Merge pull request #320 from vaclavhanzl/fix-colab-conda-all-together

Fix Colab: Install all conda packages together
aqlaboratory · May 18, 2023 · 103d037 · 103d037
2 parents 1f9270c + 410e829
commit 103d037
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/notebooks/OpenFold.ipynb b/notebooks/OpenFold.ipynb
@@ -129,6 +129,8 @@
         "      kalign2=2.04 \\\n",
         "      hhsuite=3.3.0 \\\n",
         "      python={python_version} \\\n",
+        "      openmm=7.7.0 \\\n",
+        "      pdbfixer \\\n",
         "      2>&1 1>/dev/null\n",
         "    %shell pip install -q \\\n",
         "      ml-collections==0.1.0 \\\n",
@@ -185,9 +187,6 @@
         "    %shell cp -f /content/stereo_chemical_props.txt /content/openfold/openfold/resources\n",
         "    %shell /usr/bin/python3 -m pip install -q ./openfold\n",
         "\n",
-        "    %shell conda install -y -q -c conda-forge openmm=7.7.0\n",
-        "    %shell conda install -y -q -c conda-forge pdbfixer\n",
-        "\n",
         "    if(weight_set == 'AlphaFold'):\n",
         "      %shell mkdir --parents \"{ALPHAFOLD_PARAMS_DIR}\"\n",
         "      %shell wget -O {ALPHAFOLD_PARAMS_PATH} {ALPHAFOLD_PARAM_SOURCE_URL}\n",