finalcif 142__tar.gz → 144__tar.gz

{finalcif-142 → finalcif-144}/.gitignore

@@ -221,3 +221,5 @@ test.html
 
 work/~$test.docx
 tests/examples/work/report_cu_BruecknerJK_153F40_0m-finalcif_pm.docx
+tests/examples/multi-multitable.docx
+tests/examples/report_multi-finalcif.docx

{finalcif-142 → finalcif-144}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: finalcif
-Version: 142
+Version: 144
 Summary: CIF file editor
 Project-URL: Homepage, https://dkratzert.de/finalcif.html
 Project-URL: Bug Tracker, https://github.com/dkratzert/FinalCif/issues

finalcif-144/finalcif/__init__.py

@@ -0,0 +1,2 @@
+
+VERSION = 144

{finalcif-142 → finalcif-144}/finalcif/appwindow.py

@@ -24,6 +24,7 @@ from PyQt5.QtWidgets import (QMainWindow, QShortcut, QCheckBox, QListWidgetItem,
 from gemmi import cif
 
 from finalcif import VERSION
+from finalcif.app_path import application_path
 # QtCore.QCoreApplication.setAttribute(QtCore.Qt.AA_EnableHighDpiScaling)
 # QtCore.QCoreApplication.setAttribute(QtCore.Qt.AA_ShareOpenGLContexts)
 from finalcif.cif.checkcif.checkcif import MyHTMLParser, AlertHelp, CheckCif
@@ -1104,7 +1105,7 @@ class AppWindow(QMainWindow):
             item = self.ui.docxTemplatesListWidget.item(index)
             if item.checkState() == Qt.Checked:
                 if self.templates.report_from_default_template():
-                    return 'finalcif/template/report_default.docx'
+                    return str(application_path / 'template/report_default.docx')
                 else:
                     return item.text()
 
@@ -1822,9 +1823,8 @@ class AppWindow(QMainWindow):
             self.add_ccdc_number()
             if self.cif.shx and self.cif.shx.abin and not self.cif['_platon_squeeze_void_probe_radius']:
                 show_general_warning(self, "A SQUEEZE refinement was detected.\n"
-                                           "Please import the "
-                                           "corresponding .sqf file from PLATON and\n"
-                                           "complete the _platon_squeeze_void_content information"
+                                           "Please import the corresponding .sqf file\n"
+                                           "from PLATON and complete the _platon_squeeze_void_content information "
                                            "in the 'Platon SQUEEZE voids' loop.")
         vheadlist = []
         for row_number in range(self.ui.cif_main_table.model().rowCount()):

{finalcif-142 → finalcif-144}/finalcif/cif/cif_file_io.py

@@ -356,6 +356,12 @@ class CifContainer():
             print('No hkl data found in CIF!, {}'.format(e))
             return ''
 
+    @property
+    def fab_file(self):
+        if self['_shelx_fab_file']:
+            return self['_shelx_fab_file']
+        return ''
+
     @property
     def hkl_as_cif(self) -> str:
         return HKL(self.hkl_file, self.block.name, hklf_type=self.hklf_number).hkl_as_cif
@@ -823,7 +829,7 @@ class CifContainer():
         publ_loop = self.block.find_loop('_geom_angle_publ_flag')
         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):
+                zip(label1, label2, label3, angle_val, symm1, symm2, publ_loop):
             if (without_H and (self.ishydrogen(label1) or self.ishydrogen(label2) or
                                self.ishydrogen(label3)) or (self.yes_not_set(publ))):
                 continue
@@ -895,7 +901,7 @@ 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)):
             if self.yes_not_set(publ):
                 continue
             if self.picometer:

{finalcif-142 → finalcif-144}/finalcif/displaymol/molecule2D.py

@@ -7,7 +7,7 @@ from typing import List, Union
 import numpy as np
 from PyQt5 import QtWidgets
 from PyQt5.QtCore import Qt
-from PyQt5.QtGui import QPainter, QPen, QBrush, QColor, QMouseEvent, QPalette, QImage, QResizeEvent
+from PyQt5.QtGui import QPainter, QPen, QBrush, QColor, QMouseEvent, QPalette, QImage, QResizeEvent, QWheelEvent
 
 from finalcif.cif.atoms import get_radius_from_element, element2color
 from finalcif.cif.cif_file_io import CifContainer
@@ -29,6 +29,7 @@ class MoleculeWidget(QtWidgets.QWidget):
         super().__init__(parent=parent)
         self.factor = 1.0
         self.atoms_size = 12
+        self.fontsize = 13
         self.bond_width = 2
         self.labels = False
         self.molecule_center = np.array([0, 0, 0])
@@ -56,6 +57,12 @@ class MoleculeWidget(QtWidgets.QWidget):
         self.projected_points = []
         self.zoom = 1.1
 
+    def setLabelFont(self, font_size: int):
+        if font_size < 0:
+            font_size = 1
+        self.fontsize = font_size
+        self.update()
+
     def clear(self):
         self.open_molecule(atoms=[])
 
@@ -84,7 +91,7 @@ class MoleculeWidget(QtWidgets.QWidget):
             self.painter = QPainter(self)
             self.painter.setRenderHint(QPainter.Antialiasing)
             font = self.painter.font()
-            font.setPixelSize(13)
+            font.setPixelSize(self.fontsize)
             self.painter.setFont(font)
             try:
                 self.draw()
@@ -95,6 +102,12 @@ class MoleculeWidget(QtWidgets.QWidget):
     def mousePressEvent(self, event: QMouseEvent) -> None:
         self.lastPos = event.pos()
 
