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Merged
atravitz merged 1 commit into from
May 5, 2025
Merged

adding colab installs to some notebooks #205

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51 changes: 51 additions & 0 deletions abfe_tutorial/python_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,57 @@
"## <img src=\"abfe-cycle.png\" alt=\"Drawing\" style=\"width: 400px;\"/>"
]
},
{
"cell_type": "markdown",
"id": "f9154ba7",
"metadata": {},
"source": [
"# 0. Setup for Google Colab\n",
"\n",
"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`"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6173dd67",
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" !pip install -q condacolab\n",
" import condacolab\n",
" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "2e888557",
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" import condacolab\n",
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
" condacolab.check()\n",
" except:\n",
" pass\n",
" else:\n",
" break"
]
},
{
"cell_type": "code",
"execution_count": 1,
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51 changes: 51 additions & 0 deletions ahfe_tutorial/python_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,57 @@
"## <img src=\"ahfe_cycle.png\" alt=\"Drawing\" style=\"width: 300px;\"/>"
]
},
{
"cell_type": "markdown",
"id": "e26c8170",
"metadata": {},
"source": [
"# 0. Setup for Google Colab\n",
"\n",
"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`"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "525ac910",
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" !pip install -q condacolab\n",
" import condacolab\n",
" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "808ba76a",
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" import condacolab\n",
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
" condacolab.check()\n",
" except:\n",
" pass\n",
" else:\n",
" break"
]
},
{
"cell_type": "code",
"execution_count": 1,
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51 changes: 51 additions & 0 deletions openmm_md/plain_md.ipynb
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Expand Up @@ -64,6 +64,57 @@
"| 7. NPT production (if not gas phase) | OpenFE - OpenMM + OpenMMTools | Simulation trajectory (`simulation.xtc`), Checkpoint file (`checkpoint.chk`), Log output (`simulation.log`) |\n"
]
},
{
"cell_type": "markdown",
"id": "fc27c86c",
"metadata": {},
"source": [
"# 0. Setup for Google Colab\n",
"\n",
"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`"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6559bc05",
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" !pip install -q condacolab\n",
" import condacolab\n",
" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "eb1368ca",
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" import condacolab\n",
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
" condacolab.check()\n",
" except:\n",
" pass\n",
" else:\n",
" break"
]
},
{
"cell_type": "markdown",
"id": "0eb8203a-650f-4703-b032-dbafb605061b",
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51 changes: 51 additions & 0 deletions plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,57 @@
"This notebook shows how one would go about creating a cinnabar plot of OpenFE results against known experimental values."
]
},
{
"cell_type": "markdown",
"id": "6f3d03c2",
"metadata": {},
"source": [
"# 0. Setup for Google Colab\n",
"\n",
"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`"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "04aa17bf",
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" !pip install -q condacolab\n",
" import condacolab\n",
" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6d297968",
"metadata": {},
"outputs": [],
"source": [
"# NBVAL_SKIP\n",
"# Only run this cell if on google colab\n",
"import os\n",
"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
" import condacolab\n",
" import locale\n",
" locale.getpreferredencoding = lambda: \"UTF-8\"\n",
" !mkdir inputs && cd inputs && openfe fetch rbfe-tutorial\n",
" for _ in range(3):\n",
" # Sometimes we have to re-run the check\n",
" try:\n",
" condacolab.check()\n",
" except:\n",
" pass\n",
" else:\n",
" break"
]
},
{
"cell_type": "code",
"execution_count": 1,
Expand Down
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