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()