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Merge pull request #70 from ccdc-opensource/training_exercise
build a simple google translate example around simple_report.py (NO_J…
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‎notebooks/API_Training_Exercises/01_Simple_Report.ipynb

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"```\n",
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"This script can be used for any purpose without limitation subject to the\n",
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"conditions at http://www.ccdc.cam.ac.uk/Community/Pages/Licences/v2.aspx\n",
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"\n",
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"This permission notice and the following statement of attribution must be\n",
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"included in all copies or substantial portions of this script.\n",
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"\n",
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"2024-09-11: Made available by the Cambridge Crystallographic Data Centre.\n",
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"\n",
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"```"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# International Report\n",
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"\n",
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"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",
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"You could use the ideas her to convert the 'simple_report.py script into an international report\n",
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"\n",
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"#### Prerequisites\n",
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"\n",
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"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."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"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",
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"the special utilities available for writing reports."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from ccdc.utilities import html_table\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"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"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from googletrans import Translator\n",
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"\n",
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"translator = Translator()\n",
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"def tr(text, lang):\n",
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" if lang is None:\n",
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" return text\n",
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" try:\n",
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" return translator.translate(str(text),src=\"en\",dest=lang).text\n",
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" except Exception as e:\n",
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" return text"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Let's try it out:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"\n",
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"tr(\"Mary had a little lamb\", \"ar\") # Lets try arabic!"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"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"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"def get_coordinates(molecule, round_digits=None):\n",
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" \"\"\"Yield the label and fractional coordinates of all atoms in the molecule.\n",
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"\n",
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" :param molecule: (:obj:`ccdc.molecule.Molecule`) The molecule for which to return coordinates.\n",
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" :param round_digits: (:obj:`int`) How many decimal digits coordinates should be rounded to.\n",
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" :returns: (:obj:`list`) List of the label and fractional x/y/z coordinates for each atom\n",
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" in the molecule in format ['Atom label', 'X coordinate', 'Y coordinate', 'Z coordinate'].\n",
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" \"\"\"\n",
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" for atom in molecule.atoms:\n",
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" try:\n",
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" x, y, z = atom.fractional_coordinates\n",
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" yield [atom.label,\n",
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" x if round_digits is None else round(x, round_digits),\n",
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" y if round_digits is None else round(y, round_digits),\n",
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" z if round_digits is None else round(z, round_digits)]\n",
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" except TypeError:\n",
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" continue\n",
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"\n",
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"\n",
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"def main(interface=None, lang=None):\n",
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" \"\"\"Generate a simple report based on the entry currently selected in the Mercury UI.\n",
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"\n",
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" :param interface: (:obj:`ccdc.utility.ApplicationInterface`) An ApplicationInterface instance.\n",
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" \"\"\"\n",
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" if interface is None:\n",
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" from ccdc.utilities import ApplicationInterface\n",
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" interface = ApplicationInterface()\n",
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"\n",
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" entry = interface.current_entry\n",
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"\n",
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" # Open a HTML report. This will create the file, copy the CSD Python API\n",
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" # default template for reports and fill in the headline/page title.\n",
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" with interface.html_report(title=tr('Simple report on ',lang)+ ' ' + entry.identifier) as report:\n",
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"\n",
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" # Write the section header for Entry Details\n",
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" report.write_section_header(tr('Entry Details',lang))\n",
