rdkit_fragments.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import AllChem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x1ad0763dee0>"
      ]
     },
     "execution_count": 51,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol = Chem.MolFromSmiles(\"C1CCC2(CC1)CCCC1CCCCC21\")\n",
    "def mol_with_atom_index(mol):\n",
    "    for atom in mol.GetAtoms():\n",
    "        atom.SetAtomMapNum(atom.GetIdx())\n",
    "    return mol\n",
    "mol_with_atom_index(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 52,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[CH2:1].[CH2:4][CH2:5]\n"
     ]
    },
    {
     "data": {
      "image/png": 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",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x1ad075abbc0>"
      ]
     },
     "execution_count": 52,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "atoms = [5, 4, 1]\n",
    "# smiles = Chem.MolFragmentToSmiles(mol, atoms, kekuleSmiles=True)\n",
    "smiles = Chem.MolFragmentToSmiles(mol, atoms)\n",
    "print(smiles)\n",
    "mol = Chem.MolFromSmiles(smiles)\n",
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 53,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x1ad075ab530>"
      ]
     },
     "execution_count": 53,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.MolFromSmiles(Chem.MolToSmiles(mol))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 54,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[(0, 1), (0, 2), (1, 2)]\n",
      "[CH4:1]1~[CH3:4][CH3:5]~1\n"
     ]
    }
   ],
   "source": [
    "import itertools\n",
    "\n",
    "def copy_atom(atom):\n",
    "    new_atom = Chem.Atom(atom.GetSymbol())\n",
    "    new_atom.SetFormalCharge(atom.GetFormalCharge())\n",
    "    new_atom.SetAtomMapNum(atom.GetAtomMapNum())\n",
    "    return new_atom\n",
    "\n",
    "def copy_edit_mol(mol): \n",
    "\n",
    "    new_mol = Chem.RWMol(Chem.MolFromSmiles(''))\n",
    "    for atom in mol.GetAtoms():\n",
    "        new_atom = copy_atom(atom)\n",
    "        new_mol.AddAtom(new_atom)\n",
    "\n",
    "    subset_possible_bonds = list(itertools.combinations(mol.GetAtoms(), 2))\n",
    "    subset = [(bond[0].GetIdx(), bond[1].GetIdx()) for bond in subset_possible_bonds]\n",
    "    print(subset)\n",
    "    \n",
    "    for bond in subset:\n",
    "        a1, a2 = bond[0], bond[1]\n",
    "        bond_obj = mol.GetBondBetweenAtoms(a1, a2)\n",
    "        if bond_obj:\n",
    "            new_mol.AddBond(a1, a2, order=bond_obj.GetBondType())\n",
    "        else:\n",
    "            new_mol.AddBond(a1, a2, order=Chem.BondType.UNSPECIFIED)\n",
    "\n",
    "    return new_mol\n",
    "\n",
    "\n",
    "copied_mol = copy_edit_mol(mol)\n",
    "copied_smiles = Chem.MolToSmiles(copied_mol)\n",
    "print(copied_smiles)\n",
    "copied_mol = Chem.RemoveHs(copied_mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[17:20:18] Explicit valence for atom # 0 C, 5, is greater than permitted\n"
     ]
    }
   ],
   "source": [
    "Chem.MolFromSmiles(copied_smiles)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0\n",
      "0\n",
      "1\n"
     ]
    }
   ],
   "source": [
    "for bond in copied_mol.GetBonds():\n",
    "    print(int(bond.GetBondTypeAsDouble()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[('C', 0, 4), ('C', 0, 3), ('C', 0, 3)]"
      ]
     },
     "execution_count": 57,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol = copied_mol\n",
    "[(atom.GetSymbol(), atom.GetFormalCharge(), atom.GetTotalNumHs()) for atom in mol.GetAtoms()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 58,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\n",
      "     RDKit          2D\n",
      "\n",
      " 13 13  0  0  0  0  0  0  0  0999 V2000\n",
      "    0.8660    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0\n",
      "   -0.4330    0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  4  0  0\n",
      "   -0.4330   -0.7500    0.0000 C   0  0  0  0  0  0  0  0  0  5  0  0\n",
