import gradio as gr
import gradio as gr
import os
def get_pdb(pdb_code="", filepath=""):
if pdb_code is None or pdb_code == "":
try:
return filepath.name
except AttributeError as e:
return None
else:
os.system(f"wget -qnc https://files.rcsb.org/view/{pdb_code}.pdb")
return f"{pdb_code}.pdb"
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(inp, file, public_link):
pdb_path = get_pdb(inp, file)
print("public link", public_link)
return molecule(pdb_path, public_link)
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="https://simonduerr-molstar-gradio.hf.space")
with gr.Row():
with gr.Box():
inp = gr.Textbox(
placeholder="PDB Code or upload file below", label="Input structure"
)
file = gr.File(file_count="single")
gr.Examples(["2CBA", "6VXX"], inp)
btn = gr.Button("View structure")
mol = gr.HTML()
btn.click(fn=update, inputs=[inp, file, public_link], outputs=mol)
_, _, pl = demo.launch() # use public link with share=True locally