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metal3d

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Simon Duerr commited on Aug 19, 2022

Commit

88dc70f

•

1 Parent(s): 1c9254d

fixes

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Files changed (4) hide show

README.md +5 -1
app.py +132 -31
moleculekit-1.1.1.tar.gz +0 -3
utils/voxelization.py +3 -3

README.md CHANGED Viewed

@@ -4,10 +4,14 @@ emoji: 👀
 colorFrom: indigo
 colorTo: indigo
 sdk: gradio
-sdk_version: 3.0.10
 app_file: app.py
 pinned: false
 license: mit
 ---
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces#reference

 colorFrom: indigo
 colorTo: indigo
 sdk: gradio
+sdk_version: 3.0.11
 app_file: app.py
 pinned: false
 license: mit
 ---
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces#reference
+Moleculekit is a product of Acellera https://github.com/Acellera/moleculekit and distributed under
+the HTMD Software License and free for Academics.

app.py CHANGED Viewed

@@ -52,19 +52,26 @@ def update(inp, file, mode, custom_resids, clustering_threshold):
                 return "pdb code must be 4 letters or Uniprot code does not match", ""
     identifier = os.path.basename(filepath)
     if mode == "All residues":
         ids = get_all_protein_resids(filepath)
     elif len(custom_resids)!=0:
         ids=get_all_resids_from_list(filepath,custom_resids.replace(","," "))
     else:
         ids = get_all_metalbinding_resids(filepath)
-    voxels, prot_centers, prot_N, prots = processStructures(filepath, ids)
     device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
     voxels.to(device)
-    print(voxels.shape)
     model = Model()
     model.to(device)
-    model.load_state_dict(torch.load("weights/metal_0.5A_v3_d0.2_16Abox.pth", map_location=torch.device('cpu')))
     model.eval()
     with warnings.catch_warnings():
         warnings.filterwarnings("ignore")
@@ -100,21 +107,6 @@ def update(inp, file, mode, custom_resids, clustering_threshold):
     )
-def test():
-    x = """<!DOCTYPE html>
-        <html>
-        <head>
-    <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
-    </head>
-    <body>
-    <script src="https://3Dmol.org/build/3Dmol-min.js" async></script> <div style="height: 400px; width: 400px; position: relative;" class="viewer_3Dmoljs" data-pdb="2POR" data-backgroundcolor="0xffffff" data-style="stick" ></div>
-        </body></html>"""
-    return f"""<iframe style="width: 100%; height: 480px" 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 read_mol(molpath):
     with open(molpath, "r") as fp:
@@ -134,13 +126,14 @@ def molecule(pdb, probes, cube):
         <html>
         <head>
     <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
     <style>
     body{
         font-family:sans-serif
     }
 .mol-container {
   width: 100%;
-  height: 400px;
   position: relative;
 }
 .slider{
@@ -160,16 +153,50 @@ def molecule(pdb, probes, cube):
 <script src="https://cdnjs.cloudflare.com/ajax/libs/rangeslider.js/2.3.3/rangeslider.min.js" integrity="sha512-BUlWdwDeJo24GIubM+z40xcj/pjw7RuULBkxOTc+0L9BaGwZPwiwtbiSVzv31qR7TWx7bs6OPTE5IyfLOorboQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
     </head>
     <body>
-    <div class="slidercontainer">
     <span>Isovalue </span>
     <span id="isovalue">0.5</span>
-    <input class="slider" type="range" id="rangeslider" min="0" max="1" step="0.025" value=0.5>
     </div>
     <div id="container" class="mol-container"></div>
             <script>
             let viewer = null;
             let voldata = null;
             $(document).ready(function () {
                 let element = $("#container");
                 let config = { backgroundColor: "white" };
@@ -184,8 +211,8 @@ def molecule(pdb, probes, cube):
         + cubefile
         + """`
                 voldata = new $3Dmol.VolumeData(cubefile, "cube");
-                viewer.addIsosurface(voldata, { isoval: 0.7 , color: "blue", alpha: 0.85, smoothness: 1 });
-                viewer.getModel(0).setStyle({}, {cartoon: {color: "grayCarbon"}});
                 let probes =`"""
         + probes
         + """`
@@ -207,25 +234,90 @@ def molecule(pdb, probes, cube):
                 viewer.zoomTo();
                 viewer.render();
                 viewer.zoom(0.8, 2000);
         });
         </script>
          <script>
          $("#rangeslider").rangeslider().on("change", function (el) {
                 isoval = parseFloat(el.target.value);
                 $("#isovalue").text(el.target.value)
-                viewer.addIsosurface(voldata, { isoval: parseFloat(el.target.value), color: "blue", alpha: 0.85, smoothness: 1 });
                 viewer.render();
             });
             </script>
         </body></html>"""
     )
-    return f"""<iframe style="width: 100%; height: 480px" 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>"""
 metal3d = gr.Blocks()
@@ -248,16 +340,25 @@ with metal3d:
                 clustering_threshold = gr.Slider(minimum=0.15,maximum=1, value=0.15,step=0.05, label="Clustering threshold")
                 distance_cutoff = gr.Slider(minimum=1,maximum=10, value=7,step=1, label="Clustering distance cutoff")
         btn = gr.Button("Run")
-    gr.Markdown(
-        """ <small>Inference using CPU-only, can be quite slow for more than 20 residues. Use Colab notebook for GPU acceleration</small>
-    """
-    )
     gr.Markdown("# Output")
     out = gr.Textbox(label="status")
     mol = gr.HTML()
     btn.click(fn=update, inputs=[inp, file, mode, custom_resids, clustering_threshold], outputs=[out, mol])
-metal3d.launch()

