biopolymer_alpha_notebook.ipynb

biopolymer_rc_notebook.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "colab_type": "text",
    "id": "view-in-github"
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   "source": [
    "[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gist/j-wags/4b9716cfd7c4c5efee03ff63ec6a964e/HEAD)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "jGKy7ZaVSMNK"
   },
   "source": [
    "# Let's load a protein from PDB\n",
    "\n",
    "Right now, the `Molecule.from_polymer_pdb` method can handle the canonical amino acids (26 including protonation states) in capped and uncapped forms. We may add an API to allow registration of new polymer substructures in a future release, but right now we just want to get this release out the door."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "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"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'./T4-protein.pdb'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# This code block just copies an example protein PDB into the current directory \n",
    "# for your convenience\n",
    "import shutil\n",
    "from openff.toolkit.utils import get_data_file_path\n",
    "file_path = get_data_file_path('proteins/T4-protein.pdb')\n",
    "shutil.copy(file_path, './T4-protein.pdb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "id": "Ctz4Qshz0pkz"
   },
   "outputs": [],
   "source": [
    "from openff.toolkit import Molecule, Topology\n",
    "# Load structures and perceive info\n",
    "# This PDB file must have explicit hydrogens\n",
    "protein = Molecule.from_polymer_pdb('T4-protein.pdb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "xdmbmufAEpBR",
    "outputId": "56b9f8fa-7bc6-471d-b3c2-d09122a35eee"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "OrderedDict([('atom1', 17),\n",
       "             ('atom2', 18),\n",
       "             ('bond_order', 2),\n",
       "             ('is_aromatic', False),\n",
       "             ('stereochemistry', None),\n",
       "             ('fractional_bond_order', None)])"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Let's take a look at a peptide C=O bond. The bond orders have been filled \n",
    "# in for a library of known substructures. So the information that this C=O\n",
    "# bond has an order of 2 came from the chemical components dictionary \n",
    "# published by the RCSB - _this information was NOT explicitly in the PDB file_\n",
    "protein.bonds[1].to_dict()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "protein"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "EKmJ1RuyKdHw"
   },
   "source": [
    "# \"HierarchySchemes\", AKA residues and chains\n",
    "\n",
    "Different software ecosystems have different expectations about what constitutes a \"residue\" or \"chain\". We try to be very hands-off, and allow atoms to have \"metadata\" (a dict of `(str): (str or int)`). Then we allow users to group atoms according to this metadata (for example, atoms with the same residue name, number, and chain ID could be in a single \"residue\"). Here, the \"residue\" is an instance of an OpenFF \"HierarchyElement\", and the machinery that groups them by their metadata is called a \"HierarchyScheme\".\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "nn25SwfEGM1B",
    "outputId": "e95fde0d-e291-45ea-e671-4a4dd5e5f68f"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "OrderedDict([('atomic_number', 8),\n",
       "             ('formal_charge', 0),\n",
       "             ('is_aromatic', False),\n",
       "             ('stereochemistry', None),\n",
       "             ('name', 'O'),\n",
       "             ('metadata',\n",
       "              {'residue_name': 'MET',\n",
       "               'residue_number': '0',\n",
       "               'chain_id': 'A'})])"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Check out the new \"metadata\" field that this atom has\n",
    "protein.atoms[18].to_dict()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "LQlkBQ8rsXId",
    "outputId": "a391550e-ed06-49af-a24a-8cdb7096ba9c"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'chains': HierarchyScheme with uniqueness_criteria '('chain_id',)', iterator_name 'chains', and 1 elements,\n",
