Spaces:
Sleeping
Sleeping
File size: 2,325 Bytes
e5ccf64 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 |
import gradio as gr
import torch
import pydssp
import py3Dmol
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 predict(pdb_code, pdb_file, helix, sheet, loop):
path_to_pdb = get_pdb(pdb_code=pdb_code, 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, "E": sheet, "-": loop}
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:
gr.Markdown("# Secondary structure using pyDSSP")
pdb_code = gr.Textbox(label="PDB Code")
pdb_file = gr.File(label="PDB File Upload")
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()
btn.click(
fn=predict, inputs=[pdb_code, pdb_file, helix, sheet, loop], outputs=[html]
)
gr.Examples(
[["1QYS", "#ff0000", "#00ff00", "#0000ff"]],
inputs=[pdb_code, helix, sheet, loop],
fn=predict,
)
demo.launch()
|