feature: all alphafold, reduce nSeqs that can be predicted

app.py

@@ -157,15 +157,15 @@ def make_tied_positions_for_homomers(pdb_dict_list):
     return my_dict
 
 
-def align_structures(pdb1, pdb2, lenRes):
+def align_structures(pdb1, pdb2, lenRes, index):
     """Take two structure and superimpose pdb1 on pdb2"""
     import Bio.PDB
     import subprocess
 
     pdb_parser = Bio.PDB.PDBParser(QUIET=True)
     # Get the structures
-    ref_structure = pdb_parser.get_structure("samle", pdb1)
-    sample_structure = pdb_parser.get_structure("reference", pdb2)
+    ref_structure = pdb_parser.get_structure("ref", pdb1)
+    sample_structure = pdb_parser.get_structure("sample", pdb2)
 
     aligner = Bio.PDB.CEAligner()
     aligner.set_reference(ref_structure)
@@ -173,11 +173,13 @@ def align_structures(pdb1, pdb2, lenRes):
 
     io = Bio.PDB.PDBIO()
     io.set_structure(ref_structure)
-    io.save(f"reference.pdb")
+    io.save(f"outputs/reference.pdb")
+    io.set_structure(sample_structure)
+    io.save(f"outputs/out_{index}_aligned.pdb")
     # Doing this to get around biopython CEALIGN bug
-    subprocess.call("pymol -c -Q -r cealign.pml", shell=True)
+    #subprocess.call("pymol -c -Q -r cealign.pml", shell=True)
 
-    return aligner.rms, "reference.pdb", "out_aligned.pdb"
+    return aligner.rms, "outputs/reference.pdb", f"outputs/out_{index}_aligned.pdb"
 
 
 def save_pdb(outs, filename, LEN):
@@ -196,39 +198,40 @@ def save_pdb(outs, filename, LEN):
 
 
 @ray.remote(num_gpus=1, max_calls=1)
-def run_alphafold(sequence, num_recycles):
+def run_alphafold(sequences, num_recycles):
     recycles = num_recycles
-    RUNNER, OPT = setup_af(sequence)
-
-    SEQ = re.sub("[^A-Z]", "", sequence.upper())
-    MAX_LEN = len(SEQ)
-    LEN = len(SEQ)
-
-    x = np.array([residue_constants.restype_order.get(aa, -1) for aa in SEQ])
-    x = np.pad(x, [0, MAX_LEN - LEN], constant_values=-1)
-    x = jax.nn.one_hot(x, 20)
-
-    OPT["prev"] = {
-        "init_msa_first_row": np.zeros([1, MAX_LEN, 256]),
-        "init_pair": np.zeros([1, MAX_LEN, MAX_LEN, 128]),
-        "init_pos": np.zeros([1, MAX_LEN, 37, 3]),
-    }
-
-    positions = []
+    RUNNER, OPT = setup_af(sequences[0])
     plddts = []
-    for r in range(recycles + 1):
-        outs = RUNNER(x, OPT)
-        outs = jax.tree_map(lambda x: np.asarray(x), outs)
-        positions.append(outs["prev"]["init_pos"][0, :LEN])
+    paes = []
+    for i, sequence in enumerate(sequences):
+        SEQ = re.sub("[^A-Z]", "", sequence.upper())
+        MAX_LEN = len(SEQ)
+        LEN = len(SEQ)
+
+        x = np.array([residue_constants.restype_order.get(aa, -1) for aa in SEQ])
+        x = np.pad(x, [0, MAX_LEN - LEN], constant_values=-1)
+        x = jax.nn.one_hot(x, 20)
+
+        OPT["prev"] = {
+            "init_msa_first_row": np.zeros([1, MAX_LEN, 256]),
+            "init_pair": np.zeros([1, MAX_LEN, MAX_LEN, 128]),
+            "init_pos": np.zeros([1, MAX_LEN, 37, 3]),
+        }
+
+        positions = []
+ 
+        for r in range(recycles + 1):
+            outs = RUNNER(x, OPT)
+            outs = jax.tree_map(lambda x: np.asarray(x), outs)
+            positions.append(outs["prev"]["init_pos"][0, :LEN])
+            OPT["prev"] = outs["prev"]
         plddts.append(outs["plddt"][:LEN])
-        OPT["prev"] = outs["prev"]
-        if recycles > 0:
-            print(r, plddts[-1].mean())
-    if os.path.exists("/home/duerr/phd/08_Code/ProteinMPNN"):
-        save_pdb(outs, "/home/duerr/phd/08_Code/ProteinMPNN/out.pdb", LEN)
-    else:
-        save_pdb(outs, "/home/user/app/out.pdb", LEN)
-    return plddts, outs["pae"], LEN
+        paes.append(outs["pae"])
+        if os.path.exists("/home/duerr/phd/08_Code/ProteinMPNN"):
+            save_pdb(outs, f"/home/duerr/phd/08_Code/ProteinMPNN/outputs/out_{i}.pdb", LEN)
+        else:
+            save_pdb(outs, "/home/user/app/out.pdb", LEN)
+    return plddts,paes, LEN
 
