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import gradio as gr
import sys
import random
sys.path.append("scripts/")
from foldseek_util import get_struc_seq
# Assuming 'predict_stability' is your function that predicts protein stability
def predict_stability(model_choice, organism_choice, pdb_file=None, sequence=None):
# Dummy return for illustration; replace with your actual prediction logic
return f"Predicted Stability using {model_choice} for {organism_choice}: Example Output"
def get_foldseek_seq(pdb_path):
pdb_path = pdb_path.name
parsed_seqs = get_struc_seq(
"bin/foldseek",
pdb_path,
["A"],
process_id=random.randint(0, 10000000),
)["A"]
return parsed_seqs
# Gradio Interface
with gr.Blocks() as demo:
gr.Markdown(
"""
# PLTNUM: Protein LifeTime Neural Model
**Predict the protein half-life from its sequence or PDB file.**
"""
)
gr.Image("https://github.com/sagawatatsuya/PLTNUM/blob/main/model-image.png?raw=true", label="Model Image")
# Model and Organism selection in the same row to avoid layout issues
with gr.Row():
model_choice = gr.Radio(
choices=["SaProt", "ESM-2"],
label="Select PLTNUM's base model.",
value="SaProt"
)
organism_choice = gr.Radio(
choices=["Mouse", "Human"],
label="Select the target organism.",
value="Mouse"
)
with gr.Tabs():
with gr.TabItem("Upload PDB File"):
gr.Markdown("### Upload your PDB file:")
pdb_file = gr.File(label="Upload PDB File")
output = get_foldseek_seq(pdb_file)
predict_button = gr.Button("Predict Stability")
prediction_output = gr.Textbox(label=str(output), interactive=False)
predict_button.click(fn=predict_stability, inputs=[model_choice, organism_choice, pdb_file], outputs=prediction_output)
with gr.TabItem("Enter Protein Sequence"):
gr.Markdown("### Enter the protein sequence:")
sequence = gr.Textbox(
label="Protein Sequence",
placeholder="Enter your protein sequence here...",
lines=8,
)
predict_button = gr.Button("Predict Stability")
prediction_output = gr.Textbox(label="Stability Prediction", interactive=False)
predict_button.click(fn=predict_stability, inputs=[model_choice, organism_choice, sequence], outputs=prediction_output)
gr.Markdown(
"""
### How to Use:
- **Select Model**: Choose between 'SaProt' or 'ESM-2' for your prediction.
- **Select Organism**: Choose between 'Mouse' or 'Human'.
- **Upload PDB File**: Choose the 'Upload PDB File' tab and upload your file.
- **Enter Sequence**: Alternatively, switch to the 'Enter Protein Sequence' tab and input your sequence.
- **Predict**: Click 'Predict Stability' to receive the prediction.
"""
)
gr.Markdown(
"""
### About the Tool
This tool allows researchers and scientists to predict the stability of proteins using advanced algorithms. It supports both PDB file uploads and direct sequence input.
"""
)
demo.launch()
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