstrom, zero_width_space, remove_line_endings, flatten
 
 
-def math_to_word(eq: str) -> str:
+def math_to_word(eq: str) -> BaseOxmlElement:
     """Transform a sympy equation to be printed in word document."""
     tree = etree.fromstring(eq)
     xslt = etree.parse(os.path.join(application_path, 'template/mathml2omml.xsl'))
-    transform = etree.XSLT(xslt)
+    acess_control = XSLTAccessControl(read_network=False, write_network=False)
+    transform = etree.XSLT(xslt, access_control=acess_control)
     new_dom = transform(tree)
     return new_dom.getroot()