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huhlim commited on Mar 27, 2023

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fb9e841

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1 Parent(s): f470b2d

added 3Dmol viewer to app.py

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Files changed (1) hide show

app.py +127 -16

app.py CHANGED Viewed

@@ -2,23 +2,134 @@ import gradio as gr
 import cg2all
 import os
 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)
-    return out_fn
-demo = gr.Interface(fn=runner,
-                    inputs=["file", \
-                            gr.Radio(["CalphaBasedModel", "ResidueBasedModel", "CalphaCMModel", "BackboneModel",
-                            "MainchainModel", "Martini", "PRIMO"])],
-                    outputs=["file"],
-                    examples=[["inputs/1ab1_A.calpha.pdb", "CalphaBasedModel"],
-                              ["inputs/1ab1_A.residue.pdb", "ResidueBasedModel"],
-                              ["inputs/1ab1_A.cacm.pdb", "CalphaCMModel"],
-                              ["inputs/1ab1_A.bb.pdb", "BackboneModel"],
-                              ["inputs/1ab1_A.mc.pdb", "MainchainModel"],
-                              ["inputs/1ab1_A.martini.pdb", "Martini"],
-                              ["inputs/1ab1_A.primo.pdb", "PRIMO"],
-                              ])
-demo.launch()

 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")
+            model_type = gr.Radio(
+                [
+                    "CalphaBasedModel",
+                    "ResidueBasedModel",
+                    "CalphaCMModel",
+                    "BackboneModel",
+                    "MainchainModel",
+                    "Martini",
+                    "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.cacm.pdb", "CalphaCMModel"],
+                    ["inputs/1ab1_A.bb.pdb", "BackboneModel"],
+                    ["inputs/1ab1_A.mc.pdb", "MainchainModel"],
+                    ["inputs/1ab1_A.martini.pdb", "Martini"],
+                    ["inputs/1ab1_A.primo.pdb", "PRIMO"],
+                ],
+                [input_pdb, model_type],
+            )
+        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("- CalphaCMModel: CA-trace + Residue 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("- PRIMO: [PRIMO model](https://dx.doi.org/10.1002/prot.22645)")
+    gr.Markdown("### Cite: TODO")
+app.launch()