import gradio as gr
from igfold import IgFoldRunner
import os
import random
import base64
def read_mol(molpath):
with open(molpath, "r") as fp:
lines = fp.readlines()
mol = ""
for l in lines:
mol += l
return mol
def molecule(input_pdb):
mol = read_mol(input_pdb)
byte_content = mol.encode('utf-8')
base64_content = base64.b64encode(byte_content).decode('utf-8')
x = (
"""
"""
)
return f"""
Download File
"""
def validate(seq):
alphabet = set('ACDEFGHIKLMNPQRSTVWY')
leftover = set(seq.upper()) - alphabet
return not leftover
def pred_seq(h_seq, l_seq):
h_seq = h_seq.upper().replace(' ', '')
l_seq = l_seq.upper().replace(' ', '')
print(h_seq)
h_is_valid = validate(h_seq)
l_is_valid = validate(l_seq)
if h_is_valid and l_is_valid:
sequences = {
"H": h_seq,
"L": l_seq
}
f_name = ''.join([random.choice("ACDEFGHIKLMNPQRSTVWY") for _ in range(15)])
pred_pdb = f"{f_name}.pdb"
igfold = IgFoldRunner()
igfold.fold(
pred_pdb,
sequences=sequences,
do_refine=False,
do_renum=False,
)
html = molecule(pred_pdb)
else:
html = "ERROR! Not valid sequence
"
return (html)
ex_seq = "QVQLVESGGGSVQAGGSLRLSCTASGYTIGPYCMGWFRQAPGGEREAVAAINMGGGITYYADSVKGRFTISRDNAKNTVTLQMNLKPEDTAMYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSS"
h_chain_example = "EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS"
l_chain_example = "DVVMTQTPFSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPYTFGGGTKLEIK"
with gr.Blocks() as demo:
header = gr.Label('Antibody Structure Prediction')
h_text = gr.Textbox(lines=5, label="Heavy chain")
l_text = gr.Textbox(lines=5, label="Light chain")
btn = gr.Button(value="Submit")
btn.click(pred_seq, inputs=[h_text, l_text], outputs=gr.HTML())
gr.Markdown("## Text Examples")
'''
gr.Examples(
[[h_chain_example, l_chain_example]],
[h_text, l_text],
gr.HTML(),
pred_seq,
cache_examples=True,
)
'''
if __name__ == "__main__":
demo.launch()