SumOverCharge.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x18514aa2300>"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol=Chem.MolFromSmiles('P(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3')\n",
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "def charge(mol, at_ind):\n",
    "    AllChem.ComputeGasteigerCharges(mol)\n",
    "    charges=mol.GetAtomWithIdx(at_ind).GetDoubleProp('_GasteigerCharge')\n",
    "    return charges"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "6\n",
      "-0.3232365968735926\n",
      "[2, 6, 8, 12, 14, 18]\n"
     ]
    }
   ],
   "source": [
    "startAtom=0\n",
    "initialRadii2=[]\n",
    "for i in radii1:\n",
    "    atom=mol.GetAtomWithIdx(i)\n",
    "    atIndRad2=[x.GetIdx() for x in atom.GetNeighbors()]\n",
    "    initialRadii2.append(atIndRad2)\n",
    "radii2  = set([val for sublist in initialRadii2 for val in sublist])\n",
    "radii2.remove(startAtom)\n",
    "numElement=len(radii2)\n",
    "Q2=sum([charge(mol, i) for i in radii2])\n",
    "print(numElement)\n",
    "print(Q2)\n",
    "print(list(radii2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 102,
   "metadata": {},
   "outputs": [],
   "source": [
    "#soc stands for sum over charge\n",
    "def soc(smile, startAtom):\n",
    "    mol=Chem.MolFromSmiles(smile)\n",
    "    Q0=charge(mol, startAtom)\n",
    "    print(Q0)\n",
    "    \n",
    "    atom1 = mol.GetAtomWithIdx(startAtom)\n",
    "    radii1=[x.GetIdx() for x in atom1.GetNeighbors()]\n",
    "    Q1=sum([charge(mol, i) for i in radii1])\n",
    "    print(Q1)\n",
    "    \n",
    "    initialRadii2=[]\n",
    "    for i in radii1:\n",
    "        atom2=mol.GetAtomWithIdx(i)\n",
    "        atIndRad2=[x.GetIdx() for x in atom2.GetNeighbors()]\n",
    "        initialRadii2.append(atIndRad2)\n",
    "    radii2  = set([val for sublist in initialRadii2 for val in sublist])\n",
    "    radii2.remove(startAtom)\n",
    "    numElement=len(radii2) #just to check how many atoms are there in radii2\n",
    "    Q2=sum([charge(mol, i) for i in radii2])\n",
    "    print(Q2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-0.013435687534984822\n",
      "-0.04536313583357551\n",
      "-0.3232365968735926\n"
     ]
    }
   ],
   "source": [
    "soc('P(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3', 0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-0.013164994664711785\n",
      "-0.04237728716082413\n",
      "-0.31080776820751455\n"
     ]
    }
   ],
   "source": [
    "soc('CC(C=C1)=CC=C1P(C2=CC=C(C)C=C2)C3=CC=CC=C3C', 7)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x1851640a4e0>"
      ]
     },
     "execution_count": 87,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol=Chem.MolFromSmiles('CC(C=C1)=CC=C1P(C2=CC=C(C)C=C2)C3=CC=CC=C3C')\n",
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 95,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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       "L 359.018 142.902\n",
       "L 356.579 142.902\n",
       "L 356.579 134.597\n",
       "L 347.385 134.597\n",
       "L 347.385 142.902\n",
       "L 344.947 142.902\n",
       "L 344.947 124.92\n",
       "' fill='#FF0000'/>\n",
       "<path  class='atom-2' d='M 220.581 124.819\n",
       "L 226.473 134.343\n",
       "Q 227.057 135.283, 227.997 136.985\n",
       "Q 228.937 138.686, 228.988 138.788\n",
       "L 228.988 124.819\n",
       "L 231.375 124.819\n",
       "L 231.375 142.801\n",
       "L 228.911 142.801\n",
       "L 222.587 132.388\n",
       "Q 221.851 131.168, 221.063 129.771\n",
       "Q 220.301 128.375, 220.073 127.943\n",
       "L 220.073 142.801\n",
       "L 217.736 142.801\n",
       "L 217.736 124.819\n",
       "L 220.581 124.819\n",
       "' fill='#0000FF'/>\n",
       "<path  class='atom-4' d='M 90.9825 124.92\n",
       "L 93.4207 124.92\n",
       "L 93.4207 132.565\n",
       "L 102.615 132.565\n",
       "L 102.615 124.92\n",
       "L 105.053 124.92\n",
       "L 105.053 142.902\n",
       "L 102.615 142.902\n",
       "L 102.615 134.597\n",
       "L 93.4207 134.597\n",
       "L 93.4207 142.902\n",
       "L 90.9825 142.902\n",
       "L 90.9825 124.92\n",
       "' fill='#FF0000'/>\n",
       "<path  class='atom-4' d='M 106.323 133.861\n",
       "Q 106.323 129.543, 108.457 127.13\n",
       "Q 110.59 124.717, 114.578 124.717\n",
       "Q 118.565 124.717, 120.699 127.13\n",
       "Q 122.832 129.543, 122.832 133.861\n",
       "Q 122.832 138.229, 120.673 140.718\n",
       "Q 118.514 143.182, 114.578 143.182\n",
       "Q 110.615 143.182, 108.457 140.718\n",
       "Q 106.323 138.255, 106.323 133.861\n",
       "M 114.578 141.15\n",
       "Q 117.321 141.15, 118.794 139.321\n",
       "Q 120.292 137.467, 120.292 133.861\n",
       "Q 120.292 130.33, 118.794 128.552\n",
       "Q 117.321 126.749, 114.578 126.749\n",
       "Q 111.835 126.749, 110.336 128.527\n",
       "Q 108.863 130.305, 108.863 133.861\n",
       "Q 108.863 137.493, 110.336 139.321\n",
       "Q 111.835 141.15, 114.578 141.15\n",
       "' fill='#FF0000'/>\n",
       "</svg>\n"
      ],
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x1851640ab20>"
      ]
     },
     "execution_count": 95,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol=Chem.MolFromSmiles('OC1=NC(O)=CC=C1')\n",
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [],
   "source": [
    "#trying something else, to see the atom index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit.Chem import Draw\n",
    "IPythonConsole.ipython_useSVG=True  #< set this to False if you want PNGs instead of SVGs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "metadata": {},
   "outputs": [],
   "source": [
    "def mol_with_atom_index(mol):\n",
    "    for atom in mol.GetAtoms():\n",
    "        atom.SetAtomMapNum(atom.GetIdx())\n",
    "    return mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 96,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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       "' fill='#000000'/>\n",
       "</svg>\n"
      ],
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x1851640ab20>"
      ]
     },
     "execution_count": 96,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol_with_atom_index(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-0.22227600231292152\n",
      "0.2409857793122184\n",
      "-0.536700449504709\n"
     ]
    }
   ],
   "source": [
    "#Lets get the soc's about the nitrogen\n",
    "soc('OC1=NC=CC=C1', 2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 98,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "-0.1781728805797921"
      ]
     },
     "execution_count": 98,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "charge(mol, 2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2 -0.1781728805797921\n",
      "[1, 3] 0.4270584326998369\n",
      "{0, 4, 5, 7} -0.9856415681610016\n"
     ]
    }
   ],
   "source": [
    "soc('OC1=NC(O)=CC=C1', 2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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