Create a radial network using OpenFE and Lomap Atom Mapper

lomap_radial_with_openfe.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "6db2a96e",
   "metadata": {},
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   "source": [
    "import openfe\n",
    "from rdkit import Chem\n",
    "import glob"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "e997da08",
   "metadata": {},
   "outputs": [],
   "source": [
    "mols = [openfe.SmallMoleculeComponent(Chem.MolFromMol2File(f, removeHs=False))\n",
    "        for f in glob.glob('./radial/ejm*mol2')]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "5c3ca11d",
   "metadata": {},
   "outputs": [],
   "source": [
    "# object that provides a mapping between pairs of molecules\n",
    "mapper = openfe.LomapAtomMapper()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "17af20d2",
   "metadata": {},
   "outputs": [],
   "source": [
    "# create radial network \n",
    "ln = openfe.ligand_network_planning.generate_radial_network(\n",
    "    ligands=mols[1:],\n",
    "    central_ligand=mols[0],\n",
    "    mappers=[mapper]\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "44be9b7c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ejm_45 ejm_48 {0: 0, 1: 5, 2: 4, 3: 3, 4: 2, 5: 1, 6: 19, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 20: 6, 24: 25, 25: 27, 26: 26, 27: 28, 28: 29, 29: 30, 30: 31, 31: 32}\n",
      "ejm_45 ejm_43 {0: 0, 1: 5, 2: 4, 3: 3, 4: 2, 5: 1, 6: 20, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 6, 24: 23, 25: 25, 26: 24, 27: 26, 28: 27, 29: 28, 30: 29, 31: 30, 32: 22, 33: 31}\n",
      "ejm_45 ejm_42 {0: 0, 1: 5, 2: 4, 3: 3, 4: 2, 5: 1, 6: 20, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 6, 24: 22, 25: 24, 26: 23, 27: 25, 28: 26, 29: 27, 30: 28, 31: 29, 32: 30, 33: 31}\n",
      "ejm_45 ejm_54 {0: 0, 1: 5, 2: 4, 3: 3, 4: 2, 5: 1, 6: 19, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 22, 20: 6, 24: 23, 25: 25, 26: 24, 27: 26, 28: 27, 29: 28, 30: 29, 31: 30, 32: 36, 33: 20}\n",
      "ejm_45 ejm_44 {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 31: 31, 32: 23, 33: 21}\n",
      "ejm_45 ejm_50 {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 24: 22, 25: 23, 26: 24, 27: 25, 28: 26, 29: 27, 30: 28, 31: 29, 32: 30, 33: 31}\n",
      "ejm_45 ejm_49 {0: 0, 1: 5, 2: 4, 3: 3, 4: 2, 5: 1, 6: 19, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 20: 6, 24: 26, 25: 28, 26: 27, 27: 29, 28: 30, 29: 31, 30: 32, 31: 33}\n",
      "ejm_45 ejm_47 {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 20: 19, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 31: 31}\n",
      "ejm_45 ejm_46 {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 20: 22, 24: 23, 25: 24, 26: 25, 27: 26, 28: 27, 29: 28, 30: 29, 31: 30}\n",
      "ejm_45 ejm_55 {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 21, 20: 19, 24: 22, 25: 23, 26: 24, 27: 25, 28: 26, 29: 27, 30: 28, 31: 29, 33: 20}\n",
      "ejm_45 ejm_31 {0: 0, 1: 5, 2: 4, 3: 3, 4: 2, 5: 1, 6: 20, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 6, 21: 30, 24: 21, 25: 23, 26: 22, 27: 24, 28: 25, 29: 26, 30: 27, 31: 28, 32: 29, 33: 31}\n"
     ]
    }
   ],
   "source": [
    "for edge in ln.edges:\n",
    "    # name of A/B ligand, then dictionary mapping indices of atoms in A to atoms in B\n",
    "    print(edge.componentA.name, edge.componentB.name, edge.componentA_to_componentB)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "9caef5e8",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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