                 return "pdb code must be 4 letters or Uniprot code does not match", ""
     identifier = os.path.basename(filepath)
     if mode == "All residues":
+        print('using all residues')
         ids = get_all_protein_resids(filepath)
     elif len(custom_resids)!=0:
+        print('using listed residues', custom_resids)
         ids=get_all_resids_from_list(filepath,custom_resids.replace(","," "))
     else:
+        print('using metalbinding')
         ids = get_all_metalbinding_resids(filepath)
+    print(filepath)
+    print(ids)
+    try:
+        voxels, prot_centers, prot_N, prots = processStructures(filepath, ids)
+    except Exception as e:
+        return "Error", f"""<div class="text-center mt-4"> Something went wrong with the voxelization, reset custom residues and other input fiels and check error message <br> <br> <code>{e}</code></div>"""
     device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
     voxels.to(device)
     model = Model()
     model.to(device)
+    model.load_state_dict(torch.load("weights/metal_0.5A_v3_d0.2_16Abox.pth", map_location=torch.device("cuda" if torch.cuda.is_available() else "cpu")))
     model.eval()
     with warnings.catch_warnings():
         warnings.filterwarnings("ignore")
     )
 def read_mol(molpath):
     with open(molpath, "r") as fp:
         <html>
         <head>
     <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+     <link rel="stylesheet" href="https://unpkg.com/flowbite@1.4.5/dist/flowbite.min.css" />
     <style>
     body{
         font-family:sans-serif
     }
 .mol-container {
   width: 100%;
+  height: 600px;
   position: relative;
 }
 .slider{
 <script src="https://cdnjs.cloudflare.com/ajax/libs/rangeslider.js/2.3.3/rangeslider.min.js" integrity="sha512-BUlWdwDeJo24GIubM+z40xcj/pjw7RuULBkxOTc+0L9BaGwZPwiwtbiSVzv31qR7TWx7bs6OPTE5IyfLOorboQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
     </head>
     <body>
+    <div class="slidercontainer my-8">
     <span>Isovalue </span>
     <span id="isovalue">0.5</span>
+    <input class="slider text-blue-400" type="range" id="rangeslider" min="0" max="1" step="0.05" value=0.5>
     </div>
     <div id="container" class="mol-container"></div>
+     <div class="flex items-center justify-center my-4">
+        <div class="px-4">
+        <label for="sidechain" class="relative inline-flex items-center mb-4 cursor-pointer ">
+            <input  id="sidechain"type="checkbox" class="sr-only peer">
+            <div class="w-11 h-6 bg-gray-200 rounded-full peer peer-focus:ring-4 peer-focus:ring-blue-300 dark:peer-focus:ring-blue-800 dark:bg-gray-700 peer-checked:after:translate-x-full peer-checked:after:border-white after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-blue-600"></div>
+            <span class="ml-3 text-sm font-medium text-gray-900 dark:text-gray-300">Show side chains</span>
+          </label>
+        </div>
+        <div class="px-4">
+        <label for="pdbmetal" class="relative inline-flex items-center mb-4 cursor-pointer ">
+            <input  id="pdbmetal" type="checkbox" class="sr-only peer" checked>
+            <div class="w-11 h-6 bg-gray-200 rounded-full peer peer-focus:ring-4 peer-focus:ring-blue-300 dark:peer-focus:ring-blue-800 dark:bg-gray-700 peer-checked:after:translate-x-full peer-checked:after:border-white after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-blue-600"></div>
+            <span class="ml-3 text-sm font-medium text-gray-900 dark:text-gray-300">Show PDB metals</span>
+          </label>
+        </div>
+        <div class="px-4">
+        <label for="probes" class="relative inline-flex items-center mb-4 cursor-pointer ">
+            <input  id="probes" type="checkbox" class="sr-only peer" checked>
