2022_RDKit_UGM_notebook.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "8ba104a0",
   "metadata": {},
   "source": [
    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gist/j-wags/9de19462450f45f7ec7116fbd212193e/HEAD)\n",
    "\n",
    "Handle imports"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "1fb4e51f",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "LICENSE: Could not open license file specified by OE_LICENSE environment variable \"/Users/jeffreywagner/oe_license.txt\"\n",
      "LICENSE: Could not open license file \"oe_license.txt\" in local directory\n",
      "LICENSE: N.B. OE_DIR environment variable is not set\n",
      "LICENSE: No product keys!\n",
      "LICENSE: No product keys!\n",
      "LICENSE: No product keys!\n",
      "Warning: Unable to load toolkit 'OpenEye Toolkit'. The Open Force Field Toolkit does not require the OpenEye Toolkits, and can use RDKit/AmberTools instead. However, if you have a valid license for the OpenEye Toolkits, consider installing them for faster performance and additional file format support: https://docs.eyesopen.com/toolkits/python/quickstart-python/linuxosx.html OpenEye offers free Toolkit licenses for academics: https://www.eyesopen.com/academic-licensing\n",
      "LICENSE: No product keys!\n"
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "\n",
    "from openff.toolkit import Molecule, ForceField, Topology\n",
    "from openff.units import unit\n",
    "from openff.units.openmm import from_openmm\n",
    "from io import StringIO\n",
    "from pdbfixer import PDBFixer\n",
    "import openmm.unit as omm_unit"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9a3e3115",
   "metadata": {},
   "source": [
    "Make an RDKit Molecule, and turn that into an OpenFF Molecukle"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "aa44f8b6",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "45f687a7dae64309b54d3faf150d6e9d",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": []
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "d48888c150024a5d999a603b4c728d16",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "rdmol = Chem.MolFromSmiles('CC(=O)NC1=CC=C(C=C1)O')\n",
    "\n",
    "offmol = Molecule.from_rdkit(rdmol)\n",
    "offmol.generate_conformers()\n",
    "offmol.conformers[0] += [15, 15, 15] * unit.angstrom\n",
    "\n",
    "offmol"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2d8cdd4a",
   "metadata": {},
   "source": [
    "Make another RDKit Molecule using a simple chemical reaction "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "0c720116",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<rdkit.Chem.rdchem.Mol at 0x17e79fdd0>"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "rxn = Chem.rdChemReactions.ReactionFromSmarts(\n",
    "    '[C:1]=[O]'                                     \n",
    "    + '>>'\n",
    "    + '[C:1]=[S]'\n",
    ")\n",
    "products = rxn.RunReactants([rdmol])\n",
    "\n",
    "product = products[0][0]\n",
    "Chem.SanitizeMol(product)\n",
    "product\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9a01d06c",
   "metadata": {},
   "source": [
    "Convert the product of the chemical reaction to an OpenFF Molecule"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "9d69b8b7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "0924e1e1cf1a4cc58b896bda0d7ba7a3",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "product_offmol = Molecule.from_rdkit(product)\n",
    "product_offmol.generate_conformers()\n",
    "# Offset so the visualization will be nicer\n",
    "product_offmol.conformers[0] += [7, 7, 7] * unit.angstrom\n",
    "product_offmol"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f79f3ebe",
   "metadata": {},
   "source": [
    "Load a molecule from SDF file containing several different elements and a net charge (we also cover Br and I but I but they make the AM1 calculation take too long)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "1ea09360",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "06c750dccb654c7e86dd6f1b72b876fe",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "chonpsfcl = Molecule.from_file('CHONPSFCl.sdf')\n",
    "chonpsfcl"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f42b27bc",
   "metadata": {},
   "source": [
    "Make and solvate a box containing both molecules using OpenMM"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "56aa8fd6",
   "metadata": {},
   "outputs": [],
   "source": [
    "offtop = Topology.from_molecules([offmol, product_offmol, chonpsfcl])\n",
    "offtop.box_vectors = ([2., 2., 2.,] * unit.nanometer)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "ceed4c72",
   "metadata": {},
   "outputs": [],
   "source": [
    "with StringIO() as f:\n",
    "    offtop.to_file(f)\n",
    "    f.seek(0)\n",
    "    fixer = PDBFixer(pdbfile=f)\n",
    "\n",
    "fixer.addSolvent(\n",
    "    boxVectors=offtop.box_vectors.to_openmm(),\n",
    "    positiveIon='Na+',\n",
    "    negativeIon='Cl-',\n",
    "    ionicStrength=1.0 * omm_unit.molar,\n",
    ")\n",
    "\n",
    "solvated_topology = Topology.from_openmm(\n",
    "    fixer.topology,\n",
    "    unique_molecules={\n",
    "        *offtop.molecules,\n",
    "        Molecule.from_smiles(\"O\"),\n",
    "        Molecule.from_smiles(\"[Na+]\"),\n",
    "        Molecule.from_smiles(\"[Cl-]\"),\n",
    "    },\n",
    ")\n",
    "solvated_topology.set_positions(from_openmm(fixer.positions))\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e2de8288",
   "metadata": {},
   "source": [
    "Apply the Sage force field to the molecules in the topology"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "e466d18f",
   "metadata": {},
   "outputs": [],
   "source": [
    "ff = ForceField('openff-2.0.0.offxml')\n",
    "\n",
    "interchange = ff.create_interchange(solvated_topology)\n",
    "omm_system = interchange.to_openmm()\n",
    "omm_top = interchange.to_openmm_topology()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fb6eda86",
   "metadata": {},
   "source": [
    "Generic OpenMM simulation setup + execution"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "2b03a24d",
   "metadata": {},
   "outputs": [],
   "source": [
    "import openmm\n",
    "\n",
    "# Construct and configure a Langevin integrator at 300 K with an appropriate friction constant and time-step\n",
    "integrator = openmm.LangevinIntegrator(\n",
    "    300 * openmm.unit.kelvin,\n",
    "    1 / openmm.unit.picosecond,\n",
    "    0.002 * openmm.unit.picoseconds,\n",
    ")\n",
    "\n",
    "# Combine the topology, system, integrator and initial positions into a simulation\n",
    "simulation = openmm.app.Simulation(omm_top, omm_system, integrator)\n",
    "simulation.context.setPositions(solvated_topology.get_positions().to_openmm())\n",
    "\n",
    "# Add a reporter to record the structure every 10 steps\n",
    "dcd_reporter = openmm.app.DCDReporter(\"trajectory.dcd\", 10)\n",
    "simulation.reporters.append(dcd_reporter)\n",
    "\n",
    "simulation.context.setVelocitiesToTemperature(300 * openmm.unit.kelvin)\n",
    "simulation.runForClockTime(.25 * openmm.unit.minute)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "5b5c3ffb",
   "metadata": {},
   "source": [
    "Visualize simulation using NglView"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "337106c1",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "191e4fbcbad94cd896fa75476a9276e3",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "NGLWidget(max_frame=327)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "import mdtraj, nglview\n",
    "trajectory: mdtraj.Trajectory = mdtraj.load(\n",
    "    \"trajectory.dcd\", \n",
    "    top=mdtraj.Topology.from_openmm(omm_top)\n",
    ")\n",
    "\n",
    "view = nglview.show_mdtraj(trajectory)\n",
    "view.add_ball_and_stick()\n",
    "\n",
    "view"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f109c556",
   "metadata": {},
   "source": [
    "Next steps:\n",
    "\n",
    "* Try simulating your own inputs - I (Jeff Wagner) will be on Discord if you have any questions - I'd love to hear about more use cases! (warning: pub o' clock is in about ~3 hours...)\n",
    "* If you'd like more help, please use our [Issue Tracker](https://github.com/openforcefield/openff-toolkit/issues)\n",
    "* I'll be at the hackathon tomorrow!\n",
    "* To install and run locally - \n",
    "    * Download [this gist](https://gist.github.com/j-wags/9de19462450f45f7ec7116fbd212193e)\n",
    "    * build the environment `conda env create -n openff -f environment.yaml` \n",
    "    * Activate the environment `conda activate openff` \n",
    "    * Open the notebook `jupyter-notebook`\n",
    "* or see our [installation guide](https://docs.openforcefield.org/projects/toolkit/en/stable/installation.html)\n",
    "\n",
    "Other OpenFF examples:\n",
    "* [The OpenFF Toolkit Showcase](https://github.com/openforcefield/openff-toolkit/tree/main/examples/toolkit_showcase)\n",
    "* [Automatic torsion parameter generation using BespokeFit](https://docs.openforcefield.org/projects/bespokefit/en/latest/getting-started/quick-start.html)\n",
    "* Generating parameters for a [post-translationally modified protein](https://gist.github.com/Yoshanuikabundi/66007cb9966b1455a259baaf7cd7e7c3#file-readme-md)\n"
   ]
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README.md

