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pablo-arantes · Dec 15, 2023 · 48c484a · 48c484a
1 parent 8073a74
commit 48c484a
Showing 1 changed file with 11 additions and 10 deletions.
diff --git a/Protein_2ligands.ipynb b/Protein_2ligands.ipynb
@@ -126,18 +126,19 @@
         "#@title **Install dependencies**\n",
         "#@markdown It will take a few minutes, please, drink a coffee and wait. ;-)\n",
         "# install dependencies\n",
-        "%%capture\n",
+        "import subprocess\n",
         "import sys\n",
-        "!mamba install -c conda-forge ambertools -y\n",
+        "subprocess.run(\"rm -rf /usr/local/conda-meta/pinned\", shell=True)\n",
+        "subprocess.run(\"mamba install -c conda-forge ambertools -y\", shell=True)\n",
         "import pytraj as pt\n",
-        "!pip -q install py3Dmol\n",
-        "!pip install git+https://github.com/pablo-arantes/biopandas\n",
-        "!mamba install openmm=7.7.0\n",
-        "!mamba install openmmforcefields -c conda-forge -y\n",
-        "!pip install prolif==1.1.0\n",
-        "!mamba install -c conda-forge openbabel -y\n",
-        "!mamba install -c conda-forge parmed -y\n",
-        "!pip install --upgrade MDAnalysis==2.4.2\n",
+        "subprocess.run(\"pip -q install py3Dmol\", shell=True)\n",
+        "subprocess.run(\"pip install git+https://github.com/pablo-arantes/biopandas\", shell=True)\n",
+        "subprocess.run(\"mamba install openmm=7.7.0 pdbfixer -y\", shell=True)\n",
+        "subprocess.run(\"mamba install openmmforcefields -c conda-forge -y\", shell=True)\n",
+        "subprocess.run(\"pip install prolif==1.1.0\", shell=True)\n",
+        "subprocess.run(\"mamba install -c conda-forge openbabel -y\", shell=True)\n",
+        "subprocess.run(\"mamba install -c conda-forge parmed -y\", shell=True)\n",
+        "subprocess.run(\"pip install --upgrade MDAnalysis==2.4.2\", shell=True)\n",
         "\n",
         "#load dependencies\n",
         "from openmm import app, unit\n",