 
 if os.path.exists("/home/duerr/phd/08_Code/ProteinMPNN"):
@@ -547,6 +550,8 @@ def update(
             native_score = scores.cpu().data.numpy()
             message = ""
             seq_list = []
+            seq_recovery = []
+            seq_score = []
             for temp in temperatures:
                 for j in range(NUM_BATCHES):
                     randn_2 = torch.randn(chain_M.shape, device=X.device)
@@ -724,6 +729,8 @@ def update(
                                 for i, x in enumerate(not_designed):
                                     if nd_mask[i]:
                                         chain_s += x
+                        seq_recovery.append(seq_rec_print)
+                        seq_score.append(score_print)
                         line = (
                             ">T={}, sample={}, score={}, seq_recovery={}\n{}\n".format(
                                 temp, b_ix, score_print, seq_rec_print, seq
@@ -762,7 +769,7 @@ def update(
     )
 
     fig_tadjusted.update_xaxes(side="top")
-
+    seq_dict = {"seq_list":seq_list, "recovery":seq_recovery, "seq_score":seq_score}
     return (
         message,
         fig,
@@ -771,17 +778,20 @@ def update(
         gr.File.update(value="all_probs_concat.csv", visible=True),
         pdb_path,
         gr.Dropdown.update(choices=seq_list),
-        selected_residues
+        selected_residues,
+        seq_dict
     )
 
 
-def update_AF(startsequence, pdb, num_recycles,selectedResidues):
+def update_AF(seq_dict, pdb, num_recycles,selectedResidues):
 
