main.py

import datetime
from typing import Tuple, Optional

import gradio as gr
import yaml

import mol_viewer
import run_utils


def run_wrapper(protein_file, ligand_file, other_args_file, *args) -> 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, ""

    float_locs = [-4, -3, -2]
    num_centers = 0
    for ii in float_locs:
        av = args[ii]
        if av is not None and av != "":
            num_centers += 1
            try:
                tmp = float(args[ii])
            except ValueError:
                return f"Pocket Center value {args[ii]} is not a valid number", None, ""

    if num_centers not in {0, 3}:
        return "Either none or all three pocket center values must be provided", None, ""

    other_args_dict = {}
    if other_args_file is not None:
        other_args_dict = yaml.safe_load(open(other_args_file['name'], "r"))

    output_file, pdb_text, sdf_text = run_utils.run_cli_command(
        protein_file['name'], ligand_file['name'], other_args_dict, *args,
    )

    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,
                                            interactive=True)
            with gr.Column():
                keep_local_structures = gr.Checkbox(label="Keep Local Structures", value=True, interactive=True)
                save_vis = gr.Checkbox(label="Save Visualisation", value=True, interactive=True,
                                       elem_id="save_visualisation")
        with gr.Row():
            # Add fields for pocket_center_x, pocket_center_y, pocket_center_z
            pcx = gr.Text(label="Pocket Center X", placeholder="1.23", value=None, interactive=True)
            pcy = gr.Text(label="Pocket Center Y", placeholder="4.56", value=None, interactive=True)
            pcz = gr.Text(label="Pocket Center Z", placeholder="7.89", value=None, interactive=True)
            flex_sidechains = gr.Textbox(label="Flexible Sidechains", placeholder="A:130-B:140", value=None,
                                         interactive=True,
                                         info="Specify which amino acids will be flexible. E.g., A:130-B:140 will make amino acid with id 130 in chain A, and id 140 in chain B flexible.")
        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_file = 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_file]
        # See run_utils.py:ARG_ORDER for the order of these arguments
        _inputs += [samples_per_complex, keep_local_structures, save_vis, pcx, pcy, pcz, flex_sidechains]
        _outputs = [message, output_file, viewer]
        run_btn.click(fn=run_wrapper, inputs=_inputs, outputs=_outputs, preprocess=False)

    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()