{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys\n",
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "sys.path.append('/Users/iwatobipen/develop/chemoenv/psikit/psikit')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from psikit import Psikit\n",
    "import psi4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "pk = Psikit()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "pk.read_from_smiles('c1cccnc1')\n",
    "st = ''\n",
    "for i in range(pk.mol.GetNumAtoms()):\n",
    "    st += str(i)+\" xyz\\n\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "pk.psi4.set_options({'OPT_COORDINATES':'CARTESIAN','FROZEN_CARTESIAN':st})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-246.69632927796312"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pk.energy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "c1=pk.mol.GetConformer()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-1.1798080162788467 0.5395628155681792 -0.040898689809211915\n",
      "0.06518501702779525 1.1725200495297896 -0.024197196431391794\n",
      "1.2324170131466978 0.40674272533062134 0.02136959764386789\n",
      "1.1341947566448707 -0.9870796028842717 0.049623787535432146\n",
      "-0.08808077531813244 -1.5843578108096479 0.032696378317569226\n",
      "-1.2366886542335542 -0.8565357626249066 -0.011577101627813696\n",
      "-2.090258996636217 1.123713375541261 -0.07615152943552474\n",
      "0.12525020620869629 2.2529526429691744 -0.04649351917653518\n",
      "2.2020635800742587 0.8873725333088379 0.03464869040642951\n",
      "2.029210551536477 -1.5936990336790273 0.08499205976623224\n",
      "-2.193484682172043 -1.3611919322500243 -0.02401247718906001\n"
     ]
    }
   ],
   "source": [
    "for i in range(pk.mol.GetNumAtoms()):\n",
    "    pos = c1.GetAtomPosition(i)\n",
    "    print(pos.x, pos.y, pos.z)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          3D\n",
      "\n",
      " 11 11  0  0  0  0  0  0  0  0999 V2000\n",
      "   -1.1798    0.5396   -0.0409 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.0652    1.1725   -0.0242 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.2324    0.4067    0.0214 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    1.1342   -0.9871    0.0496 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -0.0881   -1.5844    0.0327 N   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.2367   -0.8565   -0.0116 C   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.0903    1.1237   -0.0762 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.1253    2.2530   -0.0465 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.2021    0.8874    0.0346 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.0292   -1.5937    0.0850 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -2.1935   -1.3612   -0.0240 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  2  0\n",
      "  2  3  1  0\n",
      "  3  4  2  0\n",
      "  4  5  1  0\n",
      "  5  6  2  0\n",
      "  6  1  1  0\n",
      "  1  7  1  0\n",
      "  2  8  1  0\n",
      "  3  9  1  0\n",
      "  4 10  1  0\n",
      "  6 11  1  0\n",
      "M  END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(Chem.MolToMolBlock(pk.mol))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "pmol=pk.wfn.molecule()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "11\n",
      "C5H5N\n",
      "C                    -1.167454487914     0.761772792678    -0.045484422418\n",
      "C                     0.077538545393     1.394730026640    -0.028782929041\n",
      "C                     1.244770541512     0.628952702440     0.016783865035\n",
      "C                     1.146548285010    -0.764869625775     0.045038054926\n",
      "N                    -0.075727246953    -1.362147833700     0.028110645708\n",
      "C                    -1.224335125868    -0.634325785515    -0.016162834237\n",
      "H                    -2.077905468271     1.345923352651    -0.080737262045\n",
      "H                     0.137603734574     2.475162620079    -0.051079251786\n",
      "H                     2.214417108440     1.109582510419     0.030062957797\n",
      "H                     2.041564079902    -1.371489056569     0.080406327157\n",
      "H                    -2.181131153807    -1.138981955140    -0.028598209798\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(pmol.to_string(dtype='xyz', units='angstrom'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "pmol.set_units(pk.psi4.core.GeometryUnits.Angstrom)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "11\n",
      "C5H5N\n",
      "C                     0.558467286814     0.479369884597     0.055344583255\n",
      "C                    -0.136879701051     0.726450872880     0.013424718307\n",
      "C                    -0.694954000527     0.244995215113    -0.041958039092\n",
      "C                    -0.547310800252    -0.479567223669    -0.054552008614\n",
      "N                     0.133682069403    -0.709480311343    -0.013111328786\n",
      "C                     0.684628756033    -0.249209468187     0.041084281858\n",
      "H                     0.994678796710     0.848003953147     0.098387304731\n",
      "H                    -0.242913973601     1.289198698848     0.023823000261\n",
      "H                    -1.235663909075     0.430956429182    -0.074751909041\n",
      "H                    -0.973891994820    -0.858935524734    -0.097249249706\n",
      "H                     1.220271277774    -0.448653621219     0.073085054591\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(pmol.to_string(dtype='xyz'))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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