     # # run alphafold using ray
     # plddts, pae, num_res = run_alphafold(
     #    startsequence, num_recycles
     # )
-    if len(startsequence) > 700:
+    allSeqs = seq_dict['seq_list']
+    lenSeqs = len(allSeqs)
+    if len(allSeqs[0]) > 700:
         return (
             """
             <div class="p-4 mb-4 text-sm text-yellow-700 bg-orange-50 rounded-lg" role="alert">
@@ -791,21 +801,29 @@ def update_AF(startsequence, pdb, num_recycles,selectedResidues):
             plt.figure(),
             plt.figure(),
         )
-    plddts, pae, num_res = ray.get(run_alphafold.remote(startsequence, num_recycles))
-    x = np.arange(10)
+    
+    plddts, paes, num_res = ray.get(run_alphafold.remote(allSeqs, num_recycles))
+
+    sequences = {}
+    for i in range(lenSeqs):
+        rms, input_pdb, aligned_pdb = align_structures(pdb, f"outputs/out_{i}.pdb", num_res,i)
+        sequences[i]={"Seq":i,"RMSD":f"{rms:.2f}","Score":seq_dict['seq_score'][i],"Recovery":seq_dict["recovery"][i],"Mean pLDDT":f"{np.mean(plddts[i]):.4f}"}
+    results=pd.DataFrame.from_dict(sequences, orient="index")
+    print(results)
     plots = []
-    for recycle, plddts_val in enumerate(plddts):
-        if recycle == 0 or recycle == len(plddts) - 1:
-            visible = True
-        else:
-            visible = "legendonly"
+    for index, plddts_val in enumerate(plddts):
+        # if recycle == 0 or recycle == len(plddts) - 1:
+        #     visible = True
+        # else:
+        #     visible = "legendonly"
+        visible = True
         plots.append(
             go.Scatter(
                 x=np.arange(len(plddts_val)),
                 y=plddts_val,
-                hovertemplate="<i>pLDDT</i>: %{y:.2f} <br><i>Residue index:</i> %{x}<br>Recycle "
-                + str(recycle),
-                name=f"Recycle {recycle}",
+                hovertemplate="<i>pLDDT</i>: %{y:.2f} <br><i>Residue index:</i> %{x}<br>Sequence "
+                + str(index),
+                name=f"seq {index}",
                 visible=visible,
             )
         )
@@ -818,15 +836,18 @@ def update_AF(startsequence, pdb, num_recycles,selectedResidues):
         template="simple_white",
         legend=dict(yanchor="bottom", y=0.01, xanchor="left", x=0.99),
     )
-    plt.figure()
-    plt.title("Predicted Aligned Error")
-    Ln = pae.shape[0]
-    plt.imshow(pae, cmap="bwr", vmin=0, vmax=30, extent=(0, Ln, Ln, 0))
-    plt.colorbar()
-    plt.xlabel("Scored residue")
-    plt.ylabel("Aligned residue")
-    plt.savefig("pae_plot.png", dpi=300)
-    plt.close()
+    pae_plots = []
+    for i,pae in enumerate(paes):
+        plt.figure()
+        plt.title(f"Predicted Aligned Error sequence {i}")
+        Ln = pae.shape[0]
+        plt.imshow(pae, cmap="bwr", vmin=0, vmax=30, extent=(0, Ln, Ln, 0))
+        plt.colorbar()
+        plt.xlabel("Scored residue")
+        plt.ylabel("Aligned residue")
+        plt.savefig(f"outputs/pae_plot_{i}.png", dpi=300)
+        plt.close()
+        pae_plots.append(f"outputs/pae_plot_{i}.png")
     # doesnt work (likely because too large)
     # plotAF_pae = px.imshow(
     #     pae,
@@ -837,7 +858,7 @@ def update_AF(startsequence, pdb, num_recycles,selectedResidues):
     # plotAF_pae.write_html("test.html")
     # plotAF_pae.update_layout(title="Predicted Aligned Error", template="simple_white")
 
-    return molecule(pdb, "out.pdb", num_res, selectedResidues), plotAF_plddt, "pae_plot.png"
+    return molecule(input_pdb, aligned_pdb, lenSeqs, num_res, selectedResidues, allSeqs, sequences), plotAF_plddt, pae_plots, results
 
 
 def read_mol(molpath):
@@ -849,11 +870,27 @@ def read_mol(molpath):
     return mol
 
 
-def molecule(pdb, afpdb, num_res, selectedResidues):
+def molecule(input_pdb, aligned_pdb, lenSeqs, num_res, selectedResidues, allSeqs, sequences):
+
+    mol = read_mol("outputs/reference.pdb")
+    options =""
+    pred_mol = "["
+    seqdata = "{"
+    selected = "selected"
+    for i in range(lenSeqs):
+        seqdata+=str(i)+': { "score": '+sequences[i]["Score"]+', "rmsd": '+sequences[i]["RMSD"]+', "recovery": '+sequences[i]["Recovery"]+', "plddt": '+sequences[i]["Mean pLDDT"]+', "seq":"'+allSeqs[i]+'"}'
+        options+=f'<option {selected} value="{i}">sequence {i} </option>' #RMSD {sequences[i]["RMSD"]}, score {sequences[i]["Score"]}, recovery {sequences[i]["Recovery"]} pLDDT {sequences[i]["Mean pLDDT"]}
+        p=f"outputs/out_{i}_aligned.pdb"
+        pred_mol+=f"`{read_mol(p)}`"
+        selected = ""
+        if i!=lenSeqs-1:
+            pred_mol+=","
+            seqdata+=","
+    pred_mol+="]"
+    seqdata+="}"
+
+
 
