[Feature] Engineer Pathway (#256)

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#256

epdb/legacy_api.py

@@ -1815,7 +1815,7 @@ def get_model(request, package_uuid, model_uuid, c: Query[Classify]):
 
             from epdb.tasks import dispatch_eager, predict_simple
 
-            pred_res = dispatch_eager(request.user, predict_simple, mod.pk, stand_smiles)
+            _, pred_res = dispatch_eager(request.user, predict_simple, mod.pk, stand_smiles)
 
             result = []
 

epdb/logic.py

@@ -1398,6 +1398,9 @@ class SEdge(object):
         self.rule = rule
         self.probability = probability
 
+    def product_smiles(self):
+        return [p.smiles for p in self.products]
+
     def __hash__(self):
         full_hash = 0
 
@@ -1630,6 +1633,14 @@ class SPathway(object):
             # call save to update the internal modified field
             self.persist.save()
 
+    def get_edge_for_educt_smiles(self, smiles: str) -> List[SEdge]:
+        res = []
+        for e in self.edges:
+            for n in e.educts:
+                if n.smiles == smiles:
+                    res.append(e)
+        return res
+
     def _sync_to_pathway(self) -> None:
         logger.info("Updating Pathway with SPathway")
 

epdb/models.py

@@ -754,6 +754,30 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
 
     @property
     def normalized_structure(self) -> "CompoundStructure":
+        if not CompoundStructure.objects.filter(compound=self, normalized_structure=True).exists():
+            num_structs = self.structures.count()
+            stand_smiles = set()
+            for structure in self.structures.all():
+                stand_smiles.add(FormatConverter.standardize(structure.smiles))
+
+            if len(stand_smiles) != 1:
+                logger.debug(
+                    f"#Structures: {num_structs} - #Standardized SMILES: {len(stand_smiles)}"
+                )
+                logger.debug(f"Couldn't infer normalized structure for {self.name} - {self.url}")
+                raise ValueError(
+                    f"Couldn't find nor infer normalized structure for {self.name} ({self.url})"
+                )
+            else:
+                cs = CompoundStructure.create(
+                    self,
+                    stand_smiles.pop(),
+                    name="Normalized structure of {}".format(self.name),
+                    description="{} (in its normalized form)".format(self.description),
+                    normalized_structure=True,
+                )
+                return cs
+
         return CompoundStructure.objects.get(compound=self, normalized_structure=True)
 
     def _url(self):
@@ -901,57 +925,121 @@ class Compound(EnviPathModel, AliasMixin, ScenarioMixin, ChemicalIdentifierMixin
         if self in mapping:
             return mapping[self]
 
-        new_compound = Compound.objects.create(
-            package=target,
-            name=self.name,
-            description=self.description,
-            kv=self.kv.copy() if self.kv else {},
-        )
-        mapping[self] = new_compound
+        default_structure_smiles = self.default_structure.smiles
+        normalized_structure_smiles = self.normalized_structure.smiles
 
-        # Copy compound structures
-        for structure in self.structures.all():
-            if structure not in mapping:
-                new_structure = CompoundStructure.objects.create(
-                    compound=new_compound,
-                    smiles=structure.smiles,
-                    canonical_smiles=structure.canonical_smiles,
-                    inchikey=structure.inchikey,
-                    normalized_structure=structure.normalized_structure,
-                    name=structure.name,
-                    description=structure.description,
-                    kv=structure.kv.copy() if structure.kv else {},
-                )
-                mapping[structure] = new_structure
+        existing_compound = None
+        existing_normalized_compound = None
 
-                # Copy external identifiers for structure
-                for ext_id in structure.external_identifiers.all():
-                    ExternalIdentifier.objects.create(
-                        content_object=new_structure,
-                        database=ext_id.database,
-                        identifier_value=ext_id.identifier_value,
-                        url=ext_id.url,
-                        is_primary=ext_id.is_primary,
+        # Dedup check - Check if we find a direct match for a given SMILES
+        if CompoundStructure.objects.filter(
+            smiles=default_structure_smiles, compound__package=target
+        ).exists():
+            existing_compound = CompoundStructure.objects.get(
+                smiles=default_structure_smiles, compound__package=target
+            ).compound
+
+        # Check if we can find the standardized one
+        if CompoundStructure.objects.filter(
+            smiles=normalized_structure_smiles, compound__package=target
+        ).exists():
+            existing_normalized_compound = CompoundStructure.objects.get(
+                smiles=normalized_structure_smiles, compound__package=target
+            ).compound
+
+        if any([existing_compound, existing_normalized_compound]):
+            if existing_normalized_compound and existing_compound:
+                # We only have to set the mapping
+                mapping[self] = existing_compound
+                for structure in self.structures.all():
+                    if structure not in mapping:
+                        mapping[structure] = existing_compound.structures.get(
+                            smiles=structure.smiles
+                        )
+
+                return existing_compound
+
+            elif existing_normalized_compound:
+                mapping[self] = existing_normalized_compound
+
+                # Merge the structure into the existing compound
+                for structure in self.structures.all():
+                    if existing_normalized_compound.structures.filter(
+                        smiles=structure.smiles
+                    ).exists():
+                        continue
+
+                    # Create a new Structure
+                    cs = CompoundStructure.create(
+                        existing_normalized_compound,
+                        structure.smiles,
+                        name=structure.name,
+                        description=structure.description,
+                        normalized_structure=structure.normalized_structure,
                     )
 