       " 'residues': HierarchyScheme with uniqueness_criteria '('chain_id', 'residue_number', 'residue_name')', iterator_name 'residues', and 164 elements}"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# The OFFMol knows about residues and chains\n",
    "protein.hierarchy_schemes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "311Hqe8DIFuh",
    "outputId": "989f32d8-b991-4b64-9eef-1d9b2ce6fe6e"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[HierarchyElement ('A', '0', 'MET') of iterator 'residues' containing 19 atom(s),\n",
       " HierarchyElement ('A', '1', 'ASN') of iterator 'residues' containing 14 atom(s),\n",
       " HierarchyElement ('A', '2', 'ILE') of iterator 'residues' containing 19 atom(s),\n",
       " HierarchyElement ('A', '3', 'PHE') of iterator 'residues' containing 20 atom(s),\n",
       " HierarchyElement ('A', '4', 'GLU') of iterator 'residues' containing 15 atom(s)]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# We offer lightweight residue and chain iteration functionality\n",
    "protein.residues[:5]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "wHJEN5JzOEJU",
    "outputId": "f0629b69-dc31-46e6-9625-3e5712d71652"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[Atom(name=N, atomic number=7),\n",
       " Atom(name=H, atomic number=1),\n",
       " Atom(name=CA, atomic number=6),\n",
       " Atom(name=HA, atomic number=1),\n",
       " Atom(name=CB, atomic number=6),\n",
       " Atom(name=HB2, atomic number=1),\n",
       " Atom(name=HB3, atomic number=1),\n",
       " Atom(name=CG, atomic number=6),\n",
       " Atom(name=HG2, atomic number=1),\n",
       " Atom(name=HG3, atomic number=1),\n",
       " Atom(name=CD, atomic number=6),\n",
       " Atom(name=OE1, atomic number=8),\n",
       " Atom(name=OE2, atomic number=8),\n",
       " Atom(name=C, atomic number=6),\n",
       " Atom(name=O, atomic number=8)]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# The underlying atoms can be accessed using the \"particles\" iterator\n",
    "[*protein.residues[4].atoms]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "KQ_2NoF2ZoiA"
   },
   "source": [
    "## Hierarchy metadata is preserved when going to/from OpenMM, RDKit, OpenEye (not shown here), and PDB \n",
    "\n",
    "It's worth emphasizing again that we are VERY hands-off with hierarchy info handling - Our main goal is to have as few restrictions as possible. But the other side of this coin is that there are cases where we're converting to a format with limitations on their hierarchy info and information is lost or other unexpected things happen. We are adding a special docs page to help people understand this here: https://docs.openforcefield.org/projects/toolkit/en/main/users/molecule_conversion.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "ssqNn3xeWrAv",
    "outputId": "2e3fcb21-ee60-4442-e595-3163a43bbb2c"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<bound method Topology.residues of <Topology; 1 chains, 164 residues, 2634 atoms, 2654 bonds>>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Here's an example of where hierarchy info goes when converting an OFFMol\n",
    "# to OpenMM\n",
    "omm_top = protein.to_topology().to_openmm()\n",
    "omm_top.residues"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "3amen4QzanB-",
    "outputId": "e258b90a-288e-4735-9a02-b3918ddb7cd9"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Atom 100 (H51x) of chain 0 residue 5 (MET)>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "[*omm_top.atoms()][100]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "2dr_znOZZ1ar",
    "outputId": "1d4291fe-ac2d-473e-ddd8-c60d7f6a4827"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "MET 5 A\n"
     ]
    }
   ],
   "source": [
    "# Here's where hierarchy info goes in RDKit\n",
    "rd_protein = protein.to_rdkit()\n",
    "res_info = rd_protein.GetAtomWithIdx(100).GetPDBResidueInfo()\n",
    "print(res_info.GetResidueName(), res_info.GetResidueNumber(), res_info.GetChainId())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "KfReaGusabGu",
    "outputId": "403f918e-446e-4d05-a5e4-8a2c44fba23f"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ATOM      1  N   MET A   0      33.430  11.280  44.490  1.00  0.00           N1+\r\n",