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" # Assemble a list of information and labels to go into the \"Entry Details\" table\n",
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" entry_details = [\n",
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" ['<b>'+tr('Chemical name',lang)+'</b>', entry.chemical_name],\n",
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" ['<b>'+tr('Synonyms',lang)+'</b>', entry.synonyms],\n",
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" ['<b>'+tr('Formula',lang)+'</b>', entry.formula],\n",
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" ['<b>'+tr('R-factor',lang)+'</b>', entry.r_factor],\n",
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" ['<b>'+tr('Disorder',lang)+'</b>', tr(entry.disorder_details,lang)],\n",
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" ['<b>'+tr('Polymorphism',lang)+'</b>', tr(entry.polymorph,lang)],\n",
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" ['<b>'+tr('3D structure',lang)+'</b>', tr(entry.has_3d_structure,lang)],\n",
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" ['<b>'+tr('Organic',lang)+'</b>', tr(entry.is_organic,lang)],\n",
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" ['<b>'+tr('Polymeric',lang)+'</b>', tr(entry.is_polymeric,lang)],\n",
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" ['<b>'+tr('Bioactivity',lang)+'</b>', tr(entry.bioactivity,lang)],\n",
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" ['<b>'+tr('Source',lang)+'</b>', tr(entry.source,lang)],\n",
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" ['<b>'+tr('Habit',lang)+'</b>', tr(entry.habit,lang)],\n",
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" ]\n",
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" # Generate a HTML table from the entry details and write it to the report\n",
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" report.write(html_table(data=entry_details, table_id='entry_details'))\n",
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"\n",
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" # Write the section header for Fractional Coordinates\n",
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" report.write_section_header(tr('Fractional Coordinates',lang))\n",
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" # Get the coordinates of all the atoms from the entry and write them to a HTML table\n",
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" report.write(html_table(data=list(get_coordinates(entry.molecule, round_digits=3)),\n",
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" table_id='fractional_coordinates',\n",
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" header=[tr('Atom',lang), 'x', 'y', 'z']))\n",
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"\n",
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" # Write the section header for Publication Details\n",
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" report.write_section_header(tr('Publication Details',lang))\n",
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" # Assemble a list of information and labels for the Publication Details table\n",
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" publication_details = [\n",
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" ['<b>'+tr('Reference',lang)+'</b>', '%s Volume %s, %s' % (getattr(entry.publication, 'journal_name', ''),\n",
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" entry.publication.volume,\n",
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" entry.publication.year)],\n",
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" ['<b>'+tr('Authors', lang)+'</b>', entry.publication.authors],\n",
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" ['<b>'+tr('Document Object Identifier',lang)+'</b>', entry.publication.doi]\n",
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" ]\n",
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" # Write the publication details to a HTML table\n",
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" report.write(html_table(publication_details, table_id='publication_details'))\n",
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"\n",
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" # Write the section header for Basic Crystallographic Information\n",
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" report.write_section_header(tr('Basic Crystallographic Information',lang))\n",
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" # Assemble a list of basic crystal information and labels for the table\n",
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" crystallographic_data = [\n",
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" ['<b>'+tr('Crystal System',lang)+'</b>', entry.crystal.crystal_system],\n",
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" ['<b>'+tr('Space Group',lang) + '</b>', entry.crystal.spacegroup_symbol],\n",
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" ['<b>'+tr('Cell Volume',lang)+ '</b>', '%s ų' % round(entry.crystal.cell_volume, 3)],\n",
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" ['<b>Z, Z\\'</b>', entry.crystal.z_prime],\n",
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" ]\n",
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" # Write the crystallographic details to a HTML table\n",
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" report.write(html_table(crystallographic_data, table_id='crystallographic_information'))\n",
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"\n",
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" # Once the HTMLReport is closed (e.g. when the with: branch above ends),\n",
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" # it will automatically write the appropriate HTML footer."
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Lets use our function. As we are in a notebook, we will have to define a dummy interface file:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import time\n",
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"from ccdc.utilities import ApplicationInterface\n",
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"interface = ApplicationInterface(parse_commandline=False)\n",
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"interface.identifier = \"AABHTZ\"\n",
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"interface.output_html_file = f'{interface.identifier}_{time.strftime(\"%H%M%S\", time.gmtime())}_report.html'\n",
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"\n",
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"main(interface,\"ar\") # Arabic "
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Finally use Jupyter to display it:"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"from IPython.display import HTML\n",
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"HTML(interface.output_html_file)"
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]
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.20"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

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