| | 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 = ( |
| | """<!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.setStyle({}, {cartoon: { color:"spectrum"}}); |
| | viewer.addStyle({"and":[{resn:["GLY","PRO"], invert:true}, {atom:["N","C","O"], invert:true}]}, {stick: {radius:0.2, colorscheme:"WhiteCarbon"}}); |
| | viewer.addStyle({"and":[{resn:"GLY"}, {atom:"CA"}]}, {stick: {radius:0.2, colorscheme:"WhiteCarbon"}}); |
| | viewer.addStyle({"and":[{resn:"PRO"}, {atom:["C","O"], invert:true}]}, {stick: {radius:0.2, 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 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() |
| |
|