      "ATOM      2  H   MET A   0      32.860  11.870  45.090  1.00  0.00           H  \r\n",
      "ATOM      3  H2  MET A   0      32.970  10.380  44.440  1.00  0.00           H  \r\n",
      "ATOM      4  H3  MET A   0      34.270  11.280  45.050  1.00  0.00           H  \r\n",
      "ATOM      5  CA  MET A   0      33.550  11.970  43.200  1.00  0.00           C  \r\n",
      "ATOM      6  HA  MET A   0      34.090  12.890  43.410  1.00  0.00           H  \r\n",
      "ATOM      7  CB  MET A   0      34.550  11.390  42.270  1.00  0.00           C  \r\n",
      "ATOM      8 HB2  MET A   0      35.470  11.330  42.850  1.00  0.00           H  \r\n",
      "ATOM      9 HB3  MET A   0      34.320  10.370  41.960  1.00  0.00           H  \r\n",
      "ATOM     10  CG  MET A   0      34.730  12.320  41.020  1.00  0.00           C  \r\n",
      "ATOM     11 HG2  MET A   0      35.430  11.840  40.340  1.00  0.00           H  \r\n",
      "ATOM     12 HG3  MET A   0      33.720  12.350  40.620  1.00  0.00           H  \r\n",
      "ATOM     13  SD  MET A   0      35.270  14.050  41.300  1.00  0.00           S  \r\n",
      "ATOM     14  CE  MET A   0      37.050  13.800  41.760  1.00  0.00           C  \r\n",
      "ATOM     15 HE1  MET A   0      37.170  13.650  42.830  1.00  0.00           H  \r\n",
      "ATOM     16 HE2  MET A   0      37.500  12.990  41.190  1.00  0.00           H  \r\n",
      "ATOM     17 HE3  MET A   0      37.570  14.740  41.600  1.00  0.00           H  \r\n",
      "ATOM     18  C   MET A   0      32.100  12.250  42.660  1.00  0.00           C  \r\n",
      "ATOM     19  O   MET A   0      31.370  11.320  42.330  1.00  0.00           O  \r\n",
      "ATOM     20  N   ASN A   1      31.740  13.550  42.670  1.00  0.00           N  \r\n",
      "ATOM     21  H   ASN A   1      32.490  14.160  42.970  1.00  0.00           H  \r\n",
      "ATOM     22  CA  ASN A   1      30.410  14.180  42.580  1.00  0.00           C  \r\n",
      "ATOM     23  HA  ASN A   1      29.790  13.840  41.750  1.00  0.00           H  \r\n",
      "ATOM     24  CB  ASN A   1      29.680  13.970  43.910  1.00  0.00           C  \r\n",
      "ATOM     25 HB2  ASN A   1      28.610  14.090  43.760  1.00  0.00           H  \r\n",
      "ATOM     26 HB3  ASN A   1      29.880  13.020  44.410  1.00  0.00           H  \r\n",
      "ATOM     27  CG  ASN A   1      29.930  15.080  44.920  1.00  0.00           C  \r\n",
      "ATOM     28 OD1  ASN A   1      29.060  15.930  45.070  1.00  0.00           O  \r\n",
      "ATOM     29 ND2  ASN A   1      31.150  15.160  45.390  1.00  0.00           N  \r\n",
      "ATOM     30 HD21 ASN A   1      31.300  15.760  46.190  1.00  0.00           H  \r\n"
     ]
    }
   ],
   "source": [
    "# We also write this hierarchy info out to PDB if requested (this all goes \n",
    "# through OpenMM's excellent PDBFile class)\n",
    "protein.to_file('test.pdb', file_format='pdb')\n",
    "!head -n 30 test.pdb"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "_qv0_hqDZuRM"
   },
   "source": [
    "# OpenFF units \n",
    "\n",
    "We've replaced our use of OpenMM's units with a more [interoperable units package called `openff-units`](https://github.com/openforcefield/openff-units#getting-started). This is a thin wrapper over `pint` which is made to happily interoperate with `openmm.unit`, and to make it easy to implement interoperation with additional units packages in the future.\n",
    "\n",
    "When it comes to handling units, the major user-facing difference is that _getters_ will now return `openff-units` `Quantity` objects (previously they returned `openmm` `Quantity` objects). On the other hand, _setters_ are made to work with `openmm`, `pint`, or `openff-units` `Quantity` objects. \n",
    "\n",
    "https://docs.openforcefield.org/projects/toolkit/en/main/releasehistory.html#migration-guide"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "U1Xw0BQbhgji",
    "outputId": "015ce584-20e7-4938-a1c5-023877f0e395"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "openff.units.units.Quantity"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Quantities are now returned as openff-units Quantities\n",