-    rms, input_pdb, aligned_pdb = align_structures(pdb, afpdb, num_res)
-    mol = read_mol(input_pdb)
-    pred_mol = read_mol(aligned_pdb)
     x = (
         """<!DOCTYPE html>
         <html>
@@ -864,61 +901,74 @@ def molecule(pdb, afpdb, num_res, selectedResidues):
     body{
         font-family:sans-serif
     }
-.mol-container {
-  width: 100%;
-  height: 700px;
-  position: relative;
-}
-.space-x-2 > * + *{
-    margin-left: 0.5rem;
-}
-.p-1{
-    padding:0.5rem;
-}
-.w-4{
-    width:1rem;
-}
-.h-4{
-    height:1rem;
-}
-.mt-4{
-    margin-top:1rem;
-}
-select{
-    background-image:None;
-}
-</style>
-<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
+    .mol-container {
+    width: 100%;
+    height: 700px;
+    position: relative;
+    }
+    .space-x-2 > * + *{
+        margin-left: 0.5rem;
+    }
+    .p-1{
+        padding:0.5rem;
+    }
+    .w-4{
+        width:1rem;
+    }
+    .h-4{
+        height:1rem;
+    }
+    .mt-4{
+        margin-top:1rem;
+    }
+    .mol-container select{
+        background-image:None;
+    }
+    </style>
+    <script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
     </head>
     <body>  
-   
+    <div class="max-w-2xl flex items-center space-x-2 py-3">
+        <label for="seq"
+            class=" text-right whitespace-nowrap block text-base font-medium text-gray-900 dark:text-gray-400">Select
+            a sequence</label>
+        <select id="seq"
+            class="bg-gray-50 border border-gray-300 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block w-full p-2.5 dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500">
+            """+options+"""
+        </select>
+    </div>
+    <div class="font-mono bg-gray-100 py-3 px-2  font-sm rounded">
+        <code>> seq <span id="id"></span>, score <span id="score"></span>, RMSD <span id="seqrmsd"></span>, Recovery
+            <span id="recovery"></span>, pLDDT <span id="plddt"></span></code><br>
+        <p id="seqText" class="max-w-4xl font-xs block" style="word-break: break-all;">
+
+        </p>
+    </div>
     <div id="container" class="mol-container"></div>
-    <div class="flex">
-        <div class="px-4">
+    <div class="flex items-center">
+        <div class="px-4 pt-2">
         <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">
+        <div class="px-4 pt-2">
         <label for="startstructure" class="relative inline-flex items-center mb-4 cursor-pointer ">
             <input  id="startstructure" 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 input structure</span>
           </label>
         </div>
- <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">
+        <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 predicted structure
                   </button>
             </div>       
-<div class="text-sm">
-<div> RMSD AlphaFold vs. native: """
-        + f"{rms:.2f}"
-        + """Å computed using CEAlign on the aligned fragment</div>
-                        </div>
-<div class="text-sm flex items-start">
+            <div class="text-sm">
+            <div> RMSD AlphaFold vs. native: <span id="rmsd"></span> Å computed using CEAlign on the aligned fragment</div>
+                                    </div>
+            <div class="text-sm flex items-start">
                 <div class="w-1/2">
                         
