Properties on conformers

Properties_on_conformers.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem\n",
    "from rdkit.Chem.Draw import IPythonConsole\n",
    "from rdkit.Chem import rdDistGeom, rdMolAlign"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.MolFromSmiles('CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2ccccc21')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x7f47f90e8360>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "mol = Chem.AddHs(mol)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "confIds = rdDistGeom.EmbedMultipleConfs(mol, 5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "# generate 5 separate SDF files, one per each conformer\n",
    "confs = []\n",
    "for confId in confIds:\n",
    "    tempMol = Chem.Mol(mol)\n",
    "    for confId2 in reversed(confIds):\n",
    "        if (confId2 == confId):\n",
    "            continue\n",
    "        tempMol.RemoveConformer(confId2)\n",
    "    tempMol.SetIntProp('ConformerId', confId)\n",
    "    confFilename = '/tmp/bilastine_c{0:d}.sdf'.format(confId)\n",
    "    confs.append(confFilename)\n",
    "    w = Chem.SDWriter(confFilename)\n",
    "    w.write(tempMol, confId = confId)\n",
    "    w.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "for conf in confs:   # loop over my sdf files\n",
    "    suppl = Chem.SDMolSupplier(conf, removeHs = False)\n",
    "    if '_c0.sdf' in conf:\n",
    "        allconfs = suppl[0]\n",
    "    else:\n",
    "        for i, mol in enumerate(suppl):\n",
    "            allconfs.AddConformer(mol.GetConformer(), assignId = True)\n",
    "rdMolAlign.AlignMolConformers(allconfs)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "def copy_coords(source, to):\n",
    "    for i in range(source.GetNumAtoms()):\n",
    "        to.SetAtomPosition(i, source.GetAtomPosition(i))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "i = 0\n",
    "numConfs = allconfs.GetNumConformers()\n",
    "# looping again over original confs to update their coordinates from aligned allconfs\n",
    "for conf in confs:\n",
    "    suppl = Chem.SDMolSupplier(conf, removeHs = False)\n",
    "    mol = suppl[0]\n",
    "    copy_coords(allconfs.GetConformer(i), mol.GetConformer())\n",
    "    wname = conf.split('.sdf', 1)[0] + '_aligned.sdf'\n",
    "    w = Chem.SDWriter(wname)\n",
    "    w.write(mol)\n",
    "    w.close()\n",
    "    i += 1"
   ]
  }
 ],
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