import gradio as gr
from shutil import copyfile
## Modify to match format username-spacename
## Only works for hosted spaces on Huggingface, for local spaces or spaces hosted on Colab you need to use the gradio.live url with share=True as described in the last two lines
public_link = "https://simonduerr-molstar-gradio.hf.space"
import gradio as gr
import os
def get_pdb(upload_choice="PDB Code", pdb_code="", filepath=""):
urls = {
"PDB Code": {"base":"https://files.rcsb.org/view/", "suffix":".pdb"},
"AlphaFold DB": {"base":"https://alphafold.ebi.ac.uk/files/AF-", "suffix": "-F1-model_v4.pdb"},
"ESM Atlas": {"base": "https://api.esmatlas.com/fetchPredictedStructure/", "suffix":".pdb"}
}
if upload_choice=="local file":
try:
#move file to home folder to have it accessible from the web
copyfile(filepath.name, os.path.join(os.getcwd(), os.path.basename(filepath.name)))
return os.path.join(os.getcwd(), os.path.basename(filepath.name))
except AttributeError as e:
return None
else:
os.system(f"wget -qnc {urls[upload_choice]['base']}{pdb_code}{urls[upload_choice]['suffix']}")
return f"{pdb_code}{urls[upload_choice]['suffix']}"
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, public_link):
print(input_pdb)
print(public_link+'/file='+os.path.basename(input_pdb))
link = public_link+"/file="+os.path.basename(input_pdb)
x ="""
PDBe Molstar - Helper functions
"""
return f""""""
def update(upload_choice, inp, file, public_link):
pdb_path = get_pdb(upload_choice, inp, file)
return molecule(pdb_path, public_link)
def toggle_upload_input(choice):
if choice != "local file":
return gr.update(visible=True, placeholder=choice), gr.update(visible=False, value=None)
elif choice == "local file":
return gr.update(visible=False), gr.update(visible=True, value=None)
demo = gr.Blocks()
with demo:
gr.Markdown("# PDB viewer using Mol*")
gr.Markdown("""If using please cite
> David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; 10.1093/nar/gkab31.""")
public_link = gr.Variable(value=public_link)
with gr.Row():
with gr.Box():
upload_choice = gr.Radio(["PDB Code", "AlphaFold DB", "ESM Atlas","local file"], label="File source", value='PDB Code')
inp = gr.Textbox(
placeholder="PDB Code", label="Input structure"
)
file = gr.File(file_count="single", visible=False)
upload_choice.change(fn=toggle_upload_input,
inputs=[upload_choice],
outputs=[inp, file],
queue=False)
btn = gr.Button("View structure")
gr.Examples([["PDB Code", "2CBA"],["AlphaFold DB", "A0A1U8FD60"], ["ESM Atlas", "MGYP001531319262"]], [upload_choice,inp])
mol = gr.HTML()
btn.click(fn=update, inputs=[upload_choice, inp, file, public_link], outputs=mol)
_, _, pl = demo.launch() # use public link with share=True locally and uncomment below
#public_link = pl