                             <div class="font-medium mt-4 flex items-center space-x-2"><b>AF2 model of redesigned sequence</b></div>
@@ -943,21 +993,56 @@ select{
                         </div>
                     </div>
             <script>
-            let viewer = null;
-            let voldata = null;
-            $(document).ready(function () {
-                let element = $("#container");
-                let config = { backgroundColor: "white" };
-                viewer = $3Dmol.createViewer( element, config );
-                viewer.ui.initiateUI();
-                let data = `"""
+
+              function drawStructures(i, selectedResidues) {
+            $("#rmsd").text(seqs[i]["rmsd"])
+            $("#seqText").text(seqs[i]["seq"])
+            $("#seqrmsd").text(seqs[i]["rmsd"])
+            $("#id").text(i)
+            $("#score").text(seqs[i]["score"])
+            $("#recovery").text(seqs[i]["recovery"])
+            $("#plddt").text(seqs[i]["plddt"])
+
+            viewer = $3Dmol.createViewer(element, config);
+            viewer.addModel(data[i], "pdb");
+            viewer.addModel(pdb, "pdb");
+
+
+
+            viewer.getModel(1).setStyle({}, { cartoon: { colorscheme: { prop: "resi", map: colors } } })
+            viewer.getModel(0).setStyle({}, { cartoon: { colorfunc: colorAlpha } });
+            viewer.zoomTo();
+            viewer.render();
+            viewer.zoom(0.8, 2000);
+            viewer.getModel(0).setHoverable({}, true,
+                function (atom, viewer, event, container) {
+                    if (!atom.label) {
+                        atom.label = viewer.addLabel(atom.resn + atom.resi + " pLDDT=" + atom.b, { position: atom, backgroundColor: "mintcream", fontColor: "black" });
+                    }
+                },
+                function (atom, viewer) {
+                    if (atom.label) {
+                        viewer.removeLabel(atom.label);
+                        delete atom.label;
+                    }
+                }
+            );
+        }
+        let viewer = null;
+        let voldata = null;
+        let element = null;
+        let config = null;
+        let currentIndex = 0;
+            let seqs = """+seqdata+"""
+               let data = """
         + pred_mol
-        + """`  
+        + """  
                 let pdb = `"""
         + mol
         + """`  
-                viewer.addModel( data, "pdb" );
-                viewer.addModel( pdb, "pdb" );
+         var selectedResidues = """+
+                f"{selectedResidues}"
+                +"""
                 //AlphaFold code from https://gist.github.com/piroyon/30d1c1099ad488a7952c3b21a5bebc96
                 let colorAlpha = function (atom) {
                     if (atom.b < 50) {
@@ -970,9 +1055,7 @@ select{
                         return "Blue";
                     }
                 };
-                var selectedResidues = """+
-                f"{selectedResidues}"
-                +"""
+               
                 let colors = {}
                 for (let i=0; i<"""+str(num_res)+""";i++){
                 if (selectedResidues.includes(i)){
@@ -995,24 +1078,12 @@ select{
                                 }
                             }
 