Jeff's Open Force Field live demo at the 2022 RDKit UGM

CHONPSFCl.sdf

     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
   -0.3177   10.4177   17.5788 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5570   11.2140   16.4984 F   0  0  0  0  0  0  0  0  0  0  0  0
    0.8675    9.5430   17.4816 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5103    9.6872   15.8097 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    0.6584    8.4683   17.6295 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9338    9.9747   18.4138 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8354    8.9536   18.6789 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3739    9.4940   18.2485 P   0  0  2  0  0  5  0  0  0  0  0  0
    5.3764    8.3805   18.1686 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8879   10.6567   19.3632 O   0  0  0  0  0  1  0  0  0  0  0  0
    4.2192   10.2478   16.7242 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3437   10.3522   19.6783 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0186   11.3987   19.0897 S   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2070    9.7765   17.8498 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4797   10.8317   18.0037 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6995   11.0984   16.7034 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8773    9.5051   20.0798 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  3  4  1  0
  3  5  1  1
  3  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  1
  8 11  1  0
  6 12  1  0
 12 13  1  0
 13  1  1  0
  1 14  1  1
  6 15  1  6
 11 16  1  0
 12 17  1  0
M  CHG  1  10  -1
M  END
$$$$

environment.yml

channels:
  - jaimergp/label/unsupported-cudatoolkit-shim
  - conda-forge
dependencies:
  # Runtime
  - python >=3.8
  - jupyter
  - openff-toolkit =0.11.1
  - pdbfixer
  - nglview
  - ipywidgets < 8