-        if self.default_structure:
-            new_compound.default_structure = mapping.get(self.default_structure)
-            new_compound.save()
+                    mapping[structure] = cs
 
-        for a in self.aliases:
-            new_compound.add_alias(a)
-            new_compound.save()
+                    return existing_normalized_compound
 
-        # Copy external identifiers for compound
-        for ext_id in self.external_identifiers.all():
-            ExternalIdentifier.objects.create(
-                content_object=new_compound,
-                database=ext_id.database,
-                identifier_value=ext_id.identifier_value,
-                url=ext_id.url,
-                is_primary=ext_id.is_primary,
+            else:
+                raise ValueError(
+                    f"Found a CompoundStructure for {default_structure_smiles} but not for {normalized_structure_smiles} in target package {target.name}"
+                )
+        else:
+            # Here we can safely use Compound.objects.create as we won't end up in a duplicate
+            new_compound = Compound.objects.create(
+                package=target,
+                name=self.name,
+                description=self.description,
+                kv=self.kv.copy() if self.kv else {},
             )
 
+            mapping[self] = new_compound
+
+            # Copy underlying structures
+            for structure in self.structures.all():
+                if structure not in mapping:
+                    new_structure = CompoundStructure.objects.create(
+                        compound=new_compound,
+                        smiles=structure.smiles,
+                        canonical_smiles=structure.canonical_smiles,
+                        inchikey=structure.inchikey,
+                        normalized_structure=structure.normalized_structure,
+                        name=structure.name,
+                        description=structure.description,
+                        kv=structure.kv.copy() if structure.kv else {},
+                    )
+                    mapping[structure] = new_structure
+
+                    # Copy external identifiers for structure
+                    for ext_id in structure.external_identifiers.all():
+                        ExternalIdentifier.objects.create(
+                            content_object=new_structure,
+                            database=ext_id.database,
+                            identifier_value=ext_id.identifier_value,
+                            url=ext_id.url,
+                            is_primary=ext_id.is_primary,
+                        )
+
+            if self.default_structure:
+                new_compound.default_structure = mapping.get(self.default_structure)
+                new_compound.save()
+
+            for a in self.aliases:
+                new_compound.add_alias(a)
+                new_compound.save()
+
+            # Copy external identifiers for compound
+            for ext_id in self.external_identifiers.all():
+                ExternalIdentifier.objects.create(
+                    content_object=new_compound,
+                    database=ext_id.database,
+                    identifier_value=ext_id.identifier_value,
+                    url=ext_id.url,
+                    is_primary=ext_id.is_primary,
+                )
+
         return new_compound
 
     class Meta:
@@ -1112,34 +1200,44 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
         rule_type = type(self)
 
         if rule_type == SimpleAmbitRule:
-            new_rule = SimpleAmbitRule.objects.create(
+            new_rule = SimpleAmbitRule.create(
                 package=target,
                 name=self.name,
                 description=self.description,
                 smirks=self.smirks,
                 reactant_filter_smarts=self.reactant_filter_smarts,
                 product_filter_smarts=self.product_filter_smarts,
-                kv=self.kv.copy() if self.kv else {},
             )
+
+            if self.kv:
+                new_rule.kv.update(**self.kv)
+                new_rule.save()
+
         elif rule_type == SimpleRDKitRule:
-            new_rule = SimpleRDKitRule.objects.create(
+            new_rule = SimpleRDKitRule.create(
                 package=target,
                 name=self.name,
                 description=self.description,
                 reaction_smarts=self.reaction_smarts,
-                kv=self.kv.copy() if self.kv else {},
             )
+
+            if self.kv:
+                new_rule.kv.update(**self.kv)
+                new_rule.save()
+
         elif rule_type == ParallelRule:
-            new_rule = ParallelRule.objects.create(
-                package=target,
-                name=self.name,
-                description=self.description,
-                kv=self.kv.copy() if self.kv else {},
-            )
-            # Copy simple rules relationships
+            new_srs = []
             for simple_rule in self.simple_rules.all():
                 copied_simple_rule = simple_rule.copy(target, mapping)
-                new_rule.simple_rules.add(copied_simple_rule)
+                new_srs.append(copied_simple_rule)
+
+            new_rule = ParallelRule.create(
+                package=target,
+                simple_rules=new_srs,
+                name=self.name,
+                description=self.description,
+            )
+
         elif rule_type == SequentialRule:
             raise ValueError("SequentialRule copy not implemented!")
         else:
@@ -1343,6 +1441,20 @@ class ParallelRule(Rule):
                     f"Simple rule {sr.uuid} does not belong to package {package.uuid}!"
                 )
 
