{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Getting list of molecule IDs...\n",
      "Done!\n"
     ]
    }
   ],
   "source": [
    "# Make lists of the guest smiles strings and the molecule identifiers \n",
    "file = 'GDCC_hosts_guests_smiles.txt'\n",
    "\n",
    "file = open(file, 'r')\n",
    "text = file.readlines()\n",
    "file.close()\n",
    "print(\"Getting list of molecule IDs...\")   \n",
    "MoleculeIDs = [] #SAMPL6 Molecule ID \n",
    "smiles = [] #isomeric SMILES\n",
    "#Loop over lines and parse\n",
    "for line in text:\n",
    "    tmp = line.split(';') #Split into columns\n",
    "    MoleculeID = tmp[1].strip() #mol ID\n",
    "    smi = tmp[0] #smiles string\n",
    "    try:\n",
    "        MoleculeIDs.append(MoleculeID)\n",
    "        smiles.append(smi)\n",
    "    except:\n",
    "        print(\"Error storing line: %s\" % line)\n",
    "print(\"Done!\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "from openeye.oechem import *\n",
    "from openeye.oeomega import * # conformer generation\n",
    "\n",
    "for idx in range( len( smiles ) ):\n",
    "    #initialize omega, this is a conformation generator\n",
    "    omega = OEOmega()\n",
    "    #set the maximum conformer generated to 1\n",
    "    omega.SetMaxConfs(1) \n",
    "    omega.SetIncludeInput(False)\n",
    "    omega.SetStrictAtomTypes(False) #Leniency is assigning atom types\n",
    "    omega.SetStrictStereo(True) #Don't generate conformers if stereochemistry not provided\n",
    "    \n",
    "    # Generate new OEMol and parse SMILES\n",
    "    mol = OEMol()\n",
    "    OEParseSmiles( mol, smiles[idx])\n",
    "    # Generate one conformer\n",
    "    status = omega(mol)\n",
    "    if not status:\n",
    "        print(\"Error generating conformers for %s, %s.\" % (smiles[idx], MoleculeIDs[idx]))\n",
    "\n",
    "    # Write out PDB of molecule\n",
    "    ofile = oemolostream('%s.pdb'%(MoleculeIDs[idx]))\n",
    "    OEWriteMolecule(ofile, mol)\n",
    "    ofile.close()\n",
    "\n",
    "    # Write out MOL2 of molecule\n",
    "    ofile = oemolostream('%s.mol2'%(MoleculeIDs[idx]))\n",
    "    OEWriteMolecule(ofile, mol)\n",
    "    ofile.close()\n",
    "    \n",
    "    # Write out SDF of molecule\n",
    "    ofile = oemolostream('%s.sdf'%(MoleculeIDs[idx]))\n",
    "    OEWriteMolecule(ofile, mol)\n",
    "    ofile.close()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Host done: OA\n",
      "Host done: exoOA\n"
     ]
    }
   ],
   "source": [
    "hosts = ['OA', 'exoOA']\n",
    "for idx in range( len( hosts ) ):\n",
    "    inputfile = oemolistream('%s.pdb'%(hosts[idx]) )\n",
    "    mol = OEMol()\n",
    "    OEReadMolecule( inputfile, mol )\n",
    "    inputfile.close()\n",
    "\n",
    "    # Write to a SDF file\n",
    "    ofile = oemolostream( '%s.sdf'%(hosts[idx]) ) \n",
    "    OEWriteMolecule( ofile, mol)\n",
    "    ofile.close()\n",
    "\n",
    "    # Write to a PDB file\n",
    "    ofile = oemolostream(  '%s.mol2'%(hosts[idx]) )  \n",
    "    OEWriteMolecule( ofile, mol)\n",
    "    ofile.close()\n",
    "    print(\"Host done:\", hosts[idx])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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