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| 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() | |