import gradio as gr
import cg2all
import os
def read_mol(molpath):
with open(molpath, "r") as fp:
lines = fp.readlines()
mol = ""
for l in lines:
mol += l
#
mol = mol.replace("OT1", "O ")
mol = mol.replace("OT2", "OXT")
return mol
def molecule(input_pdb):
mol = read_mol(input_pdb)
x = (
"""
"""
)
return f""""""
def runner(in_pdb, model_type):
out_fn = in_pdb.name[:-4] + "-all.pdb"
ckpt_fn = f"model/{model_type}.ckpt"
cg2all.convert_cg2all(in_pdb.name, out_fn, model_type=model_type, ckpt_fn=ckpt_fn)
view = molecule(out_fn)
return out_fn, view
with gr.Blocks() as app:
gr.Markdown(
"# cg2all: conversion of coarse-grained protein structure model to all-atom structure"
)
with gr.Row():
with gr.Column():
input_pdb = gr.File(
file_count="single",
label="Input CG structure",
file_types=[".pdb", ".PDB", ".txt", ".TXT"],
)
model_type = gr.Radio(
[
"CalphaBasedModel",
"ResidueBasedModel",
"SidechainModel",
"CalphaCMModel",
"CalphaSCModel",
"BackboneModel",
"MainchainModel",
"Martini",
"Martini3",
"PRIMO",
],
label="Input CG model type",
)
#
button = gr.Button("Run")
#
gr.Examples(
[
["inputs/1ab1_A.calpha.pdb", "CalphaBasedModel"],
["inputs/1ab1_A.residue.pdb", "ResidueBasedModel"],
["inputs/1ab1_A.sc.pdb", "SidechainModel"],
["inputs/1ab1_A.cacm.pdb", "CalphaCMModel"],
["inputs/1ab1_A.casc.pdb", "CalphaSCModel"],
["inputs/1ab1_A.bb.pdb", "BackboneModel"],
["inputs/1ab1_A.mc.pdb", "MainchainModel"],
["inputs/1ab1_A.martini.pdb", "Martini"],
["inputs/1ab1_A.martini3.pdb", "Martini3"],
["inputs/1ab1_A.primo.pdb", "PRIMO"],
],
[input_pdb, model_type],
label="Monomeric coarse-grained structure",
)
gr.Examples(
[
["inputs/Q9EP54.sample.pdb", "CalphaBasedModel"],
],
[input_pdb, model_type],
label="ML(idpGAN)-generated IDP structure",
)
gr.Examples(
[
["inputs/3iyg.pdb", "CalphaBasedModel"],
],
[input_pdb, model_type],
label="Multimeric medium-resolution cryo-EM structure",
)
gr.Examples(
[
["inputs/LAF1rgg.sample.pdb", "CalphaBasedModel"],
],
[input_pdb, model_type],
label="Snapshot of COCOMO simulation of LLPS",
)
with gr.Column():
output_pdb = gr.File(file_count="single", label="Output structure")
viewer = gr.HTML()
button.click(fn=runner, inputs=[input_pdb, model_type], outputs=[output_pdb, viewer])
#
gr.Markdown("---")
gr.Markdown(
"### GitHub repository: [https://github.com/huhlim/cg2all](https://github.com/huhlim/cg2all)"
)
gr.Markdown("### Local installation: `pip install git+http://github.com/huhlim/cg2all`")
gr.Markdown("### Supported coarse-grained models")
gr.Markdown("- CalphaBasedModel: CA-trace")
gr.Markdown("- ResidueBasedModel: Residue center-of-mass")
gr.Markdown("- SidechainModel: Sidechain center-of-mass")
gr.Markdown("- CalphaCMModel: CA-trace + Residue center-of-mass")
gr.Markdown("- CalphaSCModel: CA-trace + Sidechain center-of-mass")
gr.Markdown("- BackboneModel: Backbone N, CA, and C atoms")
gr.Markdown("- MainchainModel: Backbone N, CA, C, and O atoms")
gr.Markdown("- Martini: [Martini model](http://cgmartini.nl)")
gr.Markdown("- Martini3: [Martini3 model](http://www.cgmartini.nl/index.php/martini-3-0)")
gr.Markdown("- PRIMO: [PRIMO model](https://dx.doi.org/10.1002/prot.22645)")
gr.Markdown("### Cite: TODO")
app.launch()