    "first_conformer = protein.conformers[0]\n",
    "type(first_conformer)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "V4tOa15Ph42i",
    "outputId": "16d828bb-9c65-4ef7-bb3f-75901016f864"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "openmm.unit.quantity.Quantity"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# We can convert an openff-units Quantity to openmm\n",
    "from openff.units.openmm import to_openmm, from_openmm\n",
    "type(to_openmm(first_conformer))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "csdwreNwSUOV"
   },
   "source": [
    "# (probably not that useful) Assigning residue information to a protein that we made from SMILES\n",
    "\n",
    "If we somehow have a chemical description of a protein without residue numbers/names, we can use the `perceive_residues` method to assign that information."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
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       "<path class=\"bond-6 atom-6 atom-7\" d=\"M 232.4,146.9 L 231.9,163.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-6 atom-6 atom-7\" d=\"M 231.9,163.3 L 231.4,179.7\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-6 atom-6 atom-7\" d=\"M 224.6,146.6 L 224.1,163.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-6 atom-6 atom-7\" d=\"M 224.1,163.0 L 223.6,179.5\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-7 atom-6 atom-8\" d=\"M 228.5,146.7 L 244.3,137.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-7 atom-6 atom-8\" d=\"M 244.3,137.8 L 260.2,128.8\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-8 atom-8 atom-9\" d=\"M 277.1,128.9 L 292.3,137.6\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-8 atom-8 atom-9\" d=\"M 292.3,137.6 L 307.5,146.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-9 atom-9 atom-10\" d=\"M 307.5,146.4 L 324.3,185.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-10 atom-10 atom-11\" d=\"M 324.3,185.0 L 315.7,197.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-10 atom-10 atom-11\" d=\"M 315.7,197.1 L 307.1,209.2\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-11 atom-9 atom-12\" d=\"M 307.5,146.4 L 352.4,123.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-12 atom-12 atom-13\" d=\"M 348.5,123.5 L 349.0,107.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-12 atom-12 atom-13\" d=\"M 349.0,107.1 L 349.5,90.8\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-12 atom-12 atom-13\" d=\"M 356.3,123.8 L 356.8,107.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-12 atom-12 atom-13\" d=\"M 356.8,107.4 L 357.3,91.0\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-13 atom-12 atom-14\" d=\"M 352.4,123.6 L 369.4,133.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-13 atom-12 atom-14\" d=\"M 369.4,133.6 L 386.3,143.6\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-14 atom-14 atom-15\" d=\"M 403.2,144.6 L 418.9,137.0\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-14 atom-14 atom-15\" d=\"M 418.9,137.0 L 434.5,129.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-15 atom-0 atom-16\" d=\"M 68.0,138.0 L 83.9,164.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-16 atom-0 atom-17\" d=\"M 68.0,138.0 L 53.0,165.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-17 atom-0 atom-18\" d=\"M 68.0,138.0 L 38.6,121.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-18 atom-3 atom-19\" d=\"M 146.9,153.4 L 146.1,164.5\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-18 atom-3 atom-19\" d=\"M 146.1,164.5 L 145.4,175.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-19 atom-4 atom-20\" d=\"M 195.9,119.6 L 194.6,118.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-19 atom-4 atom-20\" d=\"M 199.8,116.3 L 197.2,114.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-19 atom-4 atom-20\" d=\"M 203.8,113.1 L 199.8,109.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-19 atom-4 atom-20\" d=\"M 207.7,109.8 L 202.4,105.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-19 atom-4 atom-20\" d=\"M 211.6,106.6 L 205.0,100.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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       "<path class=\"bond-21 atom-5 atom-22\" d=\"M 171.9,83.3 L 168.3,51.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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       "<path class=\"bond-23 atom-8 atom-24\" d=\"M 268.4,102.2 L 268.3,91.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-24 atom-9 atom-25\" d=\"M 307.5,146.4 L 295.2,172.8 L 287.9,167.9 Z\" style=\"fill:#000000;fill-rule:evenodd;fill-opacity:1;stroke:#000000;stroke-width:1.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;\"/>\n",
