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adding colab installs to some notebooks (#205)
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‎abfe_tutorial/python_tutorial.ipynb

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@@ -22,6 +22,57 @@
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"## <img src=\"abfe-cycle.png\" alt=\"Drawing\" style=\"width: 400px;\"/>"
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]
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},
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{
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"cell_type": "markdown",
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"id": "f9154ba7",
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"metadata": {},
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"source": [
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"# 0. Setup for Google Colab\n",
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"\n",
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"If you are running this example in Google Colab, run the following cells to setup the environment. If you are running this notebook locally, skip down to `1. Overview`"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "6173dd67",
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"metadata": {},
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"outputs": [],
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"source": [
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"# NBVAL_SKIP\n",
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "2e888557",
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"metadata": {},
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"outputs": [],
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"source": [
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"# NBVAL_SKIP\n",
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" import condacolab\n",
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" import locale\n",
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" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
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" for _ in range(3):\n",
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" # Sometimes we have to re-run the check\n",
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" try:\n",
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" condacolab.check()\n",
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" except:\n",
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" pass\n",
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" else:\n",
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" break"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,

‎ahfe_tutorial/python_tutorial.ipynb

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@@ -22,6 +22,57 @@
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"## <img src=\"ahfe_cycle.png\" alt=\"Drawing\" style=\"width: 300px;\"/>"
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]
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},
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{
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"cell_type": "markdown",
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"id": "e26c8170",
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"metadata": {},
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"source": [
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"# 0. Setup for Google Colab\n",
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"\n",
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"If you are running this example in Google Colab, run the following cells to setup the environment. If you are running this notebook locally, skip down to `1. Overview`"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "525ac910",
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"metadata": {},
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"outputs": [],
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"source": [
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"# NBVAL_SKIP\n",
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "808ba76a",
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"metadata": {},
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"outputs": [],
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"source": [
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"# NBVAL_SKIP\n",
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" import condacolab\n",
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" import locale\n",
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" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
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" for _ in range(3):\n",
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" # Sometimes we have to re-run the check\n",
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" try:\n",
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" condacolab.check()\n",
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" except:\n",
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" pass\n",
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" else:\n",
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" break"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,

‎openmm_md/plain_md.ipynb

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@@ -64,6 +64,57 @@
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"| 7. NPT production (if not gas phase) | OpenFE - OpenMM + OpenMMTools | Simulation trajectory (`simulation.xtc`), Checkpoint file (`checkpoint.chk`), Log output (`simulation.log`) |\n"
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]
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},
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{
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"cell_type": "markdown",
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"id": "fc27c86c",
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"metadata": {},
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"source": [
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"# 0. Setup for Google Colab\n",
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"\n",
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"If you are running this example in Google Colab, run the following cells to setup the environment. If you are running this notebook locally, skip down to `1. Overview`"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "6559bc05",
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"metadata": {},
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"outputs": [],
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"source": [
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"# NBVAL_SKIP\n",
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "eb1368ca",
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"metadata": {},
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"outputs": [],
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"source": [
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"# NBVAL_SKIP\n",
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" import condacolab\n",
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" import locale\n",
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" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
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" for _ in range(3):\n",
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" # Sometimes we have to re-run the check\n",
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" try:\n",
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" condacolab.check()\n",
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" except:\n",
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" pass\n",
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" else:\n",
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" break"
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]
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},
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{
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"cell_type": "markdown",
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"id": "0eb8203a-650f-4703-b032-dbafb605061b",

‎plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb

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@@ -10,6 +10,57 @@
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"This notebook shows how one would go about creating a cinnabar plot of OpenFE results against known experimental values."
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]
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},
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{
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"cell_type": "markdown",
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"id": "6f3d03c2",
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"metadata": {},
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"source": [
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"# 0. Setup for Google Colab\n",
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"\n",
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"If you are running this example in Google Colab, run the following cells to setup the environment. If you are running this notebook locally, skip down to `1. Overview`"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "04aa17bf",
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"metadata": {},
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"outputs": [],
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"source": [
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"# NBVAL_SKIP\n",
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "6d297968",
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"metadata": {},
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"outputs": [],
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"source": [
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"# NBVAL_SKIP\n",
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"# Only run this cell if on google colab\n",
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"import os\n",
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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" import condacolab\n",
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" import locale\n",
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" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
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" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
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" for _ in range(3):\n",
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" # Sometimes we have to re-run the check\n",
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" try:\n",
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" condacolab.check()\n",
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" except:\n",
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" pass\n",
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" else:\n",
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" break"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 1,

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