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GuoJeffGuoJeff
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2 parents 616e383 + a672ffe commit 4183c8a

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5 files changed

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‎notebooks/demo_AutoDock_Vina.ipynb

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@@ -414,17 +414,16 @@
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" \"component_type\": \"dockstream\",\n",
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" \"name\": \"dockstream\",\n",
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" \"weight\": 1,\n",
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" \"model_path\": \"\",\n",
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" \"smiles\": [],\n",
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" \"specific_parameters\": {\n",
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" \"transformation\": true,\n",
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" \"transformation_type\": \"reverse_sigmoid\",\n",
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" \"low\": -12,\n",
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" \"high\": -8,\n",
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" \"k\": 0.25,\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/miniconda3/envs/DockStream/bin/python\"\n",
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" \"transformation\": {\n",
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" \"transformation_type\": \"reverse_sigmoid\",\n",
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" \"low\": -12,\n",
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" \"high\": -8,\n",
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" \"k\": 0.25\n",
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" },\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/envs/DockStream/bin/python\"\n",
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" }\n",
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"}\n",
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"```\n",
@@ -541,7 +540,7 @@
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.3"
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"version": "3.9.6"
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}
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},
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"nbformat": 4,

‎notebooks/demo_Glide.ipynb

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@@ -388,18 +388,16 @@
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" \"component_type\": \"dockstream\",\n",
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" \"name\": \"dockstream\",\n",
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" \"weight\": 1,\n",
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" \"model_path\": \"\",\n",
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" \"smiles\": [],\n",
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" \"specific_parameters\": {\n",
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" \"debug\": false,\n",
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" \"transformation\": true,\n",
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" \"transformation_type\": \"reverse_sigmoid\",\n",
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" \"low\": -20,\n",
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" \"high\": -5,\n",
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" \"k\": 0.2,\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/miniconda3/envs/DockStream/bin/python\"\n",
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" \"transformation\": {\n",
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" \"transformation_type\": \"reverse_sigmoid\",\n",
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" \"low\": -20,\n",
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" \"high\": -5,\n",
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" \"k\": 0.2\n",
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" },\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/envs/DockStream/bin/python\"\n",
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" }\n",
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"}\n",
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"```\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.11"
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"version": "3.9.6"
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}
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},
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"nbformat": 4,

‎notebooks/demo_Gold.ipynb

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" \"component_type\": \"dockstream\",\n",
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" \"name\": \"dockstream\",\n",
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" \"weight\": 1,\n",
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" \"model_path\": \"\",\n",
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" \"smiles\": [],\n",
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" \"specific_parameters\": {\n",
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" \"transformation\": true,\n",
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" \"transformation_type\": \"sigmoid\",\n",
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" \"low\": 60,\n",
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" \"high\": 100,\n",
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" \"k\": 0.25,\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/miniconda3/envs/DockStream/bin/python\"\n",
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" \"transformation\": {\n",
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" \"transformation_type\": \"sigmoid\",\n",
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" \"low\": 60,\n",
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" \"high\": 100,\n",
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" \"k\": 0.25\n",
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" },\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/envs/DockStream/bin/python\"\n",
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" }\n",
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"}\n",
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"```\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.3"
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"version": "3.9.6"
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}
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},
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"nbformat": 4,

‎notebooks/demo_Hybrid.ipynb

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]
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},
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{
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"attachments": {},
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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" \"component_type\": \"dockstream\",\n",
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" \"name\": \"dockstream\",\n",
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" \"weight\": 1,\n",
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" \"model_path\": \"\",\n",
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" \"smiles\": [],\n",
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" \"specific_parameters\": {\n",
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" \"transformation\": true,\n",
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" \"transformation_type\": \"reverse_sigmoid\",\n",
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" \"low\": -16,\n",
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" \"high\": -8,\n",
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" \"k\": 0.25,\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/miniconda3/envs/DockStream/bin/python\"\n",
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" \"transformation\": {\n",
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" \"transformation_type\": \"reverse_sigmoid\",\n",
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" \"low\": -16,\n",
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" \"high\": -8,\n",
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" \"k\": 0.25\n",
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" },\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/envs/DockStream/bin/python\"\n",
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" }\n",
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"}\n",
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"```\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.3"
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"version": "3.9.6"
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}
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},
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"nbformat": 4,

‎notebooks/demo_rDock.ipynb

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" \"component_type\": \"dockstream\",\n",
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" \"name\": \"dockstream\",\n",
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" \"weight\": 1,\n",
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" \"model_path\": \"\",\n",
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" \"smiles\": [],\n",
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" \"specific_parameters\": {\n",
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" \"transformation\": true,\n",
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" \"transformation_type\": \"reverse_sigmoid\",\n",
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" \"low\": -50,\n",
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" \"high\": -25,\n",
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" \"k\": 0.25,\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/miniconda3/envs/DockStream/bin/python\"\n",
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" \"transformation\": {\n",
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" \"transformation_type\": \"reverse_sigmoid\",\n",
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" \"low\": -50,\n",
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" \"high\": -25,\n",
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" \"k\": 0.25\n",
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" },\n",
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" \"configuration_path\": \"<absolute_path_to_DockStream_configuration>/docking.json\",\n",
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" \"docker_script_path\": \"<absolute_path_to_DockStream_source>/docker.py\",\n",
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" \"environment_path\": \"<absolute_path_to_miniconda_installation>/envs/DockStream/bin/python\"\n",
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" }\n",
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"}\n",
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"```\n",
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.8.3"
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"version": "3.9.6"
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}
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},
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"nbformat": 4,

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