Spaces:
Sleeping
Sleeping
from huggingface_hub import login | |
from esm.models.esm3 import ESM3 | |
from esm.sdk.api import ESM3InferenceClient, ESMProtein, GenerationConfig | |
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("cpu") | |
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 = ( | |
"""<!DOCTYPE html> | |
<html> | |
<head> | |
<meta http-equiv="content-type" content="text/html; charset=UTF-8" /> | |
<style> | |
body{ | |
font-family:sans-serif | |
} | |
.mol-container { | |
width: 100%; | |
height: 600px; | |
position: relative; | |
} | |
.mol-container select{ | |
background-image:None; | |
} | |
</style> | |
<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.6.3/jquery.min.js" integrity="sha512-STof4xm1wgkfm7heWqFJVn58Hm3EtS31XFaagaa8VMReCXAkQnJZ+jEy8PCC/iT18dFy95WcExNHFTqLyp72eQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script> | |
<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script> | |
</head> | |
<body> | |
<div id="container" class="mol-container"></div> | |
<script> | |
let pdb = `""" | |
+ mol | |
+ """` | |
$(document).ready(function () { | |
let element = $("#container"); | |
let config = { backgroundColor: "white" }; | |
let viewer = $3Dmol.createViewer(element, config); | |
viewer.addModel(pdb, "pdb"); | |
viewer.getModel(0).setStyle({}, { cartoon: { colorscheme:"whiteCarbon" } }); | |
viewer.zoomTo(); | |
viewer.render(); | |
viewer.zoom(0.8, 2000); | |
}) | |
</script> | |
</body></html>""" | |
) | |
return f"""<iframe style="width: 100%; height: 600px" 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>""" | |
def prediction(prompt, temperature, do_structure): | |
protein = ESMProtein(sequence=prompt) | |
protein = model.generate(protein, GenerationConfig(track="sequence", num_steps=8, temperature=temperature)) | |
if do_structure == "Yes": | |
protein = model.generate(protein, GenerationConfig(track="structure", num_steps=8)) | |
protein.to_pdb("./generation.pdb") | |
html = molecule("./generation.pdb") | |
seq = protein.sequence | |
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") | |
return seq, protein.sequence, html, html1, "./round_tripped.pdb", "./generation.pdb", | |
else: | |
f = open("./empty.pdb", "w") | |
f.write("\n") | |
f.close() | |
return protein.sequence, "Inverse folding and re-generation not enabled", "<h3>Structure reconstruction not enabled</h3>", "<h3>Inverse folding and re-generation not enabled</h3>", "./empty.pdb", "./empty.pdb" | |
reps = [ | |
{ | |
"model": 0, | |
"chain": "", | |
"resname": "", | |
"style": "stick", | |
"color": "whiteCarbon", | |
"residue_range": "", | |
"around": 0, | |
"byres": False, | |
"visible": False | |
} | |
] | |
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"), gr.Radio(["Yes", "No"], label="Reconstruct structure", info="Choose wheter to reconstruct structure or not, allowing also inverse folding-powered double check")], outputs = [gr.Textbox(label="Originally predicted sequence", show_copy_button=True),gr.Textbox(label="Inverse folding predicted sequence", show_copy_button=True),gr.HTML(label="Predicted 3D structure"),gr.HTML(label="Inverse-folding predicted 3D structure"), Molecule3D(label="Inverse-folding predicted molecular structure", reps=reps), Molecule3D(label="Predicted molecular structure", reps=reps)], title="""<h1 align='center'>Proteins with ESM</h1> | |
<h2 align='center'>Predict the whole sequence and 3D structure of masked protein sequences!</h2> | |
<h3 align='center'>Support this space with a ⭐ on <a href='https://github.com/AstraBert/proteins-w-esm'>GitHub</a></h3> | |
<h3 align='center'>Support Evolutionary Scale's ESM with a ⭐ on <a href='https://github.com/evolutionaryscale/esm'>GitHub</a></h3>""", examples = [["___________________________________________________DQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPP___________________________________________________________", 0.7, "No"], ["__________________________________________________________AGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVRE___________________________", 0.2, "Yes"], ["__________KTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLH________", 0.5, "Yes",]], cache_examples=False) | |
demo.launch() |