Spaces:
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Simon Duerr
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e5ccf64
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Parent(s):
ff6c561
first commit
Browse files- app.py +74 -0
- requirements.txt +4 -0
app.py
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import gradio as gr
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import torch
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import pydssp
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import py3Dmol
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import os
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def get_pdb(pdb_code="", filepath=""):
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try:
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return filepath.name
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except AttributeError as e:
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if pdb_code is None or pdb_code == "":
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return None
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else:
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os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb")
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return f"{pdb_code}.pdb"
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def get_offset(pdb):
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pdb_multiline = pdb.split("\n")
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for line in pdb_multiline:
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if line.startswith("ATOM"):
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return int(line[22:27])
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def predict(pdb_code, pdb_file, helix, sheet, loop):
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path_to_pdb = get_pdb(pdb_code=pdb_code, filepath=pdb_file)
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pdb = open(path_to_pdb, "r").read()
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offset = get_offset(pdb)
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coord = torch.tensor(pydssp.read_pdbtext(pdb))
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secondary_struct = pydssp.assign(coord)
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view = py3Dmol.view(width=400, height=400)
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view.addModel(pdb, "pdb")
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colormap = {"H": helix, "E": sheet, "-": loop}
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colors = {i + offset: colormap[resi] for i, resi in enumerate(secondary_struct)}
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view.setStyle({"cartoon": {"colorscheme": {"prop": "resi", "map": colors}}})
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view.zoomTo()
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output = view._make_html().replace("'", '"')
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x = f"""<!DOCTYPE html><html> {output} </html>""" # do not use ' in this input
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return f"""<iframe style="width: 100%; height:420px" name="result" allow="midi; geolocation; microphone; camera;
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display-capture; encrypted-media;" sandbox="allow-modals allow-forms
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allow-scripts allow-same-origin allow-popups
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allow-top-navigation-by-user-activation allow-downloads" allowfullscreen=""
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allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""
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with gr.Blocks() as demo:
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gr.Markdown("# Secondary structure using pyDSSP")
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pdb_code = gr.Textbox(label="PDB Code")
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pdb_file = gr.File(label="PDB File Upload")
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with gr.Row():
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helix = gr.ColorPicker(label="helix")
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sheet = gr.ColorPicker(label="sheet")
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loop = gr.ColorPicker(label="loop")
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btn = gr.Button(label="Run")
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html = gr.HTML()
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btn.click(
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fn=predict, inputs=[pdb_code, pdb_file, helix, sheet, loop], outputs=[html]
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)
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gr.Examples(
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[["1QYS", "#ff0000", "#00ff00", "#0000ff"]],
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inputs=[pdb_code, helix, sheet, loop],
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fn=predict,
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)
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demo.launch()
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requirements.txt
ADDED
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@@ -0,0 +1,4 @@
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+
torch
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gradio
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py3Dmol
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git+https://github.com/ShintaroMinami/PyDSSP.git
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