ctrl click pockets network and default isolevel value

ippisite/ippidb/management/commands/update_mrc_files.py

@@ -18,6 +18,17 @@ def dir_path(string):
         raise NotADirectoryError(string)
 
 
+def isolevel_float(arg):
+    """ Type function for argparse - a float within some predefined bounds """
+    try:
+        f = float(arg)
+    except ValueError:
+        raise argparse.ArgumentTypeError("Must be a floating point number")
+    if f < 0 or f > 1.0:
+        raise argparse.ArgumentTypeError("Argument must be < 1.0 and > 0")
+    return f
+
+
 class Command(AppCommand):
     """
     Command to update mrc files
@@ -26,7 +37,12 @@ class Command(AppCommand):
     help = "liste all mrc files in a directory and update files in the database"
 
     def __init__(
-        self, stdout=None, stderr=None, no_color=False, force_color=False, task=None,
+        self,
+        stdout=None,
+        stderr=None,
+        no_color=False,
+        force_color=False,
+        task=None,
     ):
         super(Command, self).__init__(
             stdout=stdout, stderr=stderr, no_color=no_color, force_color=force_color
@@ -38,7 +54,10 @@ class Command(AppCommand):
 
     def add_arguments(self, parser):
         parser.add_argument(
-            "-mp", "--mrcpath", type=dir_path, help="root directory with all mrc files",
+            "-mp",
+            "--mrcpath",
+            type=dir_path,
+            help="root directory with all mrc files",
         )
         parser.add_argument(
             "-pa",
@@ -61,6 +80,14 @@ class Command(AppCommand):
             dest="label",
             help="label for files, used as label in the interface",
         )
+        parser.add_argument(
+            "-di",
+            "--default_isolevel",
+            dest="default_isolevel",
+            help="isolevel default value",
+            default=0.7,
+            type=isolevel_float,
+        )
 
     def handle(self, *args, **options):
         """
@@ -75,7 +102,9 @@ class Command(AppCommand):
         if typefile == "druggability":
             storage_path = Chain.mrc_file.field.storage.path("content/mrc_files")
         else:
-            storage_path = InteractFile.interact_file.field.storage.path("content/interact_files")
+            storage_path = InteractFile.interact_file.field.storage.path(
+                "content/interact_files"
+            )
         if not os.path.exists(storage_path):
             os.makedirs(storage_path)
         list_files = glob.glob(os.path.join(mrcpath, pattern))
@@ -108,13 +137,18 @@ class Command(AppCommand):
                     with open(data, "rb") as f:
                         dbchains[0].mrc_file.delete()
                         dbchains[0].mrc_file.save(os.path.basename(data), File(f))
+                        dbchains[0].default_isolevel = options["default_isolevel"]
+                        dbchains[0].save()
                 else:
                     interactfile, created = InteractFile.objects.get_or_create(
-                        chain=dbchains[0], label=label
+                        chain=dbchains[0],
+                        label=label,
                     )
                     with open(data, "rb") as f:
                         interactfile.interact_file.delete()
                         interactfile.interact_file.save(os.path.basename(data), File(f))
+                    interactfile.default_isolevel=options["default_isolevel"]
+                    interactfile.save()
                 self.stdout.write(
                     self.style.SUCCESS(
                         "File mrc {}, have been saved in Chain, pdb: {}, chain: {}".format(
@@ -126,7 +160,8 @@ class Command(AppCommand):
                 self.stdout.write(
                     self.style.WARNING(
                         "WARNING: Chain, pdb: {}, chain: {} doesn't exist".format(
-                            pdb, chain,
+                            pdb,
+                            chain,
                         )
                     )
                 )

ippisite/ippidb/migrations/0068_auto_20210310_1052.py

+# Generated by Django 2.2.1 on 2021-03-10 10:52
+
+from django.db import migrations, models
+
+
+def init_isolevel(apps, schema_editor):
+    Chain = apps.get_model("ippidb", "Chain")
+    InteractFile = apps.get_model("ippidb", "InteractFile")
+    Chains = Chain.objects.all()
+    if Chains:
+        for Chain in Chains:
+            Chain.default_isolevel = 0.5
+            Chain.save()
+    InteractFiles = InteractFile.objects.all()
+    if InteractFiles:
+        for InteractFile in InteractFiles:
+            if InteractFile.label == "all":
+                InteractFile.default_isolevel = 0.7
+                InteractFile.save()
+            if InteractFile.label == "hydrophobic":
+                InteractFile.default_isolevel = 0.3
+                InteractFile.save()
+            if InteractFile.label == "hbond donor-acceptor":
+                InteractFile.default_isolevel = 0.3
+                InteractFile.save()
+            if InteractFile.label == "negative":
+                InteractFile.default_isolevel = 0.08
+                InteractFile.save()
+            if InteractFile.label == "positive":
+                InteractFile.default_isolevel = 0.05
+                InteractFile.save()
+            if InteractFile.label == "backbone":
+                InteractFile.default_isolevel = 0.18
+                InteractFile.save()
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("ippidb", "0067_metainformation_normalize_factor"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="chain",
+            name="default_isolevel",
+            field=models.FloatField(default=0.7, verbose_name="Default isolevel value"),
+        ),
+        migrations.AddField(
+            model_name="interactfile",
+            name="default_isolevel",
+            field=models.FloatField(default=0.7, verbose_name="Default isolevel value"),
+        ),
+        migrations.RunPython(init_isolevel, reverse_code=migrations.RunPython.noop),
+    ]