       "<path class=\"bond-25 atom-10 atom-26\" d=\"M 324.3,185.0 L 351.4,172.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-26 atom-10 atom-27\" d=\"M 324.3,185.0 L 351.0,203.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-27 atom-11 atom-28\" d=\"M 304.7,231.0 L 308.8,239.7\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-27 atom-11 atom-28\" d=\"M 308.8,239.7 L 312.9,248.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-28 atom-14 atom-29\" d=\"M 394.7,159.3 L 394.7,170.4\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-28 atom-14 atom-29\" d=\"M 394.7,170.4 L 394.7,181.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-29 atom-15 atom-30\" d=\"M 434.5,129.5 L 421.7,100.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-30 atom-15 atom-31\" d=\"M 434.5,129.5 L 452.5,105.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"bond-31 atom-15 atom-32\" d=\"M 434.5,129.5 L 461.4,148.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
       "<path class=\"atom-2\" d=\"M 93.9 72.2 Q 93.9 67.8, 96.1 65.3 Q 98.3 62.8, 102.4 62.8 Q 106.4 62.8, 108.6 65.3 Q 110.8 67.8, 110.8 72.2 Q 110.8 76.7, 108.6 79.2 Q 106.4 81.8, 102.4 81.8 Q 98.3 81.8, 96.1 79.2 Q 93.9 76.7, 93.9 72.2 M 102.4 79.7 Q 105.2 79.7, 106.7 77.8 Q 108.2 75.9, 108.2 72.2 Q 108.2 68.6, 106.7 66.7 Q 105.2 64.9, 102.4 64.9 Q 99.5 64.9, 98.0 66.7 Q 96.5 68.5, 96.5 72.2 Q 96.5 75.9, 98.0 77.8 Q 99.5 79.7, 102.4 79.7 \" fill=\"#FF0000\"/>\n",
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       "<path class=\"atom-8\" d=\"M 264.5 114.8 L 270.6 124.5 Q 271.2 125.5, 272.2 127.3 Q 273.1 129.0, 273.2 129.1 L 273.2 114.8 L 275.6 114.8 L 275.6 133.2 L 273.1 133.2 L 266.6 122.5 Q 265.8 121.3, 265.0 119.9 Q 264.3 118.4, 264.0 118.0 L 264.0 133.2 L 261.6 133.2 L 261.6 114.8 L 264.5 114.8 \" fill=\"#0000FF\"/>\n",
       "<path class=\"atom-11\" d=\"M 291.0 220.0 Q 291.0 215.6, 293.2 213.1 Q 295.3 210.6, 299.4 210.6 Q 303.5 210.6, 305.7 213.1 Q 307.9 215.6, 307.9 220.0 Q 307.9 224.5, 305.7 227.1 Q 303.5 229.6, 299.4 229.6 Q 295.4 229.6, 293.2 227.1 Q 291.0 224.5, 291.0 220.0 M 299.4 227.5 Q 302.3 227.5, 303.8 225.6 Q 305.3 223.7, 305.3 220.0 Q 305.3 216.4, 303.8 214.6 Q 302.3 212.7, 299.4 212.7 Q 296.6 212.7, 295.1 214.5 Q 293.6 216.4, 293.6 220.0 Q 293.6 223.8, 295.1 225.6 Q 296.6 227.5, 299.4 227.5 \" fill=\"#FF0000\"/>\n",
       "<path class=\"atom-13\" d=\"M 345.3 79.9 Q 345.3 75.4, 347.5 73.0 Q 349.7 70.5, 353.7 70.5 Q 357.8 70.5, 360.0 73.0 Q 362.2 75.4, 362.2 79.9 Q 362.2 84.4, 360.0 86.9 Q 357.8 89.4, 353.7 89.4 Q 349.7 89.4, 347.5 86.9 Q 345.3 84.4, 345.3 79.9 M 353.7 87.4 Q 356.6 87.4, 358.1 85.5 Q 359.6 83.6, 359.6 79.9 Q 359.6 76.2, 358.1 74.4 Q 356.6 72.6, 353.7 72.6 Q 350.9 72.6, 349.4 74.4 Q 347.9 76.2, 347.9 79.9 Q 347.9 83.6, 349.4 85.5 Q 350.9 87.4, 353.7 87.4 \" fill=\"#FF0000\"/>\n",
       "<path class=\"atom-14\" d=\"M 390.7 139.4 L 396.7 149.2 Q 397.3 150.2, 398.3 151.9 Q 399.3 153.6, 399.3 153.8 L 399.3 139.4 L 401.8 139.4 L 401.8 157.9 L 399.2 157.9 L 392.7 147.2 Q 392.0 145.9, 391.2 144.5 Q 390.4 143.1, 390.2 142.6 L 390.2 157.9 L 387.8 157.9 L 387.8 139.4 L 390.7 139.4 \" fill=\"#0000FF\"/>\n",
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       "<path class=\"atom-18\" d=\"M 22.7 107.3 L 25.2 107.3 L 25.2 115.2 L 34.7 115.2 L 34.7 107.3 L 37.2 107.3 L 37.2 125.8 L 34.7 125.8 L 34.7 117.3 L 25.2 117.3 L 25.2 125.8 L 22.7 125.8 L 22.7 107.3 \" fill=\"#000000\"/>\n",
       "<path class=\"atom-19\" d=\"M 137.4 177.1 L 139.9 177.1 L 139.9 184.9 L 149.4 184.9 L 149.4 177.1 L 151.9 177.1 L 151.9 195.6 L 149.4 195.6 L 149.4 187.0 L 139.9 187.0 L 139.9 195.6 L 137.4 195.6 L 137.4 177.1 \" fill=\"#000000\"/>\n",