+        # Deduplication check
+        query = ParallelRule.objects.annotate(
+            srs_count=Count("simple_rules", filter=Q(simple_rules__in=simple_rules), distinct=True)
+        )
+
+        existing_rule_qs = query.filter(
+            srs_count=len(simple_rules),
+        )
+
+        if existing_rule_qs.exists():
+            if existing_rule_qs.count() > 1:
+                logger.error(f"Found more than one reaction for given input! {existing_rule_qs}")
+            return existing_rule_qs.first()
+
         r = ParallelRule()
         r.package = package
 
@@ -1524,31 +1636,44 @@ class Reaction(EnviPathModel, AliasMixin, ScenarioMixin, ReactionIdentifierMixin
         if self in mapping:
             return mapping[self]
 
-        # Create new reaction
-        new_reaction = Reaction.objects.create(
-            package=target,
-            name=self.name,
-            description=self.description,
-            multi_step=self.multi_step,
-            medline_references=self.medline_references,
-            kv=self.kv.copy() if self.kv else {},
-        )
-        mapping[self] = new_reaction
+        copied_reaction_educts = []
+        copied_reaction_products = []
+        copied_reaction_rules = []
 
         # Copy educts (reactant compounds)
         for educt in self.educts.all():
             copied_educt = educt.copy(target, mapping)
-            new_reaction.educts.add(copied_educt)
+            copied_reaction_educts.append(copied_educt)
 
         # Copy products
         for product in self.products.all():
             copied_product = product.copy(target, mapping)
-            new_reaction.products.add(copied_product)
+            copied_reaction_products.append(copied_product)
 
         # Copy rules
         for rule in self.rules.all():
             copied_rule = rule.copy(target, mapping)
-            new_reaction.rules.add(copied_rule)
+            copied_reaction_rules.append(copied_rule)
+
+        new_reaction = Reaction.create(
+            package=target,
+            name=self.name,
+            description=self.description,
+            educts=copied_reaction_educts,
+            products=copied_reaction_products,
+            rules=copied_reaction_rules,
+            multi_step=self.multi_step,
+        )
+
+        if self.medline_references:
+            new_reaction.medline_references = self.medline_references
+            new_reaction.save()
+
+        if self.kv:
+            new_reaction.kv = self.kv
+            new_reaction.save()
+
+        mapping[self] = new_reaction
 
         # Copy external identifiers
         for ext_id in self.external_identifiers.all():
@@ -1666,14 +1791,12 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
         while len(queue):
             current = queue.pop()
             processed.add(current)
-
             nodes.append(current.d3_json())
 
-            for e in self.edges:
-                if current in e.start_nodes.all():
-                    for prod in e.end_nodes.all():
-                        if prod not in queue and prod not in processed:
-                            queue.append(prod)
+            for e in self.edges.filter(start_nodes=current).distinct():
+                for prod in e.end_nodes.all():
+                    if prod not in queue and prod not in processed:
+                        queue.append(prod)
 
         # We shouldn't lose or make up nodes...
         assert len(nodes) == len(self.nodes)
@@ -1838,6 +1961,8 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
             return mapping[self]
 
         # Start copying the pathway
+        # Its safe to use .objects.create here as Pathways itself aren't
+        # deduplicated
         new_pathway = Pathway.objects.create(
             package=target,
             name=self.name,
@@ -1975,6 +2100,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
                 else None,
                 "uncovered_functional_groups": False,
             },
+            "is_engineered_intermediate": self.kv.get("is_engineered_intermediate", False),
         }
 
     @staticmethod
@@ -3762,23 +3888,29 @@ class JobLog(TimeStampedModel):
     done_at = models.DateTimeField(null=True, blank=True, default=None)
     task_result = models.TextField(null=True, blank=True, default=None)
 
