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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "6a7a5d41-e6d7-4efa-a481-3182963ca888",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Collecting gradio_client\n",
" Downloading gradio_client-1.3.0-py3-none-any.whl.metadata (7.1 kB)\n",
"Requirement already satisfied: fsspec in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from gradio_client) (2024.6.1)\n",
"Requirement already satisfied: httpx>=0.24.1 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from gradio_client) (0.27.0)\n",
"Collecting huggingface-hub>=0.19.3 (from gradio_client)\n",
" Downloading huggingface_hub-0.24.7-py3-none-any.whl.metadata (13 kB)\n",
"Requirement already satisfied: packaging in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from gradio_client) (24.1)\n",
"Requirement already satisfied: typing-extensions~=4.0 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from gradio_client) (4.12.2)\n",
"Requirement already satisfied: websockets<13.0,>=10.0 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from gradio_client) (12.0)\n",
"Requirement already satisfied: anyio in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from httpx>=0.24.1->gradio_client) (4.4.0)\n",
"Requirement already satisfied: certifi in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from httpx>=0.24.1->gradio_client) (2024.7.4)\n",
"Requirement already satisfied: httpcore==1.* in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from httpx>=0.24.1->gradio_client) (1.0.5)\n",
"Requirement already satisfied: idna in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from httpx>=0.24.1->gradio_client) (3.7)\n",
"Requirement already satisfied: sniffio in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from httpx>=0.24.1->gradio_client) (1.3.1)\n",
"Requirement already satisfied: h11<0.15,>=0.13 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from httpcore==1.*->httpx>=0.24.1->gradio_client) (0.14.0)\n",
"Requirement already satisfied: filelock in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from huggingface-hub>=0.19.3->gradio_client) (3.15.4)\n",
"Requirement already satisfied: pyyaml>=5.1 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from huggingface-hub>=0.19.3->gradio_client) (6.0.1)\n",
"Requirement already satisfied: requests in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from huggingface-hub>=0.19.3->gradio_client) (2.32.3)\n",
"Requirement already satisfied: tqdm>=4.42.1 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from huggingface-hub>=0.19.3->gradio_client) (4.66.5)\n",
"Requirement already satisfied: exceptiongroup>=1.0.2 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from anyio->httpx>=0.24.1->gradio_client) (1.2.2)\n",
"Requirement already satisfied: charset-normalizer<4,>=2 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from requests->huggingface-hub>=0.19.3->gradio_client) (3.3.2)\n",
"Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/danielkovtun/mamba-m1/envs/pinder/lib/python3.10/site-packages (from requests->huggingface-hub>=0.19.3->gradio_client) (2.2.2)\n",
"Downloading gradio_client-1.3.0-py3-none-any.whl (318 kB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m318.7/318.7 kB\u001b[0m \u001b[31m3.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0ma \u001b[36m0:00:01\u001b[0m\n",
"\u001b[?25hDownloading huggingface_hub-0.24.7-py3-none-any.whl (417 kB)\n",
"\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m417.5/417.5 kB\u001b[0m \u001b[31m11.2 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n",
"\u001b[?25hInstalling collected packages: huggingface-hub, gradio_client\n",
"Successfully installed gradio_client-1.3.0 huggingface-hub-0.24.7\n"
]
}
],
"source": [
"!pip install gradio_client"
]
},
{
"cell_type": "markdown",
"id": "549b9b2c-3074-446b-962e-90c8efd2bd59",
"metadata": {},
"source": [
"# PINDER inference and evaluation template API examples"
]
},
{
"cell_type": "markdown",
"id": "b979671e-97d6-4c52-bc6e-279a09d722c8",
"metadata": {},
"source": [
"## Run inference via predict endpoint"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "2c0171fa-ee2a-40b7-8578-aa8516b4ece9",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Loaded as API: https://danielkovtun-pinder-inference-template.hf.space/ ✔\n",
"/private/var/folders/tt/x223wxwj6dzg3vjjgc_6y5bm0000gn/T/gradio/0cda59c2805986a9e5956ed00cb552b3c86f05915da91e6e14a0a31b962e664b/3g9w_R--3g9w_L.pdb 1.2273471355438232\n"
]
}
],
"source": [
"from gradio_client import Client, handle_file\n",
"from pathlib import Path\n",
"\n",
"uri = \"https://danielkovtun-pinder-inference-template.hf.space/\"\n",
"# If running docker container locally\n",
"dev_uri = \"http://localhost:7860/\"\n",
"client = Client(uri)\n",
"result = client.predict(\n",
" receptor_pdb=handle_file(\"./3g9w_R.pdb\"),\n",
" ligand_pdb=handle_file(\"./3g9w_L.pdb\"),\n",
" receptor_fasta=None, # optional in this implementation\n",
" ligand_fasta=None,\n",
" api_name=\"/predict\"\n",
")\n",
"output_pdb, runtime = Path(result[0]), result[1]\n",
"print(output_pdb, runtime)\n"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "c530fde1-7f57-4991-a53e-b3855657f9fc",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(PosixPath('pinder-inference-outputs/3g9w_R--3g9w_L.pdb'), True)"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import shutil\n",
"\n",
"local_dir = Path(\"./pinder-inference-outputs\")\n",
"local_dir.mkdir(exist_ok=True, parents=True)\n",
"\n",
"output_pdb = Path(shutil.copy(output_pdb, local_dir))\n",
"output_pdb, output_pdb.is_file() \n",
"\n"
]
},
{
"cell_type": "markdown",
"id": "b3c1c03e-74c1-4010-b385-e4366d43cd6f",
"metadata": {},
"source": [
"## Fetch evaluation metrics via evaluate endpoint"
]
},
{
"cell_type": "code",
"execution_count": 13,
"id": "e5e26250-f20d-484d-84e2-320cdfef830a",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Loaded as API: http://localhost:7860/ ✔\n"
]
},
{
"data": {
"text/plain": [
"{'headers': ['system', 'L_rms', 'I_rms', 'F_nat', 'DOCKQ', 'CAPRI_class'],\n",
" 'data': [['3g9w__A1_Q71LX4--3g9w__D1_P05556',\n",
" 34.781349182128906,\n",
" 15.405366897583008,\n",
" 0.0,\n",
" 0.021916405918697517,\n",
" 'Incorrect']],\n",
" 'metadata': None}"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"client = Client(uri)\n",
"result = client.predict(\n",
" system_id=\"3g9w__A1_Q71LX4--3g9w__D1_P05556\",\n",
" prediction_pdb=handle_file(\"3g9w_R--3g9w_L.pdb\"),\n",
" api_name=\"/evaluate\"\n",
")\n",
"metrics, pred_native, runtime = result\n",
"metrics"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "eef0d108-5d76-4bef-bd0c-4952d433ccaf",
"metadata": {},
"outputs": [
{
"data": {
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"<table border=\"1\" class=\"dataframe\">\n",
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" <th></th>\n",
" <th>system</th>\n",
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" <th>I_rms</th>\n",
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"text/plain": [
" system L_rms I_rms F_nat DOCKQ \\\n",
"0 3g9w__A1_Q71LX4--3g9w__D1_P05556 34.781349 15.405367 0.0 0.021916 \n",
"\n",
" CAPRI_class \n",
"0 Incorrect "
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import pandas as pd\n",
"\n",
"metric_df = pd.DataFrame(metrics[\"data\"], columns=metrics[\"headers\"])\n",
"metric_df"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "pinder",
"language": "python",
"name": "pinder"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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