+    def wheelEvent(self, event: QWheelEvent):
+        if event.angleDelta().y() > 0:
+            self.setLabelFont(self.fontsize + 2)
+        elif event.angleDelta().y() < 0:
+            self.setLabelFont(self.fontsize - 2)
+
     def save_image(self, filename: Path, image_scale=1.5):
         image = QImage(self.size() * image_scale, QImage.Format_RGB32)
         image.fill(Qt.white)
@@ -285,6 +298,7 @@ def display(atoms: List[Atomtuple]):
     render_widget = MoleculeWidget(None)
     t1 = time.perf_counter()
     render_widget.open_molecule(atoms, labels=False)
+    render_widget.labels = True
     print(f'Time to display molecule: {time.perf_counter() - t1:5.4} s')
     # add and show
     window.setCentralWidget(render_widget)

{finalcif-142 → finalcif-144}/finalcif/report/templated_report.py

@@ -40,7 +40,7 @@ from finalcif.report.report_text import (math_to_word, gstr, format_radiation, _
 from finalcif.report.symm import SymmetryElement
 from finalcif.tools.misc import (isnumeric, this_or_quest, timessym, angstrom, protected_space,
                                  less_or_equal, halbgeviert, minus_sign, ellipsis_mid, _angstrom_to_x, angstrom_to_pm,
-                                 angstrom_to_nanometers)
+                                 angstrom_to_nanometers, do_nothing)
 from finalcif.tools.options import Options
 from finalcif.tools.space_groups import SpaceGroups
 
@@ -577,10 +577,10 @@ class Formatter(ABC):
         radiation_wavelength = cif['_diffrn_radiation_wavelength']
         try:
             resolution_angst = float(radiation_wavelength) / (2 * sin(radians(float(theta_max))))
-            if not cif.picometer:
-                d_max = f' ({resolution_angst:.2f}{protected_space}{angstrom})'
-            else:
+            if cif.picometer:
                 d_max = f' ({angstrom_to_pm(str(resolution_angst)):.2}{protected_space}pm)'
+            else:
+                d_max = f' ({resolution_angst:.2f}{protected_space}{angstrom})'
             # 2theta range:
             return f"{2 * float(theta_min):.2f} to {2 * float(theta_max):.2f}{d_max}"
         except ValueError:
@@ -1041,8 +1041,8 @@ class TemplatedReport():
         jinja_env = jinja2.Environment()
         jinja_env.globals.update(strip=str.strip)
         jinja_env.filters['inv_article'] = report_text.get_inf_article
-        jinja_env.filters['to_pm'] = angstrom_to_pm
-        jinja_env.filters['to_nm'] = angstrom_to_nanometers
+        jinja_env.filters['to_pm'] = angstrom_to_pm if self.options.use_picometers else do_nothing
+        jinja_env.filters['to_nm'] = angstrom_to_nanometers if self.options.use_picometers else do_nothing
         jinja_env.filters['float_num'] = report_text.format_float_with_decimal_places
         # foo[1,2] bar[3]:
         jinja_env.filters['ref_num'] = self.count_reference

{finalcif-142 → finalcif-144}/finalcif/tools/misc.py

@@ -98,15 +98,28 @@ def grouper(inputs, n, fillvalue=None):
 
 
 def angstrom_to_pm(angstrom: str) -> str:
-    return _angstrom_to_x(angstrom, factor=100)
+    try:
+        return _angstrom_to_x(angstrom, factor=100)
+    except ValueError:
+        return '?'
 
 
 def angstrom_to_pm_squared(angstrom: str) -> str:
-    return _angstrom_to_x(angstrom, factor=100 ** 2)
+    try:
+        return _angstrom_to_x(angstrom, factor=100 ** 2)
+    except ValueError:
+        return '?'
 
 
 def angstrom_to_nanometers(angstrom: str) -> str:
-    return _angstrom_to_x(angstrom, factor=0.001)
+    try:
+        return _angstrom_to_x(angstrom, factor=0.001)
+    except ValueError:
+        return '?'
+
+
+def do_nothing(value: str) -> str:
+    return value
 
 
 def _angstrom_to_x(value: str, factor: float = 100) -> str:

{finalcif-142 → finalcif-144}/finalcif/tools/shred.py

@@ -26,9 +26,12 @@ class ShredCIF():
                                                             suffix='_' + self._cif.block.name + '-finalcif.res')
             hklfile_path = self._cif.finalcif_file_prefixed(prefix='',
                                                             suffix='_' + self._cif.block.name + '-finalcif.hkl')
+            fabfile_path = self._cif.finalcif_file_prefixed(prefix='',
+                                                            suffix='_' + self._cif.block.name + '-finalcif.fab')
         else:
             resfile_path = self._cif.finalcif_file.with_suffix('.res')
             hklfile_path = self._cif.finalcif_file.with_suffix('.hkl')
+            fabfile_path = self._cif.finalcif_file.with_suffix('.fab')
         res_data = None
         hkl_data = None
         if not self._cif:
@@ -51,6 +54,8 @@ class ShredCIF():
             hkl_data = self.format_hkl_data(hkl_data)
             if not self._write_hkl_file(hklfile_path, hkl_data):
                 return None
+        if fab_data := self._cif.fab_file:
+            self._write_hkl_file(fabfile_path, fab_data)
         self._show_info(resfile_path, hklfile_path, res_data, hkl_data)
 
     @staticmethod

finalcif-142/finalcif/__init__.py

@@ -1,2 +0,0 @@
-
-VERSION = 142