+            <div class="w-11 h-6 bg-gray-200 rounded-full peer peer-focus:ring-4 peer-focus:ring-blue-300 dark:peer-focus:ring-blue-800 dark:bg-gray-700 peer-checked:after:translate-x-full peer-checked:after:border-white after:absolute after:top-0.5 after:left-[2px] after:bg-white after:border-gray-300 after:border after:rounded-full after:h-5 after:w-5 after:transition-all dark:border-gray-600 peer-checked:bg-blue-600"></div>
+            <span class="ml-3 text-sm font-medium text-gray-900 dark:text-gray-300">Show Probes</span>
+          </label>
+        </div>
+        </div>
+     <div class="flex items-center justify-center my-4">
+ <button type="button" class="text-gray-900 bg-white hover:bg-gray-100 border border-gray-200 focus:ring-4 focus:outline-none focus:ring-gray-100 font-medium rounded-lg text-sm px-5 py-2.5 text-center inline-flex items-center dark:focus:ring-gray-600 dark:bg-gray-800 dark:border-gray-700 dark:text-white dark:hover:bg-gray-700 mr-2 mb-2" id="download">
+                    <svg class="w-6 h-6 mr-2 -ml-1" fill="none" stroke="currentColor" viewBox="0 0 24 24" xmlns="http://www.w3.org/2000/svg"><path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M4 16v1a3 3 0 003 3h10a3 3 0 003-3v-1m-4-4l-4 4m0 0l-4-4m4 4V4"></path></svg>
+                    Download predictions
+                  </button>
+              </div>
             <script>
             let viewer = null;
             let voldata = null;
+            let shape = null;
+            let sidechain = null;
+            let metal = null;
             $(document).ready(function () {
                 let element = $("#container");
                 let config = { backgroundColor: "white" };
         + cubefile
         + """`
                 voldata = new $3Dmol.VolumeData(cubefile, "cube");
+                shape = viewer.addIsosurface(voldata, { isoval: 0.5 , color: "blue", alpha: 0.85, smoothness: 1 });
+                viewer.getModel(0).setStyle({}, {cartoon: {}});
                 let probes =`"""
         + probes
         + """`
                 viewer.zoomTo();
                 viewer.render();
                 viewer.zoom(0.8, 2000);
+                $("#sidechain").change(function () {
+                    if (this.checked) {
+                        BB = ["C", "O", "N"]
+                        viewer.getModel(0).setStyle( {"and": [{resn: ["GLY", "PRO"], invert: true},{atom: BB, invert: true},]},{stick: {hidden:false, colorscheme: "WhiteCarbon", radius: 0.3}, cartoon: {}});
+                        viewer.render()
+                         $("#pdbmetal").prop( "checked", false );
+                    } else {
+                        BB = ["C", "O", "N"]
+                        viewer.getModel(0).setStyle({"and": [{resn: ["GLY", "PRO"], invert: true},{atom: BB, invert: true},]},{stick: {colorscheme: "WhiteCarbon",hidden:true, radius: 0.3}, cartoon: {}});
+                        viewer.render()
+                         $("#pdbmetal").prop( "checked", false );
+                    }
+                });
+                 $("#pdbmetal").change(function () {
+                    if (this.checked) {
+                        viewer.getModel(0).setStyle({ "resn": ["ZN","MG","NA","FE", "NI","MN","CA", "CU", "CU1"] }, { "sphere": {hidden:false}});
+                        viewer.render()
+                    } else {
+                        viewer.getModel(0).setStyle({ "resn": ["ZN","MG","NA","FE","NI", "MN","CA", "CU", "CU1"] }, { "sphere": {hidden:true}});
+                        viewer.render()
+                    }
+                });
+                $("#probes").change(function () {
+                    if (this.checked) {
+                        viewer.getModel(1).setStyle({ "resn": "ZN" }, { "sphere": { }});
+                        viewer.addStyle()
+                        viewer.render()
+                    } else {
+                        viewer.getModel(1).setStyle({});
+                        viewer.render()
+                    }
+                });