ippisite/ippidb/models/targetcentric.py

@@ -132,6 +132,9 @@ class Chain(models.Model):
         verbose_name="pdb file content with only one chain", default="no pdb file"
     )
     mrc_file = models.FileField(upload_to=content, blank=True)
+    default_isolevel = models.FloatField(
+        default=0.7, verbose_name="Default isolevel value"
+    )
 
     class Meta:
         unique_together = ("pdb", "pdb_chain_id")
@@ -156,6 +159,9 @@ class InteractFile(models.Model):
     chain = models.ForeignKey(Chain, on_delete=models.CASCADE)
     label = models.CharField(max_length=250, blank=False, null=False)
     interact_file = models.FileField(upload_to=contentinteract, blank=True)
+    default_isolevel = models.FloatField(
+        default=0.7, verbose_name="Default isolevel value"
+    )
 
     def __unicode__(self):
         return "{}".format(self.interact_file)

ippisite/ippidb/serializer.py

@@ -57,7 +57,7 @@ class ChainDistanceSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = Chain
-        fields = ("id", "pdb_chain_id", "protein", "pdb")
+        fields = ("id", "pdb_chain_id", "protein", "pdb", "default_isolevel")
 
 
 class PartnerDistanceSerializer(serializers.ModelSerializer):
@@ -121,6 +121,7 @@ class ChainSerializer(serializers.ModelSerializer):
             "cavity_set",
             "partner_set",
             "mrc_file",
+            "default_isolevel",
             "interactfile_set",
         )
 

ippisite/ippidb/static/js/targetcentric.js

@@ -448,13 +448,13 @@ function loadNGL(url, callback){
                                                                                         opaqueBack: false,
                                                                                         smooth: 2,
                                                                                         color: filecolor(indexchain, indexfile),
-                                                                                        isolevel: 0.7,
+                                                                                        isolevel: interactfile.default_isolevel,
                                                                                         isolevelType: 'value',});
                                     });
                                     var divvalueslider = createElement("div", {}, {}, "",  {'id': baseName(interactfile.interact_file) + "_interact_isolevel"});
-                                    divvalueslider.innerHTML = 'current value for ' + interactfile.label + ': 0.7';
+                                    divvalueslider.innerHTML = 'current value for ' + interactfile.label + ': ' + interactfile.default_isolevel;
                                     divchain.appendChild(divvalueslider);
-                                    var isolevel = createElement("input", {type: "range", value: 70, min: 0, max: 100, step: 1},
+                                    var isolevel = createElement("input", {type: "range", value: interactfile.default_isolevel*100, min: 0, max: 100, step: 1},
                                                                  {},"form-control-range",{'id': baseName(interactfile.interact_file) + "_interact_isolevelslide"});
                                     isolevel.oninput = function(e) {
                                         $('#' + baseName(interactfile.interact_file) + "_interact_isolevel").html('current value for ' + interactfile.label + ': ' + parseFloat(e.target.value)/100);
@@ -485,7 +485,7 @@ function loadNGL(url, callback){
                                                                             opaqueBack: false,
                                                                             smooth: 2,
                                                                             color: filecolor(indexchain, -1),
-                                                                            isolevel: 0.7,
+                                                                            isolevel: chain.default_isolevel,
                                                                             isolevelType: 'value',});
                         });
                     
@@ -493,11 +493,11 @@ function loadNGL(url, callback){
                     var labelslider = createElement("label", {}, {}, "", {'for':'isolevel' + chain.pdb_chain_id});
                     labelslider.innerHTML = 'Adjust predictive surface druggable on chain ' + chain.pdb_chain_id;
                     var divvalueslider = createElement("div", {}, {}, "",  {'id': 'valueisolevel' + chain.pdb_chain_id});
-                    divvalueslider.innerHTML = 'current value: 0.7'
+                    divvalueslider.innerHTML = 'current value: '+ chain.default_isolevel
                     divchainmrc.appendChild(labelslider);
                     divchainmrc.appendChild(divvalueslider);
                     var isolevel = createElement("input", {
-                        type: "range", value: 70, min: 0, max: 100, step: 1
+                        type: "range", value: chain.default_isolevel*100, min: 0, max: 100, step: 1
                     }, {},"form-control-range",{'id':'isolevel' + chain.pdb_chain_id});
                     isolevel.oninput = function(e) {
                         $('#valueisolevel' + chain.pdb_chain_id).html('current value: ' + parseFloat(e.target.value)/100);

ippisite/ippidb/static/js/targetcentrict_networks.js

@@ -71,6 +71,9 @@ var node_trace = function(nodes, edges) {
     return [trace_edges, trace_PL, trace_HD, dict_nodes, [size_PL, size_HD]]
 };
 
