build a simple google translate example around simple_report.py (NO_J…

notebooks/API_Training_Exercises/01_Simple_Report.ipynb

@@ -0,0 +1,378 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "```\n",
+    "This script can be used for any purpose without limitation subject to the\n",
+    "conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
+    "\n",
+    "This permission notice and the following statement of attribution must be\n",
+    "included in all copies or substantial portions of this script.\n",
+    "\n",
+    "2024-09-11: Made available by the Cambridge Crystallographic Data Centre.\n",
+    "\n",
+    "```"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# International Report\n",
+    "\n",
+    "This notebook talks through how to create a report that reports a CSD entry ... but uses google translate to translate headings into the language of user choice.\n",
+    "You could use the ideas her to convert the 'simple_report.py script into an international report\n",
+    "\n",
+    "#### Prerequisites\n",
+    "\n",
+    "First install the CSD Python API and googletrans into your conda or pip environment. This should only be needed the before you run the script."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Now we are ready to start some python coding. We need to import some modules. We are writing a script that ultimately will be used in Mercury so we will want some of \n",
+    "the special utilities available for writing reports."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ccdc.utilities import html_table\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We can create a translator for the script to use, and define our language of choice. Lets write a little function to do the translation"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from googletrans import Translator\n",
+    "\n",
+    "translator = Translator()\n",
+    "def tr(text, lang):\n",
+    "    if lang is None:\n",
+    "        return text\n",
+    "    try:\n",
+    "        return translator.translate(str(text),src=\"en\",dest=lang).text\n",
+    "    except Exception as e:\n",
+    "        return text"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Let's try it out:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'ماري لديها خروف صغير'"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "\n",
+    "tr(\"Mary had a little lamb\", \"ar\")  # Lets try arabic!"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "So now we can create a report on a CSD entry that is international. The following function will work in a Mercury API script. Note how it defines an interface object"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_coordinates(molecule, round_digits=None):\n",
+    "    \"\"\"Yield the label and fractional coordinates of all atoms in the molecule.\n",
+    "\n",
+    "    :param molecule: (:obj:`ccdc.molecule.Molecule`) The molecule for which to return coordinates.\n",
+    "    :param round_digits: (:obj:`int`) How many decimal digits coordinates should be rounded to.\n",
+    "    :returns: (:obj:`list`) List of the label and fractional x/y/z coordinates for each atom\n",
+    "        in the molecule in format ['Atom label', 'X coordinate', 'Y coordinate', 'Z coordinate'].\n",
+    "    \"\"\"\n",
+    "    for atom in molecule.atoms:\n",
+    "        try:\n",
+    "            x, y, z = atom.fractional_coordinates\n",
+    "            yield [atom.label,\n",
+    "                   x if round_digits is None else round(x, round_digits),\n",
+    "                   y if round_digits is None else round(y, round_digits),\n",
+    "                   z if round_digits is None else round(z, round_digits)]\n",
+    "        except TypeError:\n",
+    "            continue\n",
+    "\n",
+    "\n",
+    "def main(interface=None, lang=None):\n",
