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Fix notebook: Colab now has python 3.8, fix imports, mitigate UTF-8 glitch #285

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merged 4 commits into from Apr 10, 2023
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Fix notebook: Colab now has python 3.8, fix imports, mitigate UTF-8 glitch #285

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9c38e95
Fix notebook: Colab now has python 3.8, fix imports, mitigate UTF-8 g…
vaclavhanzl Mar 5, 2023
c84fd44
Fix notebook: Better mitigation of the ANSI_X3.4-1968 problem in Colab
vaclavhanzl Mar 6, 2023
007ab6f
Fix notebook: Also save the protein to zip when relaxation is off
vaclavhanzl Mar 6, 2023
1fafb86
Improve notebook: Make install/import independent of relax_prediction
vaclavhanzl Mar 6, 2023
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50 changes: 27 additions & 23 deletions notebooks/OpenFold.ipynb
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Expand Up @@ -121,10 +121,11 @@
" %env PATH=/opt/conda/bin:{PATH}\n",
"\n",
" # Install the required versions of all dependencies.\n",
" %shell conda install -y -q conda==4.13.0\n",
" %shell conda install -y -q -c conda-forge -c bioconda \\\n",
" kalign2=2.04 \\\n",
" hhsuite=3.3.0 \\\n",
" python=3.7 \\\n",
" python=3.8 \\\n",
" 2>&1 1>/dev/null\n",
" %shell pip install -q \\\n",
" ml-collections==0.1.0 \\\n",
Expand Down Expand Up @@ -180,15 +181,12 @@
" %shell cp -f /content/stereo_chemical_props.txt /content/openfold/openfold/resources\n",
" %shell /usr/bin/python3 -m pip install -q ./openfold\n",
"\n",
" if(relax_prediction):\n",
" %shell conda install -y -q -c conda-forge \\\n",
" openmm=7.5.1 \\\n",
" pdbfixer=1.7\n",
" \n",
" # Apply OpenMM patch.\n",
" %shell pushd /opt/conda/lib/python3.7/site-packages/ && \\\n",
" patch -p0 < /content/openfold/lib/openmm.patch && \\\n",
" popd\n",
" %shell conda install -y -q -c conda-forge openmm=7.5.1\n",
" # Apply OpenMM patch.\n",
" %shell pushd /opt/conda/lib/python3.8/site-packages/ && \\\n",
" patch -p0 < /content/openfold/lib/openmm.patch && \\\n",
" popd\n",
" %shell conda install -y -q -c conda-forge pdbfixer=1.7\n",
"\n",
" if(weight_set == 'AlphaFold'):\n",
" %shell mkdir --parents \"{ALPHAFOLD_PARAMS_DIR}\"\n",
Expand Down Expand Up @@ -222,8 +220,8 @@
"import unittest.mock\n",
"import sys\n",
"\n",
"sys.path.insert(0, '/usr/local/lib/python3.7/site-packages/')\n",
"sys.path.append('/opt/conda/lib/python3.7/site-packages')\n",
"sys.path.insert(0, '/usr/local/lib/python3.8/site-packages/')\n",
"sys.path.append('/opt/conda/lib/python3.8/site-packages')\n",
"\n",
"# Allows us to skip installing these packages\n",
"unnecessary_modules = [\n",
Expand All @@ -247,6 +245,14 @@
"import numpy as np\n",
"import py3Dmol\n",
"import torch\n",
"import shutil\n",
"\n",
"# Prevent shell magic being broken by openmm, prevent this cryptic error:\n",
"# \"NotImplementedError: A UTF-8 locale is required. Got ANSI_X3.4-1968\"\n",
"import locale\n",
"def getpreferredencoding(do_setlocale = True):\n",
" return \"UTF-8\"\n",
"locale.getpreferredencoding = getpreferredencoding\n",
"\n",
"# A filthy hack to avoid slow Linear layer initialization\n",
"import openfold.model.primitives\n",
Expand All @@ -267,9 +273,8 @@
"from openfold.data.tools import jackhmmer\n",
"from openfold.model import model\n",
"from openfold.np import protein\n",
"if(relax_prediction):\n",
" from openfold.np.relax import relax\n",
" from openfold.np.relax import utils\n",
"from openfold.np.relax import relax\n",
"from openfold.np.relax.utils import overwrite_b_factors\n",
"from openfold.utils.import_weights import import_jax_weights_\n",
"from openfold.utils.tensor_utils import tensor_tree_map\n",
"\n",
Expand Down Expand Up @@ -571,14 +576,13 @@
" relaxed_pdb, _, _ = amber_relaxer.process(\n",
" prot=unrelaxed_proteins[best_model_name]\n",
" )\n",
"\n",
" # Write out the prediction\n",
" pred_output_path = os.path.join(output_dir, 'selected_prediction.pdb')\n",
" with open(pred_output_path, 'w') as f:\n",
" f.write(relaxed_pdb)\n",
"\n",
" best_pdb = relaxed_pdb\n",
"\n",
" # Write out the prediction\n",
" pred_output_path = os.path.join(output_dir, 'selected_prediction.pdb')\n",
" with open(pred_output_path, 'w') as f:\n",
" f.write(best_pdb)\n",
"\n",
" pbar.update(n=1) # Finished AMBER relax.\n",
"\n",
"# Construct multiclass b-factors to indicate confidence bands\n",
Expand All @@ -590,7 +594,7 @@
" banded_b_factors.append(idx)\n",
" break\n",
"banded_b_factors = np.array(banded_b_factors)[:, None] * final_atom_mask\n",
"to_visualize_pdb = utils.overwrite_b_factors(best_pdb, banded_b_factors)\n",
"to_visualize_pdb = overwrite_b_factors(best_pdb, banded_b_factors)\n",
"\n",
"# --- Visualise the prediction & confidence ---\n",
"show_sidechains = True\n",
Expand Down Expand Up @@ -688,7 +692,7 @@
"\n",
"\n",
"# --- Download the predictions ---\n",
"!zip -q -r {output_dir}.zip {output_dir}\n",
"shutil.make_archive(base_name='prediction', format='zip', root_dir=output_dir)\n",
"files.download(f'{output_dir}.zip')"
],
"execution_count": null,
Expand Down