PDBAtomResidueInfo

PDBAtomResidueInfo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem import rdDistGeom\n",
    "from rdkit.Chem.Draw import IPythonConsole"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.MolFromSmiles('c1ccccn1')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rdDistGeom.EmbedMolecule(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "elem_count = {}\n",
    "for a in mol.GetAtoms():\n",
    "    n = elem_count.get(a.GetAtomicNum(), 0)\n",
    "    n += 1\n",
    "    elem_count[a.GetAtomicNum()] = n\n",
    "    n = min(n, 99)\n",
    "    mi = Chem.AtomPDBResidueInfo()\n",
    "    mi.SetResidueName('MOL')\n",
    "    mi.SetResidueNumber(1)\n",
    "    atom_name = '{0:>2s}{1:<2d}'.format(a.GetSymbol(), n)\n",
    "    mi.SetIsHeteroAtom(True)\n",
    "    mi.SetName(atom_name)\n",
    "    mi.SetOccupancy(0.0)\n",
    "    mi.SetTempFactor(0.0)\n",
    "    a.SetMonomerInfo(mi)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "HETATM    1  C1  MOL     1      -1.011   0.850  -0.017  0.00  0.00           C  \n",
      "HETATM    2  C2  MOL     1       0.159   1.321  -0.598  0.00  0.00           C  \n",
      "HETATM    3  C3  MOL     1       1.251   0.462  -0.564  0.00  0.00           C  \n",
      "HETATM    4  C4  MOL     1       1.052  -0.805  -0.026  0.00  0.00           C  \n",
      "HETATM    5  C5  MOL     1      -0.213  -1.342  -0.195  0.00  0.00           C  \n",
      "HETATM    6  N1  MOL     1      -1.238  -0.486   0.039  0.00  0.00           N  \n",
      "CONECT    1    2    2    6\n",
      "CONECT    2    3\n",
      "CONECT    3    4    4\n",
      "CONECT    4    5\n",
      "CONECT    5    6    6\n",
      "END\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print(Chem.MolToPDBBlock(mol))"
   ]
  }
 ],
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