+    "    \"\"\"Generate a simple report based on the entry currently selected in the Mercury UI.\n",
+    "\n",
+    "    :param interface: (:obj:`ccdc.utility.ApplicationInterface`) An ApplicationInterface instance.\n",
+    "    \"\"\"\n",
+    "    if interface is None:\n",
+    "        from ccdc.utilities import ApplicationInterface\n",
+    "        interface = ApplicationInterface()\n",
+    "\n",
+    "    entry = interface.current_entry\n",
+    "\n",
+    "    # Open a HTML report. This will create the file, copy the CSD Python API\n",
+    "    # default template for reports and fill in the headline/page title.\n",
+    "    with interface.html_report(title=tr('Simple report on ',lang)+ ' ' + entry.identifier) as report:\n",
+    "\n",
+    "        # Write the section header for Entry Details\n",
+    "        report.write_section_header(tr('Entry Details',lang))\n",
+    "        # Assemble a list of information and labels to go into the \"Entry Details\" table\n",
+    "        entry_details = [\n",
+    "            ['<b>'+tr('Chemical name',lang)+'</b>', entry.chemical_name],\n",
+    "            ['<b>'+tr('Synonyms',lang)+'</b>', entry.synonyms],\n",
+    "            ['<b>'+tr('Formula',lang)+'</b>', entry.formula],\n",
+    "            ['<b>'+tr('R-factor',lang)+'</b>', entry.r_factor],\n",
+    "            ['<b>'+tr('Disorder',lang)+'</b>', tr(entry.disorder_details,lang)],\n",
+    "            ['<b>'+tr('Polymorphism',lang)+'</b>', tr(entry.polymorph,lang)],\n",
+    "            ['<b>'+tr('3D structure',lang)+'</b>', tr(entry.has_3d_structure,lang)],\n",
+    "            ['<b>'+tr('Organic',lang)+'</b>', tr(entry.is_organic,lang)],\n",
+    "            ['<b>'+tr('Polymeric',lang)+'</b>', tr(entry.is_polymeric,lang)],\n",
+    "            ['<b>'+tr('Bioactivity',lang)+'</b>', tr(entry.bioactivity,lang)],\n",
+    "            ['<b>'+tr('Source',lang)+'</b>', tr(entry.source,lang)],\n",
+    "            ['<b>'+tr('Habit',lang)+'</b>', tr(entry.habit,lang)],\n",
+    "        ]\n",
+    "        # Generate a HTML table from the entry details and write it to the report\n",
+    "        report.write(html_table(data=entry_details, table_id='entry_details'))\n",
+    "\n",
+    "        # Write the section header for Fractional Coordinates\n",
+    "        report.write_section_header(tr('Fractional Coordinates',lang))\n",
+    "        # Get the coordinates of all the atoms from the entry and write them to a HTML table\n",
+    "        report.write(html_table(data=list(get_coordinates(entry.molecule, round_digits=3)),\n",
+    "                                table_id='fractional_coordinates',\n",
+    "                                header=[tr('Atom',lang), 'x', 'y', 'z']))\n",
+    "\n",
+    "        # Write the section header for Publication Details\n",
+    "        report.write_section_header(tr('Publication Details',lang))\n",
+    "        # Assemble a list of information and labels for the Publication Details table\n",
+    "        publication_details = [\n",
+    "            ['<b>'+tr('Reference',lang)+'</b>', '%s Volume %s, %s' % (getattr(entry.publication, 'journal_name', ''),\n",
+    "                                                       entry.publication.volume,\n",
+    "                                                       entry.publication.year)],\n",
+    "            ['<b>'+tr('Authors', lang)+'</b>', entry.publication.authors],\n",
+    "            ['<b>'+tr('Document Object Identifier',lang)+'</b>', entry.publication.doi]\n",
+    "        ]\n",
+    "        # Write the publication details to a HTML table\n",
+    "        report.write(html_table(publication_details, table_id='publication_details'))\n",
+    "\n",
+    "        # Write the section header for Basic Crystallographic Information\n",
+    "        report.write_section_header(tr('Basic Crystallographic Information',lang))\n",
