Round-trip a molecule with dummy atoms through a PDB block

DummyPDBAtoms.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "RDKit WARNING: [13:18:47] Enabling RDKit 2020.03.1dev1 jupyter extensions\n"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit.Chem import rdDepictor"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.MolFromSmiles(\"C1CCCCC1*\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rdDepictor.Compute2DCoords(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f4e6fcf7620>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "pdb_block = Chem.MolToPDBBlock(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "HETATM    1  C1  UNL     1       0.321  -1.299   0.000  1.00  0.00           C  \n",
      "HETATM    2  C2  UNL     1      -1.179  -1.299   0.000  1.00  0.00           C  \n",
      "HETATM    3  C3  UNL     1      -1.929   0.000   0.000  1.00  0.00           C  \n",
      "HETATM    4  C4  UNL     1      -1.179   1.299   0.000  1.00  0.00           C  \n",
      "HETATM    5  C5  UNL     1       0.321   1.299   0.000  1.00  0.00           C  \n",
      "HETATM    6  C6  UNL     1       1.071  -0.000   0.000  1.00  0.00           C  \n",
      "HETATM    7  *1  UNL     1       2.571   0.000   0.000  1.00  0.00           *  \n",
      "CONECT    1    2    6\n",
      "CONECT    2    3\n",
      "CONECT    3    4\n",
      "CONECT    4    5\n",
      "CONECT    5    6\n",
      "CONECT    6    7\n",
      "END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(pdb_block)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol_from_pdb = Chem.MolFromPDBBlock(pdb_block.replace(\" *\", \"AT\"),\n",
    "                                    sanitize=False, proximityBonding=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "[a.SetAtomicNum(0) for a in mol_from_pdb.GetAtoms() if a.GetAtomicNum() == 85];"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "rdkit.Chem.rdmolops.SanitizeFlags.SANITIZE_NONE"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Chem.SanitizeMol(mol_from_pdb)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f4e98296990>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol_from_pdb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "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": "3.6.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}