notebooks/model_notebooks/OpenFold.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "pc5-mbsX9PZC"
   },
   "source": [
    "# OpenFold"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from prtm import protein\n",
    "from prtm import visual\n",
    "from prtm.query import caching\n",
    "from prtm.models.openfold import config\n",
    "from prtm.models.openfold.modeling import OpenFoldForFolding\n",
    "from prtm.models.openfold.np.relax import relax"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "caching.set_db_path(\"../cached_queries_for_testing.db\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "sequence = 'MAAHKGAEHHHKAAEHHEQAAKHHHAAAEHHEKGEHEQAAHHADTAYAHHKHAEEHAAQAAKHDAEHHAPKPH'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "folder = OpenFoldForFolding(model_name=\"finetuning_no_templ_ptm-1\", random_seed=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "predicted_protein, aux_output = folder(sequence)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "amber_relaxer = relax.AmberRelaxation(\n",
    "    max_iterations=0,\n",
    "    tolerance=2.39,\n",
    "    stiffness=10.0,\n",
    "    exclude_residues=[],\n",
    "    max_outer_iterations=20,\n",
    "    use_gpu=False,\n",
    ")\n",
    "relaxed_pdb, _, _ = amber_relaxer.process(\n",
    "    prot=predicted_protein, cif_output=False\n",
    ")\n",
    "relaxed_prediction = protein.Protein37.from_pdb_string(relaxed_pdb)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "relaxed_prediction.show()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "visual.view_superimposed_structures(predicted_protein, relaxed_prediction)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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   "name": "OpenFold.ipynb",
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