+    "        # Assemble a list of basic crystal information and labels for the table\n",
+    "        crystallographic_data = [\n",
+    "            ['<b>'+tr('Crystal System',lang)+'</b>', entry.crystal.crystal_system],\n",
+    "            ['<b>'+tr('Space Group',lang) + '</b>', entry.crystal.spacegroup_symbol],\n",
+    "            ['<b>'+tr('Cell Volume',lang)+ '</b>', '%s ų' % round(entry.crystal.cell_volume, 3)],\n",
+    "            ['<b>Z, Z\\'</b>', entry.crystal.z_prime],\n",
+    "        ]\n",
+    "        # Write the crystallographic details to a HTML table\n",
+    "        report.write(html_table(crystallographic_data, table_id='crystallographic_information'))\n",
+    "\n",
+    "    # Once the HTMLReport is closed (e.g. when the with: branch above ends),\n",
+    "    # it will automatically write the appropriate HTML footer."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Lets use our function. As we are in a notebook, we will have to define a dummy interface file:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import time\n",
+    "from ccdc.utilities import ApplicationInterface\n",
+    "interface = ApplicationInterface(parse_commandline=False)\n",
+    "interface.identifier = \"AABHTZ\"\n",
+    "interface.output_html_file = f'{interface.identifier}_{time.strftime(\"%H%M%S\", time.gmtime())}_report.html'\n",
+    "\n",
+    "main(interface,\"ar\") # Arabic "
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Finally use Jupyter to display it:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<!DOCTYPE html>\n",
+       "<html>\n",
+       "\t<head>\n",
+       "\t\t<style type=\"text/css\">\n",
+       "\t\t\tbody { font-family: Calibri, Verdana, sans-serif; padding: 1.5em; font-size: 1.2em}\n",
+       "\t\t\t#ccdc_logo { float: right; margin: -2em 1.5em 1.5em 1.5em; }\n",
+       "\t\t\tp { text-align: justify; }\n",
+       "\t\t\th1 { text-align: left; font-size: 1.8em; font-weight: bold; }\n",
+       "\t\t\th2 { text-align: left; font-size: 1.5em; font-weight: bold; }\n",
+       "\t\t\ttable { width: 100%; margin:auto; border: 1px solid; border-collapse:collapse; }\n",
+       "\t\t\tth { padding: .2em; font-weight: bold; }\n",
+       "\t\t\ttd { padding: .2em; }\n",
+       "\t\t\ttable, th, td { border: 1px solid; }\n",
+       "\t\t\ttr:nth-child(even) { background: #ccc; }\n",
+       "        </style>\n",
+       "\t\t<meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\"/>\n",
+       "\t\t<title>تقرير بسيط عن AABHTZ</title>\n",
+       "    </head>\n",
+       "\t<body>\n",
+       "<img src=\"ccdc_logo_180x180_with_text.png\" id=\"ccdc_logo\" alt=\"CCDC\" />\n",
+       "<h1 id=\"report_header\">تقرير بسيط عن AABHTZ</h1>\n",
+       "<h2 id=\"\">تفاصيل الدخول</h2>\n",
+       "<table id=\"entry_details\">\n",
+       "    <tr><td><b>الاسم الكيميائي</b></td><td>4-Acetoamido-3-(1-acetyl-2-(2,6-dichlorobenzylidene)hydrazine)-1,2,4-triazole</td></tr>\n",
+       "    <tr><td><b>المرادفات</b></td><td>()</td></tr>\n",
+       "    <tr><td><b>صيغة</b></td><td>C13 H12 Cl2 N6 O2</td></tr>\n",
+       "    <tr><td><b>عامل r</b></td><td>4.1</td></tr>\n",
+       "    <tr><td><b>اضطراب</b></td><td>لا أحد</td></tr>\n",
+       "    <tr><td><b>تعدد الأشكال</b></td><td>لا أحد</td></tr>\n",
+       "    <tr><td><b>هيكل ثلاثي الأبعاد</b></td><td>حقيقي</td></tr>\n",
+       "    <tr><td><b>عضوي</b></td><td>حقيقي</td></tr>\n",
+       "    <tr><td><b>البوليمرية</b></td><td>خطأ شنيع</td></tr>\n",
+       "    <tr><td><b>النشاط الحيوي</b></td><td>لا أحد</td></tr>\n",
+       "    <tr><td><b>مصدر</b></td><td>لا أحد</td></tr>\n",
+       "    <tr><td><b>عادة</b></td><td>لا أحد</td></tr>\n",
+       "</table>\n",
+       "<h2 id=\"\">إحداثيات كسرية</h2>\n",
+       "<table id=\"fractional_coordinates\">\n",
+       "    <tr><th>ذرة</th><th>x</th><th>y</th><th>z</th></tr>\n",
