Tutorial/Advanced_customisation.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import chemcoord as cc"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Settings"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Settings can be seen here:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'defaults': {'use_lookup': False,\n",
       "  'atomic_radius_data': 'atomic_radius_cc',\n",
       "  'viewer': 'gv.exe'}}"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cc.configuration.settings"
   ]
  },
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    "A configuration file can be written with:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "cc.configuration.write_configuration_file('./example_configuration_file', overwrite=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[defaults]\n",
       "use_lookup = False\n",
       "atomic_radius_data = atomic_radius_cc\n",
       "viewer = gv.exe\n",
       "\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%less example_configuration_file"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "It is read automatically during startup from ``'~/.chemcoordrc'``.\n",
    "Otherwise it is possible to explicitly call ``cc.configuration.read_configuration_file(...)``"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "!rm example_configuration_file"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Inheritance\n",
    "\n",
    "You can safely inherit from the classes in this module"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "class my_tailored_class(cc.Cartesian):\n",
    "    def my_number_one_method(self):\n",
    "        return 1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "chemcoord.cartesian_coordinates.cartesian_class_main.Cartesian"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "molecule = cc.Cartesian.read_xyz('MIL53_small.xyz')\n",
    "type(molecule)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Notice how all old methods from Cartesian return an object of your tailored class"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "__main__.my_tailored_class"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "my_molecule = my_tailored_class.read_xyz('MIL53_small.xyz')\n",
    "type(my_molecule)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "__main__.my_tailored_class"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(my_molecule.get_inertia()['transformed_Cartesian'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "1"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "my_molecule.get_inertia()['transformed_Cartesian'].my_number_one_method()"
   ]
  }
 ],
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