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, h_seq, l_seq):
mol = read_mol(input_pdb)
byte_content = mol.encode('utf-8')
base64_content = base64.b64encode(byte_content).decode('utf-8')
x = (
"""
"""
)
return f"""
"""
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)
print(l_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(num_models = 1)
igfold.fold(
pred_pdb,
sequences=sequences,
do_refine=False,
do_renum=False
)
html = molecule(pred_pdb, h_seq, l_seq)
else:
html = "ERROR! Not valid sequence
"
return (html)
with gr.Blocks() as demo:
gr.Markdown('# Antibody Structure Prediction')
gr.Markdown("## Examples")
html = """
H-chain: QVQLKESGPGLVAPSQSLSITCTVSGFSLSSYGVSWVRQPPGKGLEWLGVIWGDGSTNYHPNLMSRLSISKDISKSQVLFKLNSLQTDDTATYYCVTLDYWGQGTSVTVSS
L-chain: DVVMTQTPLSLPVSLGDQASISCRSSQSLVHRNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGLYFCFQTTYVPNTFGGGTKLEIK
H-chain: EVQLLESGGGLVQPGGSLRLSCAASGFTFSLYWMGWVRQAPGKGLEWVSSISSSGGVTPYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKLGELGWFDPWGQGTLVTVSS
L-chain: DIQMTQSPSSLSASVGDRVTITCRASQGISSYLNWYQQKPGKAPKLLIYYASNLQNGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIK
H-chain: EVQLVQSGPEVKKPGTSVKVSCKASGFTFMSSAVQWVRQARGQRLEWIGWIVIGSGNTNYAQKFQERVTITRDMSTSTAYMELSSLRSEDTAVYYCAAPYCSSISCNDGFDIWGQGTMVTVS
L-chain: EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPITFGQGTKLEIK
"""
gr.HTML(value = html)
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())
if __name__ == "__main__":
demo.launch()