+var pathurl = window.location.pathname.split( '/' );
+pathurl.pop();
+var base_url = window.location.origin + pathurl.join('/')
 
 var build_trace = function(nodes, edges) {
     traces = node_trace(nodes, edges);
@@ -99,26 +102,34 @@ $.ajax({
     Plotly.newPlot('myDiv', [data[0], data[1], data[2]], layout, {scrollZoom: true});
     $(".loader").remove();
     ippidb_plot.on('plotly_click', function(datapoints){
-      var curvenumber = datapoints.points[0].curveNumber - 1;
-      var pointnumber = datapoints.points[0].pointNumber;
-      var colors = [repeatElement("#4e79a7", connect_ippidb[0].length), 
-              repeatElement("#de425b", connect_ippidb[1].length)];
-      var opacity = [repeatElement(0.2, connect_ippidb[0].length), 
-              repeatElement(0.2, connect_ippidb[1].length)];
-      colors[curvenumber][pointnumber] = '#488f31';
-      opacity[curvenumber][pointnumber] = 1;
-      for (var i=0; i < connect_ippidb[curvenumber][pointnumber].length; i++){
-          var curvenumber2 = connect_ippidb[curvenumber][pointnumber][i][0];
-          var pointnumber2 = connect_ippidb[curvenumber][pointnumber][i][1];
-          colors[curvenumber2][pointnumber2] = '#488f31';
-          opacity[curvenumber2][pointnumber2] = 1;
-      }
-      var update_PL = {'marker':{color: colors[0], size: data[4][0], line: {width: 1,
-                                                                     color: 'DarkSlateGrey'}, opacity: opacity[0], symbol: 1}};
-      var update_HD = {'marker':{color: colors[1], size: data[4][1], line: {width: 1,
-                                                                     color: 'DarkSlateGrey'}, opacity: opacity[1]}};
-      Plotly.restyle('myDiv', update_PL, 1);
-      Plotly.restyle('myDiv', update_HD, 2);
+      if (datapoints.event.button == 0) {
+        if (datapoints.event.ctrlKey) {
+          window.open(base_url + "/?pdbsearch=" + datapoints.points[0].text.split("-")[0], '_blank');
+        } else {
+          var curvenumber = datapoints.points[0].curveNumber - 1;
+          var pointnumber = datapoints.points[0].pointNumber;
+          var colors = [repeatElement("#4e79a7", connect_ippidb[0].length), 
+                  repeatElement("#de425b", connect_ippidb[1].length)];
+          var opacity = [repeatElement(0.2, connect_ippidb[0].length), 
+                  repeatElement(0.2, connect_ippidb[1].length)];
+          colors[curvenumber][pointnumber] = '#488f31';
+          opacity[curvenumber][pointnumber] = 1;
+          for (var i=0; i < connect_ippidb[curvenumber][pointnumber].length; i++){
+              var curvenumber2 = connect_ippidb[curvenumber][pointnumber][i][0];
+              var pointnumber2 = connect_ippidb[curvenumber][pointnumber][i][1];
+              colors[curvenumber2][pointnumber2] = '#488f31';
+              opacity[curvenumber2][pointnumber2] = 1;
+          }
+          var update_PL = {'marker':{color: colors[0], size: data[4][0], line: {width: 1,
+                                                                         color: 'DarkSlateGrey'}, opacity: opacity[0], symbol: 1}};
+          var update_HD = {'marker':{color: colors[1], size: data[4][1], line: {width: 1,
+                                                                         color: 'DarkSlateGrey'}, opacity: opacity[1]}};
+          Plotly.restyle('myDiv', update_PL, 1);
+          Plotly.restyle('myDiv', update_HD, 2);
+        };
+      };
+      
+      
     });
 
     $('.search-button').click(function() {

ippisite/ippidb/templates/targetcentric_networks.html

@@ -35,6 +35,10 @@
               <span>Vicinity network of the PPI pocketome: Displays pockets having a pocket similarity index (PSI) with at least one other pocket above 0.65 
                     <br><br>Vicinity network of PPI pockets (non-redundant): Same as above but by only considering similar pockets within proteins having a different Uniprot ID. 
                      The purpose is this network is to highlight unforeseen vicinities within the PPI pocketome.
+                     <br> <br>
+                     mouse left-click pocket to show closest pockets
+                     <br>
+                     mouse left-click + ctrl key on pocket to load details on protein (pockets, 3d structure, pockets descriptors...)
               </span>
             </a>
           </p>