-                viewer.getModel(1).setStyle({},{ cartoon: {colorscheme:{prop:"resi",map:colors} } })
-                viewer.getModel(0).setStyle({}, { cartoon: { colorfunc: colorAlpha } });
-                viewer.zoomTo();
-                viewer.render();
-                viewer.zoom(0.8, 2000);
-                viewer.getModel(0).setHoverable({}, true,
-                    function (atom, viewer, event, container) {
-                        if (!atom.label) {
-                            atom.label = viewer.addLabel(atom.resn+atom.resi+" pLDDT=" + atom.b, { position: atom, backgroundColor: "mintcream", fontColor: "black" });
-                        }
-                    },
-                    function (atom, viewer) {
-                        if (atom.label) {
-                            viewer.removeLabel(atom.label);
-                            delete atom.label;
-                        }
-                    }
-                );
+             $(document).ready(function () {
+                element = $("#container");
+                config = { backgroundColor: "white" };
+                //viewer.ui.initiateUI();
+ 
+                drawStructures(currentIndex, selectedResidues)
                 $("#sidechain").change(function () {
                     if (this.checked) {
                         BB = ["C", "O", "N"]
@@ -1037,7 +1108,12 @@ select{
                         viewer.render()
                     }
                 });
-
+                $("#seq").change(function () {
+                    drawStructures(this.value, selectedResidues)
+                    currentIndex = this.value
+                    $("#sidechain").prop( "checked", false );
+                    $("#startstructure").prop( "checked", true );
+                });
                 $("#startstructure").change(function () {
                     if (this.checked) {
                          $("#sidechain").prop( "checked", false );
@@ -1052,9 +1128,7 @@ select{
                     }
                 });
                 $("#download").click(function () {
-                    download(\""""
-        + aligned_pdb
-        + """\", data);
+                    download("outputs/out_" + currentIndex + "_aligned.pdb", data);
                 })
         });
         function download(filename, text) {
@@ -1070,7 +1144,7 @@ select{
         </body></html>"""
     )
 
-    return f"""<iframe style="width: 800px; height: 1000px" name="result" allow="midi; geolocation; microphone; camera; 
+    return f"""<iframe style="width: 800px; height: 1300px" 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="" 
@@ -1117,7 +1191,7 @@ with proteinMPNN:
                 )
             with gr.Row():
                 num_seqs = gr.Slider(
-                    minimum=1, maximum=50, value=1, step=1, label="Number of sequences"
+                    minimum=1, maximum=15, value=1, step=1, label="Number of sequences"
                 )
                 sampling_temp = gr.Radio(
                     choices=[0.1, 0.15, 0.2, 0.25, 0.3],
@@ -1222,20 +1296,24 @@ with proteinMPNN:
             with gr.Row():
                 with gr.Row():
                     chosen_seq = gr.Dropdown(
-                        choices=[], label="Select a sequence for validation"
+                        choices=[], label="Select a sequence for validation",
+                        visible=False
                     )
                     num_recycles = gr.Dropdown(
                         choices=[0, 1, 3, 5], value=3, label="num Recycles"
                     )
-                btnAF = gr.Button("Run AF2 on sequence")
+                btnAF = gr.Button("Run AlphaFold on all sequences")
             with gr.Row():
                 mol = gr.HTML()
                 with gr.Column():
+                    gr.Markdown("## Metrics")
+                    results = gr.Dataframe(nteractive=False, row_count=(0, 'dynamic'), headers=["Seq","RMSD","Score","Recovery","Mean pLDDT"])
                     plotAF_plddt = gr.Plot(label="pLDDT")
                     # remove maxh80 class from css
-                    plotAF_pae = gr.Image(label="PAE") #gr.Plot(label="PAE")
+                    plotAF_pae = gr.Gallery(label="PAE plots") #gr.Plot(label="PAE")
     tempFile = gr.Variable()
     selectedResidues = gr.Variable()
+    seq_dict = gr.Variable()
     btn.click(
         fn=update,
         inputs=[
@@ -1258,13 +1336,14 @@ with proteinMPNN:
             all_probs,
             tempFile,
             chosen_seq,
-            selectedResidues
+            selectedResidues,
+            seq_dict
         ],
     )
     btnAF.click(
         fn=update_AF,
-        inputs=[chosen_seq, tempFile, num_recycles, selectedResidues],
-        outputs=[mol, plotAF_plddt, plotAF_pae],
+        inputs=[seq_dict, tempFile, num_recycles, selectedResidues],
+        outputs=[mol, plotAF_plddt, plotAF_pae, results],
     )
     examples.click(fn=set_examples, inputs=examples, outputs=examples.components)
     gr.Markdown(

outputs/README.md

@@ -0,0 +1 @@
+Files are only saved here temporarily, they are not visible to the author

packages.txt

@@ -1 +0,0 @@
-pymol