      "    0.9993    1.0853    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.1651   -0.7500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    2.1651    0.7500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.9993   -1.0853    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.1830    2.0490    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.9184    0.5413    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.2402    1.6117    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.1830   -2.0490    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "    0.2402   -1.6117    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "   -1.9184   -0.5413    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0\n",
      "  1  2  0  0\n",
      "  1  3  0  0\n",
      "  2  3  1  0\n",
      "  1  4  1  0\n",
      "  1  5  1  0\n",
      "  1  6  1  0\n",
      "  1  7  1  0\n",
      "  2  8  1  0\n",
      "  2  9  1  0\n",
      "  2 10  1  0\n",
      "  3 11  1  0\n",
      "  3 12  1  0\n",
      "  3 13  1  0\n",
      "M  END\n",
      "\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[17:20:18] UFFTYPER: Unrecognized atom type: C_6 (0)\n",
      "[17:20:18] UFFTYPER: Unrecognized atom type: C_5 (1)\n",
      "[17:20:18] UFFTYPER: Unrecognized atom type: C_5 (2)\n"
     ]
    }
   ],
   "source": [
    "copied_mol2 = Chem.AddHs(copied_mol)\n",
    "AllChem.EmbedMolecule(copied_mol2,randomSeed=0xf00d)\n",
    "print(Chem.MolToMolBlock(copied_mol2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "<class 'rdkit.Chem.rdchem.BondType'>\n"
     ]
    }
   ],
   "source": [
    "print(type(Chem.BondType.ZERO))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 60,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['AROMATIC',\n",
       " 'DATIVE',\n",
       " 'DATIVEL',\n",
       " 'DATIVEONE',\n",
       " 'DATIVER',\n",
       " 'DOUBLE',\n",
       " 'FIVEANDAHALF',\n",
       " 'FOURANDAHALF',\n",
       " 'HEXTUPLE',\n",
       " 'HYDROGEN',\n",
       " 'IONIC',\n",
       " 'ONEANDAHALF',\n",
       " 'OTHER',\n",
       " 'QUADRUPLE',\n",
       " 'QUINTUPLE',\n",
       " 'SINGLE',\n",
       " 'THREEANDAHALF',\n",
       " 'THREECENTER',\n",
       " 'TRIPLE',\n",
       " 'TWOANDAHALF',\n",
       " 'UNSPECIFIED',\n",
       " 'ZERO',\n",
       " '__abs__',\n",
       " '__add__',\n",
       " '__and__',\n",
       " '__bool__',\n",
       " '__ceil__',\n",
       " '__class__',\n",
       " '__delattr__',\n",
       " '__dir__',\n",
       " '__divmod__',\n",
       " '__doc__',\n",
       " '__eq__',\n",
       " '__float__',\n",
       " '__floor__',\n",
       " '__floordiv__',\n",
       " '__format__',\n",
       " '__ge__',\n",
       " '__getattribute__',\n",
       " '__getnewargs__',\n",
       " '__gt__',\n",
       " '__hash__',\n",
       " '__index__',\n",
       " '__init__',\n",
       " '__init_subclass__',\n",
       " '__int__',\n",
       " '__invert__',\n",
       " '__le__',\n",
       " '__lshift__',\n",
       " '__lt__',\n",
       " '__mod__',\n",
       " '__module__',\n",
       " '__mul__',\n",
       " '__ne__',\n",
       " '__neg__',\n",
       " '__new__',\n",
       " '__or__',\n",
       " '__pos__',\n",
       " '__pow__',\n",
       " '__radd__',\n",
       " '__rand__',\n",
       " '__rdivmod__',\n",
       " '__reduce__',\n",
       " '__reduce_ex__',\n",
       " '__repr__',\n",
       " '__rfloordiv__',\n",
       " '__rlshift__',\n",
       " '__rmod__',\n",
       " '__rmul__',\n",
       " '__ror__',\n",
       " '__round__',\n",
       " '__rpow__',\n",
       " '__rrshift__',\n",
       " '__rshift__',\n",
       " '__rsub__',\n",
       " '__rtruediv__',\n",
       " '__rxor__',\n",
       " '__setattr__',\n",
       " '__sizeof__',\n",
       " '__slots__',\n",
       " '__str__',\n",
       " '__sub__',\n",
       " '__subclasshook__',\n",
       " '__truediv__',\n",
       " '__trunc__',\n",
       " '__xor__',\n",
       " 'bit_length',\n",
       " 'conjugate',\n",
       " 'denominator',\n",
       " 'from_bytes',\n",
       " 'imag',\n",
       " 'name',\n",
       " 'names',\n",
       " 'numerator',\n",
       " 'real',\n",
       " 'to_bytes',\n",
       " 'values']"
      ]
     },
     "execution_count": 60,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dir(Chem.BondType)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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