+       "    <tr><td>Cl1</td><td>-0.336</td><td>0.1</td><td>0.106</td></tr>\n",
+       "    <tr><td>Cl2</td><td>-0.641</td><td>-0.308</td><td>0.327</td></tr>\n",
+       "    <tr><td>C1</td><td>-0.478</td><td>0.039</td><td>0.231</td></tr>\n",
+       "    <tr><td>C2</td><td>-0.573</td><td>0.134</td><td>0.342</td></tr>\n",
+       "    <tr><td>C3</td><td>-0.685</td><td>0.092</td><td>0.448</td></tr>\n",
+       "    <tr><td>C4</td><td>-0.702</td><td>-0.045</td><td>0.445</td></tr>\n",
+       "    <tr><td>C5</td><td>-0.607</td><td>-0.139</td><td>0.33</td></tr>\n",
+       "    <tr><td>C6</td><td>-0.49</td><td>-0.101</td><td>0.218</td></tr>\n",
+       "    <tr><td>C7</td><td>-0.384</td><td>-0.194</td><td>0.089</td></tr>\n",
+       "    <tr><td>N1</td><td>-0.367</td><td>-0.298</td><td>0.135</td></tr>\n",
+       "    <tr><td>N2</td><td>-0.263</td><td>-0.38</td><td>0.01</td></tr>\n",
+       "    <tr><td>C8</td><td>-0.186</td><td>-0.365</td><td>-0.175</td></tr>\n",
+       "    <tr><td>N3</td><td>-0.22</td><td>-0.386</td><td>-0.335</td></tr>\n",
+       "    <tr><td>N4</td><td>-0.115</td><td>-0.36</td><td>-0.484</td></tr>\n",
+       "    <tr><td>C9</td><td>-0.025</td><td>-0.326</td><td>-0.406</td></tr>\n",
+       "    <tr><td>N5</td><td>-0.064</td><td>-0.327</td><td>-0.21</td></tr>\n",
+       "    <tr><td>N6</td><td>0.002</td><td>-0.284</td><td>-0.074</td></tr>\n",
+       "    <tr><td>C10</td><td>-0.031</td><td>-0.161</td><td>0.074</td></tr>\n",
+       "    <tr><td>C11</td><td>0.041</td><td>-0.124</td><td>0.222</td></tr>\n",
+       "    <tr><td>O1</td><td>-0.11</td><td>-0.088</td><td>0.079</td></tr>\n",
+       "    <tr><td>C12</td><td>-0.239</td><td>-0.486</td><td>0.072</td></tr>\n",
+       "    <tr><td>C13</td><td>-0.331</td><td>-0.509</td><td>0.255</td></tr>\n",
+       "    <tr><td>O2</td><td>-0.145</td><td>-0.554</td><td>-0.03</td></tr>\n",
+       "    <tr><td>H1</td><td>-0.558</td><td>0.232</td><td>0.347</td></tr>\n",
+       "    <tr><td>H2</td><td>-0.752</td><td>0.157</td><td>0.531</td></tr>\n",
+       "    <tr><td>H3</td><td>-0.784</td><td>-0.078</td><td>0.53</td></tr>\n",
+       "    <tr><td>H4</td><td>-0.326</td><td>-0.175</td><td>-0.032</td></tr>\n",
+       "    <tr><td>H5</td><td>0.057</td><td>-0.296</td><td>-0.469</td></tr>\n",
+       "    <tr><td>H6</td><td>0.046</td><td>-0.34</td><td>-0.057</td></tr>\n",
+       "    <tr><td>H7</td><td>0.081</td><td>-0.036</td><td>0.217</td></tr>\n",
+       "    <tr><td>H8</td><td>0.105</td><td>-0.198</td><td>0.189</td></tr>\n",
+       "    <tr><td>H9</td><td>-0.006</td><td>-0.107</td><td>0.333</td></tr>\n",
+       "    <tr><td>H10</td><td>-0.313</td><td>-0.598</td><td>0.275</td></tr>\n",
+       "    <tr><td>H11</td><td>-0.329</td><td>-0.451</td><td>0.374</td></tr>\n",
+       "    <tr><td>H12</td><td>-0.413</td><td>-0.525</td><td>0.243</td></tr>\n",
+       "</table>\n",
+       "<h2 id=\"\">تفاصيل النشر</h2>\n",
+       "<table id=\"publication_details\">\n",
+       "    <tr><td><b>مرجع</b></td><td> Volume 5, 1976</td></tr>\n",
+       "    <tr><td><b>المؤلفون</b></td><td>P.-E.Werner</td></tr>\n",
+       "    <tr><td><b>معرف كائن المستند</b></td><td>None</td></tr>\n",
+       "</table>\n",
+       "<h2 id=\"\">المعلومات البلورية الأساسية</h2>\n",
+       "<table id=\"crystallographic_information\">\n",
+       "    <tr><td><b>نظام البلورة</b></td><td>triclinic</td></tr>\n",
+       "    <tr><td><b>مجموعة الفضاء</b></td><td>P-1</td></tr>\n",
+       "    <tr><td><b>حجم الخلية</b></td><td>769.978 ų</td></tr>\n",
+       "    <tr><td><b>Z, Z'</b></td><td>1.0</td></tr>\n",
+       "</table>\n",
+       "\n",
+       "</body>\n",
+       "</html>\n"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from IPython.display import HTML\n",
+    "HTML(interface.output_html_file)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.20"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}