[Fix] AppDomain Leftovers (#161)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#161

epdb/management/commands/localize_urls.py

@@ -1,8 +1,10 @@
 from django.apps import apps
 from django.core.management.base import BaseCommand
 
-from django.db.models import F, Value
+from django.db.models import F, Value, TextField, JSONField
-from django.db.models.functions import Replace
+from django.db.models.functions import Replace, Cast
+
+from epdb.models import EnviPathModel
 
 
 class Command(BaseCommand):
@@ -49,3 +51,14 @@ class Command(BaseCommand):
             obj_cls.objects.update(
                 url=Replace(F("url"), Value(options["old"]), Value(options["new"]))
             )
+            if issubclass(obj_cls, EnviPathModel):
+                obj_cls.objects.update(
+                    kv=Cast(
+                        Replace(
+                            Cast(F("kv"), output_field=TextField()),
+                            Value(options["old"]),
+                            Value(options["new"]),
+                        ),
+                        output_field=JSONField(),
+                    )
+                )

epdb/views.py

@@ -1454,12 +1454,20 @@ def package_rule(request, package_uuid, rule_uuid):
                 logger.info(
                     f"Rule {current_rule.uuid} returned multiple product sets on {smiles}, picking the first one."
                 )
-
+            # Some Rules are touching unrelated areas which might result in ~ indicating
-            smirks = f"{stand_smiles}>>{'.'.join(sorted(res[0]))}"
+            # any bond (-, =, #). For drawing we need a concrete bond. -> use single bond
+            product_smiles = [x.replace("~", "-") for x in res[0]]
+            smirks = f"{stand_smiles}>>{'.'.join(sorted(product_smiles))}"
             # Usually the functional groups are a mapping of fg -> count
             # As we are doing it on the fly here fake a high count to ensure that its properly highlighted
-            educt_functional_groups = {x: 1000 for x in current_rule.reactants_smarts}
+
-            product_functional_groups = {x: 1000 for x in current_rule.products_smarts}
+            if isinstance(current_rule, SimpleAmbitRule):
+                educt_functional_groups = {current_rule.reactants_smarts: 1000}
+                product_functional_groups = {current_rule.products_smarts: 1000}
+            else:
+                educt_functional_groups = {x: 1000 for x in current_rule.reactants_smarts}
+                product_functional_groups = {x: 1000 for x in current_rule.products_smarts}
+
             return HttpResponse(
                 IndigoUtils.smirks_to_svg(
                     smirks,
@@ -1993,9 +2001,42 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid):
 
     if request.method == "GET":
         is_image_request = request.GET.get("image")
+        is_highlight_request = request.GET.get("highlight", False)
+        is_highlight_reactivity = request.GET.get("highlightReactivity", False)
         if is_image_request:
             if is_image_request == "svg":
-                svg_data = current_node.as_svg
+                # TODO optimize this chain
+                if is_highlight_request:
+                    # User functional groups covered by the model training data
+                    fgs = {}
+                    if current_pathway.setting:
+                        if current_pathway.setting.model:
+                            if current_pathway.setting.model.app_domain:
+                                fgs = current_pathway.setting.model.app_domain.functional_groups
+
+                    svg_data = IndigoUtils.mol_to_svg(
+                        current_node.default_node_label.smiles, functional_groups=fgs
+                    )
+                elif is_highlight_reactivity:
+                    # Use reactant smarts to show all reaction sites
+                    # set a high count to obtain a strong color
+                    ad_data = current_node.get_app_domain_assessment_data()
+                    fgs = {}
+                    for t in ad_data.get("assessment", {}).get("transformations", []):
+                        r = Rule.objects.get(url=t["rule"]["url"])
+
+                        if isinstance(r, SimpleAmbitRule):
+                            fgs[r.reactants_smarts] = 1000
+                        else:
+                            for sr in r.srs:
+                                fgs[sr.reactants_smarts] = 1000
+
+                    svg_data = IndigoUtils.mol_to_svg(
+                        current_node.default_node_label.smiles, functional_groups=fgs
+                    )
+                else:
+                    svg_data = current_node.as_svg
+
                 return HttpResponse(svg_data, content_type="image/svg+xml")
 
         context = get_base_context(request)

static/js/pps.js

@@ -646,8 +646,8 @@ function handleAssessmentResponse(depict_url, data) {
     var reactivityCentersImgSrc = null;
 
     if (data['assessment']['node'] !== undefined) {
-        functionalGroupsImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "'>";
+        functionalGroupsImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "&highlight=true'>";
-        reactivityCentersImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "'>"
+        reactivityCentersImgSrc = "<img width='400' src='" + data['assessment']['node']['image'] + "&highlightReactivity=true'>"
     } else {
         functionalGroupsImgSrc = "<img width='400' src=\"" + depict_url + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "\">";
         reactivityCentersImgSrc = "<img width='400' src=\"" + depict_url + "?smiles=" + encodeURIComponent(data['assessment']['smiles']) + "\">"
@@ -784,4 +784,4 @@ function handleAssessmentResponse(depict_url, data) {
 
     $("#appDomainAssessmentResultTable").append(res);
 
-}
+}

utilities/chem.py

@@ -729,6 +729,7 @@ class IndigoUtils(object):
         height: int = 0,
         educt_functional_groups: Dict[str, int] = None,
         product_functional_groups: Dict[str, int] = None,
+        debug: bool = False,
     ):
         if educt_functional_groups is None:
             educt_functional_groups = {}
@@ -739,6 +740,11 @@ class IndigoUtils(object):
         i = Indigo()
         renderer = IndigoRenderer(i)
 
+        if debug:
+            i.setOption("render-atom-ids-visible", True)
+            i.setOption("render-bond-ids-visible", False)
+            i.setOption("render-atom-bond-ids-from-one", True)
+
         i.setOption("render-output-format", "svg")
         i.setOption("render-coloring", True)
         i.setOption("render-image-size", width, height)