+                  $("#download").click(function () {
+                    download("protein.pdb", data);
+                    download("metaldensity.cube", cubefile);
+                    download("probes.pdb", probes);
+                })
         });
+         function download(filename, text) {
+            var element = document.createElement("a");
+            element.setAttribute("href", "data:text/plain;charset=utf-8," + encodeURIComponent(text));
+            element.setAttribute("download", filename);
+            element.style.display = "none";
+            document.body.appendChild(element);
+            element.click();
+            document.body.removeChild(element);
+        }
         </script>
          <script>
          $("#rangeslider").rangeslider().on("change", function (el) {
                 isoval = parseFloat(el.target.value);
                 $("#isovalue").text(el.target.value)
+                console.log("Change isosurface to "+el.target.value)
+                viewer.removeShape(shape)
+                shape=viewer.addIsosurface(voldata, { isoval: parseFloat(el.target.value), color: "blue", alpha: 0.85, smoothness: 1 });
                 viewer.render();
             });
             </script>
         </body></html>"""
     )
+    return f"""<iframe style="width: 100%; height: 1000px" 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 set_examples(example):
+    n,code, resids = example
+    return [
+        n,
+        code,
+        resids
+    ]
 metal3d = gr.Blocks()
                 clustering_threshold = gr.Slider(minimum=0.15,maximum=1, value=0.15,step=0.05, label="Clustering threshold")
                 distance_cutoff = gr.Slider(minimum=1,maximum=10, value=7,step=1, label="Clustering distance cutoff")
         btn = gr.Button("Run")
+    n = gr.Textbox(label="Label",visible=False)
+    examples = gr.Dataset(components=[n,inp, custom_resids],
+    samples=[["HCA2", "2CBA", ""],
+                                     ["Nickel in GB1 dimer", "6F5N", ""],
+                                     ["Zebrafish palmitoyltransferase ZDHHC15B PDB", "6BMS", ""],
+                                     ["Human palmitoyltransferase ZDHHC23 AlphaFold", "Q8IYP9", "280,273,263,260,274,277,274,287"]],
+                           )
+    examples.click(fn=set_examples, inputs=examples, outputs=examples.components)
+    #gr.Markdown(
+    #    """ <small>Inference using CPU-only, can be quite slow for more than 20 residues. Use Colab notebook for GPU acceleration</small>
+    #"""
+    #)
     gr.Markdown("# Output")
     out = gr.Textbox(label="status")
     mol = gr.HTML()
     btn.click(fn=update, inputs=[inp, file, mode, custom_resids, clustering_threshold], outputs=[out, mol])
+metal3d.launch(share=True)

moleculekit-1.1.1.tar.gz DELETED Viewed

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:7751777ae97868b5194c6a0c5c9785867964c43befb8ea963db0642cf80a208d
-size 6434734

utils/voxelization.py CHANGED Viewed

@@ -177,7 +177,7 @@ def processStructures(pdb_file, resids, clean=True):
     # load molecule using MoleculeKit
     try:
-        prot = Molecule('files/2CBA.pdb')
     except:
         raise IOError("could not read pdbfile")
@@ -196,8 +196,8 @@ def processStructures(pdb_file, resids, clean=True):
     envs = []
     results = [voxelize_single_notcentered(x) for x in environments]
-    voxels = torch.empty(len(results), 8, 32, 32, 32, device="cpu")
     vox_env, prot_centers_list, prot_n_list, envs = zip(*results)

     # load molecule using MoleculeKit
     try:
+        prot = Molecule(pdb_file)
     except:
         raise IOError("could not read pdbfile")
     envs = []
     results = [voxelize_single_notcentered(x) for x in environments]
+    device = "cuda" if torch.cuda.is_available() else "cpu"
+    voxels = torch.empty(len(results), 8, 32, 32, 32, device=device)
     vox_env, prot_centers_list, prot_n_list, envs = zip(*results)