       "<path class=\"atom-20\" d=\"M 211.2 82.7 L 213.7 82.7 L 213.7 90.5 L 223.2 90.5 L 223.2 82.7 L 225.7 82.7 L 225.7 101.2 L 223.2 101.2 L 223.2 92.6 L 213.7 92.6 L 213.7 101.2 L 211.2 101.2 L 211.2 82.7 \" fill=\"#000000\"/>\n",
       "<path class=\"atom-21\" d=\"M 198.4 48.8 L 200.9 48.8 L 200.9 56.7 L 210.4 56.7 L 210.4 48.8 L 212.9 48.8 L 212.9 67.3 L 210.4 67.3 L 210.4 58.7 L 200.9 58.7 L 200.9 67.3 L 198.4 67.3 L 198.4 48.8 \" fill=\"#000000\"/>\n",
       "<path class=\"atom-22\" d=\"M 159.8 31.7 L 162.3 31.7 L 162.3 39.5 L 171.8 39.5 L 171.8 31.7 L 174.3 31.7 L 174.3 50.1 L 171.8 50.1 L 171.8 41.6 L 162.3 41.6 L 162.3 50.1 L 159.8 50.1 L 159.8 31.7 \" fill=\"#000000\"/>\n",
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       "<path class=\"atom-29\" d=\"M 387.4 182.9 L 389.9 182.9 L 389.9 190.7 L 399.4 190.7 L 399.4 182.9 L 401.9 182.9 L 401.9 201.4 L 399.4 201.4 L 399.4 192.8 L 389.9 192.8 L 389.9 201.4 L 387.4 201.4 L 387.4 182.9 \" fill=\"#000000\"/>\n",
       "<path class=\"atom-30\" d=\"M 409.7 80.9 L 412.2 80.9 L 412.2 88.8 L 421.7 88.8 L 421.7 80.9 L 424.2 80.9 L 424.2 99.4 L 421.7 99.4 L 421.7 90.9 L 412.2 90.9 L 412.2 99.4 L 409.7 99.4 L 409.7 80.9 \" fill=\"#000000\"/>\n",
       "<path class=\"atom-31\" d=\"M 453.2 85.4 L 455.7 85.4 L 455.7 93.3 L 465.1 93.3 L 465.1 85.4 L 467.6 85.4 L 467.6 103.9 L 465.1 103.9 L 465.1 95.4 L 455.7 95.4 L 455.7 103.9 L 453.2 103.9 L 453.2 85.4 \" fill=\"#000000\"/>\n",
       "<path class=\"atom-32\" d=\"M 462.8 146.0 L 465.3 146.0 L 465.3 153.8 L 474.8 153.8 L 474.8 146.0 L 477.3 146.0 L 477.3 164.5 L 474.8 164.5 L 474.8 155.9 L 465.3 155.9 L 465.3 164.5 L 462.8 164.5 L 462.8 146.0 \" fill=\"#000000\"/>\n",
       "</svg>"
      ],
      "text/plain": [
       "<IPython.core.display.SVG object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "ala_ser = Molecule.from_smiles('CC(=O)N[C@@H](C)C(=O)N[C@@H](CO)C(=O)NC')\n",
    "ala_ser"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "id": "kZA8qZV7gwo9"
   },
   "outputs": [],
   "source": [
    "ala_ser.generate_conformers()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "ED0efjzmR-zW",
    "outputId": "369fbf10-af60-48d5-e4ee-b249a030cc3e"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{}"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# The atoms of this molecule initially have no metadata\n",
    "ala_ser.atoms[0].metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "dLbXUk3QTIWe",
    "outputId": "b13a2663-9af1-48fc-d2fa-803b318e6905"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'residue_name': 'ACE', 'residue_number': 1, 'atom_name': 'CH3'}"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# But we can add standard protein residue metadata using the perceive_residues method\n",
    "ala_ser.perceive_residues()\n",
    "ala_ser.atoms[0].metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "R48ZsItsTPAH",
    "outputId": "73b5f154-6c4b-460f-f934-9e0715cc95f0"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[HierarchyElement ('None', 1, 'ACE') of iterator 'residues' containing 6 atom(s),\n",
       " HierarchyElement ('None', 2, 'ALA') of iterator 'residues' containing 10 atom(s),\n",
       " HierarchyElement ('None', 3, 'SER') of iterator 'residues' containing 11 atom(s),\n",
       " HierarchyElement ('None', 4, 'NME') of iterator 'residues' containing 6 atom(s)]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ala_ser.residues"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "6yS4BapCTkee"
   },
   "source": [
    "# Iterators like `topology.topology_molecules` and `topology.topology_atoms` are being deprecated\n",
    "\n",
    "The difference between `Topology.reference_molecules` and `Topology.topology_molecules` managed to confuse everyone, and would have added a lot of complexity by keeping them around in this refactor. While the code still takes advantage of knowing which molecules are identical to each other, it now does so outside the public API. \n",
    "\n",
    "Since we didn't give a lot of warning for this, the old code paths will still exist for a few months, but you'll get these annoying deprecation warnings. To reach the new recommended API points, just take out the `topology_` part of the method name. So for example, `topology.topology_atoms` should now be accessed as `topology.atoms`. The objects that are returned are no longer weird views of atoms (`TopologyAtoms`), instead they're just the same atoms as you'd get from calling `Molecule.atoms`. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "pVsPUNtLTSiQ",
