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