from huggingface_hub import login
from esm.models.esm3 import ESM3
from esm.sdk.api import ESM3InferenceClient, ESMProtein, GenerationConfig
import spaces
import os
import gradio as gr
from gradio_molecule3d import Molecule3D
# This will prompt you to get an API key from huggingface hub, make one with
# "Read" or "Write" permission and copy it back here.
TOKEN = os.getenv("HF_TOKEN")
login(TOKEN)
# This will download the model weights and instantiate the model on your machine.
model: ESM3InferenceClient = ESM3.from_pretrained("esm3_sm_open_v1").to("cuda")
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)
x = (
"""
"""
)
return f""""""
@spaces.GPU(duration=300)
def prediction(prompt, temperature):
protein = ESMProtein(sequence=prompt)
protein = model.generate(protein, GenerationConfig(track="sequence", num_steps=8, temperature=temperature))
seq = protein.sequence
protein = model.generate(protein, GenerationConfig(track="structure", num_steps=8))
protein.to_pdb("./generation.pdb")
protein.sequence = None
protein = model.generate(protein, GenerationConfig(track="sequence", num_steps=8))
protein.coordinates = None
protein = model.generate(protein, GenerationConfig(track="structure", num_steps=8))
protein.to_pdb("./round_tripped.pdb")
html1 = molecule("./round_tripped.pdb")
html = molecule("./generation.pdb")
return seq, protein.sequence, html, html1, "./generation.pdb", "./round_tripped.pdb"
demo = gr.Interface(fn = prediction, inputs = [gr.Textbox(label="Masked protein sequence", info="Use '_' as masking character", value="___________________________________________________DQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPP___________________________________________________________"), gr.Slider(0,1,label="Temperature")], outputs = [gr.Textbox(label="Originally predicted sequence"),gr.Textbox(label="Inverse folding predicted sequence"),gr.HTML(label="Predicted 3D structure"),gr.HTML(label="Inverse-folding predicted 3D structure"), Molecule3D(label="Predicted molecular structure"), Molecule3D(label="Inverse-folding predicted molecular structure")], title="""Proteins with ESM
Predict the whole sequence and 3D structure of masked protein sequences!
Support this space with a ⭐ on GitHub
Support Evolutionary Scale's ESM with a ⭐ on GitHub
""", examples = [["___________________________________________________DQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPP___________________________________________________________", 0.7], ["__________________________________________________________AGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVRE___________________________", 0.2], ["__________KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH________", 0.5]], cache_examples=False)
if __name__ == '__main__':
demo.launch()