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import datetime
from typing import Tuple, Optional
import gradio as gr
import mol_viewer
import run_utils
def run_wrapper(protein_file, ligand_file, other_args_file, *args, **kwargs) -> Tuple[str, Optional[str], str]:
if protein_file is None:
return "Protein file is missing! Must provide a protein file in PDB format", None, ""
if ligand_file is None:
return "Ligand file is missing! Must provide a ligand file in SDF format", None, ""
if other_args_file is not None:
kwargs["other_arg_file"] = other_args_file.name
output_file, pdb_text, sdf_text = run_utils.run_cli_command(
protein_file.name, ligand_file.name, *args, **kwargs
)
output_viz = "No visualisation created"
if pdb_text:
output_viz = mol_viewer.gen_3dmol_vis(pdb_text, sdf_text)
message = f"Calculation completed at {datetime.datetime.now()}"
return message, output_file, output_viz
def run():
with gr.Blocks(title="DiffDock-Pocket Web") as demo:
gr.Markdown("# DiffDock-Pocket")
gr.Markdown("""Run [DiffDock-Pocket](https://github.com/plainerman/DiffDock-Pocket) for a single protein and ligand.
We have provided the most important inputs as UI elements. """)
with gr.Row():
protein_pdb = gr.File(label="Protein PDB (required)", file_types=[".pdb"])
ligand_sdf = gr.File(label="Ligand SDF (required)", file_types=[".sdf"])
with gr.Row():
samples_per_complex = gr.Number(label="Samples Per Complex", value=1, minimum=1, maximum=100, precision=0)
with gr.Column():
keep_local_structures = gr.Checkbox(label="Keep Local Structures", value=True)
save_vis = gr.Checkbox(label="Save Visualisation", value=True)
with gr.Row():
gr.Markdown("""Additional values can be included in "Other arguments", and will be passed
to [inference.py](https://github.com/plainerman/DiffDock-Pocket/blob/main/inference.py).
Must be a YAML file without any nesting. """)
other_args = gr.File(label="Other arguments (Optional, YML)", file_types=[".yml", ".yaml"], value=None)
with gr.Row():
run_btn = gr.Button("Run DiffDock-Pocket")
with gr.Row():
message = gr.Text(label="Run message", interactive=False)
with gr.Row():
output_file = gr.File(label="Output Files")
with gr.Row():
init_value = "Rank1 Reverse Processed Protein will be visualised here"
viewer = gr.HTML(value=init_value, label="Protein Viewer", show_label=True)
_inputs = [protein_pdb, ligand_sdf, other_args, samples_per_complex, keep_local_structures, save_vis]
_outputs = [message, output_file, viewer]
run_btn.click(fn=run_wrapper, inputs=_inputs, outputs=_outputs)
demo.launch(server_name="0.0.0.0", server_port=7860, share=False)
if __name__ == "__main__":
run_utils.set_env_variables()
run_utils.configure_logging()
run()
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