fortecube_text.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "narrow-madness",
   "metadata": {},
   "outputs": [],
   "source": [
    "from psikit import Psikit\n",
    "import fortecubeview\n",
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "boxed-sense",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Optimizer: Optimization complete!\n",
      "CubeViewer: listing cube files from the directory /home/iwatobipen/dev/sandbox/rdk/psi4test/tmp1\n",
      "Reading 8 cube files\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "c20b9e5a490c42ceb8e656a6762e24d5",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HTML(value=''), Renderer(camera=OrthographicCamera(bottom=-2.5, children=(DirectionalLight(colo…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "41215fc213594edeb62497ef7830d5ff",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HTML(value='\\n        <style>\\n           .jupyter-widgets-output-area .output_scroll {\\n                heigh…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "bd108b7cd82640f3b68e7770c7f6adac",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(Select(description='Cube files:', options=('/home/iwatobipen/dev/sandbox/rdk/psi4test/tm…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<fortecubeview.cube_viewer.CubeViewer at 0x7f857e092fd0>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pk = Psikit()\n",
    "pk.tempdir ='/home/iwatobipen/dev/sandbox/rdk/psi4test/tmp1'\n",
    "os.mkdir(pk.tempdir)\n",
    "pk.read_from_smiles('c1ccccc1N(=O)=O')\n",
    "pk.optimize()\n",
    "pk.create_cube_files(gridspace=0.5)\n",
    "fortecubeview.plot(path=pk.tempdir, width=600, height=300, colorscheme='national', sumlevel=0.7)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "comprehensive-storage",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Optimizer: Optimization complete!\n",
      "CubeViewer: listing cube files from the directory /home/iwatobipen/dev/sandbox/rdk/psi4test/tmp2\n",
      "Reading 8 cube files\n"
     ]
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "dc5683d4803d46b5b1bb6f1908ccbe3d",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "VBox(children=(HTML(value=''), Renderer(camera=OrthographicCamera(bottom=-2.5, children=(DirectionalLight(colo…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "3aef4d93243547bab46c611b3c252ebb",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HTML(value='\\n        <style>\\n           .jupyter-widgets-output-area .output_scroll {\\n                heigh…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "36f14047af044044aed955b0544f8b44",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "interactive(children=(Select(description='Cube files:', options=('/home/iwatobipen/dev/sandbox/rdk/psi4test/tm…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/plain": [
       "<fortecubeview.cube_viewer.CubeViewer at 0x7f860f519690>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pk = Psikit()\n",
    "pk.tempdir ='/home/iwatobipen/dev/sandbox/rdk/psi4test/tmp2'\n",
    "os.mkdir(pk.tempdir)\n",
    "pk.read_from_smiles('c1cc(O)ccc1')\n",
    "pk.optimize()\n",
    "pk.create_cube_files(gridspace=0.5)\n",
    "fortecubeview.plot(path=pk.tempdir, width=600, height=300, colorscheme='national', sumlevel=0.7)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "straight-yukon",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "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": "3.7.9"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}