Spaces:
Sleeping
Sleeping
Change pocket center inputs to be text
Browse files
main.py
CHANGED
@@ -15,6 +15,20 @@ def run_wrapper(protein_file, ligand_file, other_args_file, *args) -> Tuple[str,
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if ligand_file is None:
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return "Ligand file is missing! Must provide a ligand file in SDF format", None, ""
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other_args_dict = {}
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if other_args_file is not None:
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other_args_dict = yaml.safe_load(open(other_args_file['name'], "r"))
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@@ -49,10 +63,11 @@ def run():
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elem_id="save_visualisation")
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with gr.Row():
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# Add fields for pocket_center_x, pocket_center_y, pocket_center_z
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pcx = gr.
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pcy = gr.
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pcz = gr.
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flex_sidechains = gr.Textbox(label="Flexible Sidechains", placeholder="A:130-B:140", value=None,
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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.")
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with gr.Row():
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gr.Markdown("""Additional values can be included in "Other arguments", and will be passed
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if ligand_file is None:
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return "Ligand file is missing! Must provide a ligand file in SDF format", None, ""
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float_locs = [-4, -3, -2]
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num_centers = 0
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for ii in float_locs:
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av = args[ii]
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if av is not None and av != "":
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num_centers += 1
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try:
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tmp = float(args[ii])
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except ValueError:
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return f"Pocket Center value {args[ii]} is not a valid number", None, ""
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if num_centers not in {0, 3}:
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return "Either none or all three pocket center values must be provided", None, ""
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other_args_dict = {}
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if other_args_file is not None:
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other_args_dict = yaml.safe_load(open(other_args_file['name'], "r"))
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elem_id="save_visualisation")
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with gr.Row():
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# Add fields for pocket_center_x, pocket_center_y, pocket_center_z
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pcx = gr.Text(label="Pocket Center X", placeholder="1.23", value=None, interactive=True)
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pcy = gr.Text(label="Pocket Center Y", placeholder="4.56", value=None, interactive=True)
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pcz = gr.Text(label="Pocket Center Z", placeholder="7.89", value=None, interactive=True)
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flex_sidechains = gr.Textbox(label="Flexible Sidechains", placeholder="A:130-B:140", value=None,
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interactive=True,
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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.")
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with gr.Row():
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gr.Markdown("""Additional values can be included in "Other arguments", and will be passed
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