    "outputId": "8e80f371-ca67-4d08-8b56-adfa1ae651e7"
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/jeffreywagner/conda/envs/offtk-0-11-0-rc/lib/python3.9/site-packages/openff/toolkit/topology/topology.py:51: TopologyDeprecationWarning: Topology.topology_atoms is deprecated. Use Topology.atoms instead.\n",
      "  warnings.warn(\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "2667"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "top = Topology.from_molecules([protein, ala_ser])\n",
    "# This will emit a deprecation warning\n",
    "len([*top.topology_atoms])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "oLGpLhr2VgJT",
    "outputId": "cc26da2e-bb7c-4f27-978e-cf0b1b129a93"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2667"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# This will give the same result with no deprecation warning\n",
    "len([*top.atoms])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "7ldyVVBrURoE",
    "outputId": "010efca5-a648-4de5-949a-326582415a45"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[2634, 33]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# The molecules returned by Topology.molecules are now just full copies of the input molecules.\n",
    "[mol.n_atoms for mol in top.molecules]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "ioiDXIPocXLu",
    "outputId": "5a8bbca3-fd7e-4680-804f-6607f4bdc7b6"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[164, 4]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# You can still access hierarchy iterators on the underlying molecules\n",
    "[len(mol.residues) for mol in top.molecules]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "UclsjlOhWFje",
    "outputId": "b6b4107f-6ede-4ecf-ee58-bdc919437972"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "168"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Hierarchies also expose the underlying hierarchy iterators through this crummy API.\n",
    "# This simply returns the result of calling the desired hierarchy iterator on each \n",
    "# molecule in the order that they appear in the hierarchy. \n",
    "len([*top.hierarchy_iterator('residues')])\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "759GW-yxWJnm"
   },
   "source": [
    "# Now we can make Interchange objects\n",
    "\n",
    "We finally have our first alternative to `ForceField.create_openmm_system` - It's `ForceField.create_interchange`. Interchange is very cool, we're building it to replace ParmEd in workflows and do other things good too. See [the docs](https://docs.openforcefield.org/projects/interchange/en/latest/using/intro.html) for details.\n",
    "\n",
    "We also have a protein force field that can be used for testing - It's a port of AMBER's ff14SB in SMIRNOFF format. Due to the difference between atomtype-based parameterization and the chemical perception-based parameterization, this force field is gigantic. So it takes a while (~60 seconds) to apply, and while we've tested it a reasonable amount there may still be energy-affecting bugs to shake out."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "TWzNie0_Vv3_",
    "outputId": "7afd9e8a-aaf3-41e5-9b5e-8cbf454cbd79"
   },
   "outputs": [],
   "source": [
    "from openff.toolkit import ForceField\n",
    "ff = ForceField('ff14sb_off_impropers_0.0.3.offxml')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {
    "id": "dXxgTjNHXuU2"
   },
   "outputs": [],
   "source": [
    "# Make the topology periodic\n",
    "from openff.units import unit\n",
    "top.box_vectors = [10., 10., 10.] * unit.nanometer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {
    "id": "4HXMuaJ8X_r3"
   },
   "outputs": [],
   "source": [
    "interchange = ff.create_interchange(top)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "S98SVBCsYYF7",
    "outputId": "0d7f46e4-5bae-449c-c788-4610f09f9766"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Interchange with 6 potential handlers, periodic topology with 2667 atoms."
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "interchange"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "0XpTTQJehuxz",
    "outputId": "7e1a1d9a-a5a1-4a8d-a10e-59d726cd6815"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Potential(parameters={'k': <Quantity(868.0, 'kilocalorie / angstrom ** 2 / mole')>, 'length': <Quantity(1.01, 'angstrom')>}, map_key=None)"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Interchange contains the underlying parameters\n",
    "[*interchange['Bonds'].potentials.values()][0]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "Qw22uF-Wf4Gr",
    "outputId": "cea011fd-c75e-4725-f4e4-682a8bd7d3e6"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[[3.3429999999999995 1.128 4.449000000000001] [3.2859999999999996 1.187 4.509] [3.2969999999999997 1.038 4.443999999999999] ... [-0.460730402913539 -0.22444411880710183 0.01874313443855259] [-0.5825801296383424 -0.1305705161684031 0.10692123816470528] [-0.5482891464956796 -0.0988002309477765 -0.07205858865949857]] nanometer\n"
     ]
    }
   ],
   "source": [
    "# Because both input molecules had positions (T4 was loaded from PDB and ala_ser \n",
    "# had conformer generation run), the resulting Interchange object has positions.\n",
    "print(interchange.positions)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "9XGZw35oYyqK",
    "outputId": "d12d3b0a-8deb-4e3e-96ca-b405fab70307"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x1731a1570> >,\n",
       " <Topology; 2 chains, 172 residues, 2667 atoms, 2686 bonds>)"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# The Interchange can export to an OpenMM system, which is pretty much the \n",
    "# same as you'd get by using ForceField.create_openmm_system. It also contains\n",
    "# an OpenFF Topology object (a copy of the one that made it) that can be turned\n",
    "# into an OpenMM Topology\n",
    "(interchange.to_openmm(), interchange.topology.to_openmm())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {
    "id": "3pA-8EtoKJRn"
   },
   "outputs": [],
   "source": [
    "# As a little taste of what's to come, it can also export to prmtop and inpcrd.\n",
    "# This is better validated for small molecules than for proteins, there's more \n",
    "# development to come here\n",
    "interchange.to_prmtop('proteins.prmtop')\n",
    "interchange.to_inpcrd('proteins.inpcrd')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "hqQxl12-CS5u",
    "outputId": "d213a437-3cc0-4e3d-95c7-d9bac0d3009a"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "%VERSION  VERSION_STAMP = V0001.000  DATE = 07/07/22  13:23:29\r\n",
      "%FLAG TITLE\r\n",
      "%FORMAT(20a4)\r\n",
      "\r\n",
      "%FLAG POINTERS\r\n",
      "%FORMAT(10I8)\r\n",
      "    2667     293    1345    1341    3039    1805    6743    6142       0       0\r\n",
      "   14634     168    1341    1805    6142     276     448     924       1       0\r\n",
      "       0       0       0       0       0       0       0       1    2667       0\r\n",
      "       0       0\r\n"
     ]
    }
   ],
   "source": [
    "!head proteins.prmtop"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {
    "colab": {
     "base_uri": "https://localhost:8080/"
    },
    "id": "Cos00kdOC6NJ",
    "outputId": "13645f28-5ac9-40b2-9984-8e6c33192f04"
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\r\n",
      " 2667  0.0000000e+00\r\n",
      "  33.4300000  11.2800000  44.4900000  32.8600000  11.8700000  45.0900000\r\n",
      "  32.9700000  10.3800000  44.4400000  34.2700000  11.2800000  45.0500000\r\n",
      "  33.5500000  11.9700000  43.2000000  34.0900000  12.8900000  43.4100000\r\n",
      "  34.5500000  11.3900000  42.2700000  35.4700000  11.3300000  42.8500000\r\n",
      "  34.3200000  10.3700000  41.9600000  34.7300000  12.3200000  41.0200000\r\n",
      "  35.4300000  11.8400000  40.3400000  33.7200000  12.3500000  40.6200000\r\n",
      "  35.2700000  14.0500000  41.3000000  37.0500000  13.8000000  41.7600000\r\n",
      "  37.1700000  13.6500000  42.8300000  37.5000000  12.9900000  41.1900000\r\n"
     ]
    }
   ],
   "source": [
    "!head proteins.inpcrd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "id": "XkffoOC5C8jL"
   },
   "outputs": [],
   "source": []
  }
 ],
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   "include_colab_link": true,
   "name": "biopolymer_alpha_notebook.ipynb",
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  "kernelspec": {
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environment.yml

name: test
channels:
  - jaimergp/label/unsupported-cudatoolkit-shim
  - conda-forge

dependencies:
    # Base depends
  - python
  - pip

    # Testing
  - pytest
  - pytest-cov
  - pytest-xdist
  - pytest-rerunfailures
  - nbval
  - codecov
  - coverage
  - numpy
  - networkx
  - ambertools
  - rdkit
  - packaging
    # Removed until a compatible release is made
# - openmmforcefields
  - openmm >=7.6
  - openff-toolkit
  - nglview
  - notebook
  - openff-amber-ff-ports
  - openff-forcefields
  - openff-units >=0.1.6
  - openff-utilities
  - smirnoff99Frosst
  - cachetools
  - cached-property
  - pyyaml
  - toml
  - bson
  - msgpack-python
  - xmltodict
  - python-constraint
  - qcelemental
  - qcportal >=0.15
  - qcengine
  - mdtraj
  - distributed