+    TERMINAL_STATES = [
+        "SUCCESS",
+        "FAILURE",
+        "REVOKED",
+        "IGNORED",
+    ]
+
+    def is_in_terminal_state(self):
+        return self.status in self.TERMINAL_STATES
+
     def check_for_update(self):
+        if self.is_in_terminal_state():
+            return
+
         async_res = self.get_result()
         new_status = async_res.state
 
-        TERMINAL_STATES = [
-            "SUCCESS",
-            "FAILURE",
-            "REVOKED",
-            "IGNORED",
-        ]
-
-        if new_status != self.status and new_status in TERMINAL_STATES:
+        if new_status != self.status and new_status in self.TERMINAL_STATES:
             self.status = new_status
             self.done_at = async_res.date_done
 
             if new_status == "SUCCESS":
-                self.task_result = async_res.result
+                self.task_result = str(async_res.result) if async_res.result else None
 
             self.save()
 
@@ -3789,3 +3921,13 @@ class JobLog(TimeStampedModel):
         from celery.result import AsyncResult
 
         return AsyncResult(str(self.task_id))
+
+    def parsed_result(self):
+        if not self.is_in_terminal_state() or self.task_result is None:
+            return None
+
+        import ast
+
+        if self.job_name == "engineer_pathways":
+            return ast.literal_eval(self.task_result)
+        return self.task_result

epdb/tasks.py

@@ -36,7 +36,7 @@ def dispatch_eager(user: "User", job: Callable, *args, **kwargs):
         log.task_result = str(x) if x else None
         log.save()
 
-        return x
+        return log, x
     except Exception as e:
         logger.exception(e)
         raise e
@@ -52,7 +52,7 @@ def dispatch(user: "User", job: Callable, *args, **kwargs):
         log.status = "INITIAL"
         log.save()
 
-        return x.result
+        return log
     except Exception as e:
         logger.exception(e)
         raise e
@@ -175,6 +175,7 @@ def predict(
 
     except Exception as e:
         pw.kv.update({"status": "failed"})
+        pw.kv.update(**{"error": str(e)})
         pw.save()
 
         if JobLog.objects.filter(task_id=self.request.id).exists():
@@ -284,3 +285,71 @@ def identify_missing_rules(
     buffer.seek(0)
 
     return buffer.getvalue()
+
+
+@shared_task(bind=True, queue="background")
+def engineer_pathways(self, pw_pks: List[int], setting_pk: int, target_package_pk: int):
+    from utilities.misc import PathwayUtils
+
+    setting = Setting.objects.get(pk=setting_pk)
+    # Temporarily set model_threshold to 0.0 to keep all tps
+    setting.model_threshold = 0.0
+
+    target = Package.objects.get(pk=target_package_pk)
+
+    intermediate_pathways = []
+    predicted_pathways = []
+
+    for pw in Pathway.objects.filter(pk__in=pw_pks):
+        pu = PathwayUtils(pw)
+
+        eng_pw, node_to_snode_mapping, intermediates = pu.engineer(setting)
+
+        # If we've found intermediates, do the following
+        # - Get a copy of the original pathway and add intermediates
+        # - Store the predicted pathway for further investigation
+        if len(intermediates):
+            copy_mapping = {}
+            copied_pw = pw.copy(target, copy_mapping)
+            copied_pw.name = f"{copied_pw.name} (Engineered)"
+            copied_pw.description = f"The original Pathway can be found here: {pw.url}"
+            copied_pw.save()
+
+            for inter in intermediates:
+                start = copy_mapping[inter[0]]
+                end = copy_mapping[inter[1]]
+                start_snode = inter[2]
+                end_snode = inter[3]
+                for idx, intermediate_edge in enumerate(inter[4]):
+                    smiles_to_node = {}
+
+                    snodes_to_create = list(
+                        set(intermediate_edge.educts + intermediate_edge.products)
+                    )
+
+                    for snode in snodes_to_create:
+                        if snode == start_snode or snode == end_snode:
+                            smiles_to_node[snode.smiles] = start if snode == start_snode else end
+                            continue
+
+                        if snode.smiles not in smiles_to_node:
+                            n = Node.create(copied_pw, smiles=snode.smiles, depth=snode.depth)
+                            # Used in viz to highlight intermediates
+                            n.kv.update({"is_engineered_intermediate": True})
+                            n.save()
+                            smiles_to_node[snode.smiles] = n
+
+                    Edge.create(
+                        copied_pw,
+                        [smiles_to_node[educt.smiles] for educt in intermediate_edge.educts],
+                        [smiles_to_node[product.smiles] for product in intermediate_edge.products],
+                        rule=intermediate_edge.rule,
+                    )
+
+            # Persist the predicted pathway
+            pred_pw = pu.spathway_to_pathway(target, eng_pw, name=f"{pw.name} (Predicted)")
+
+            intermediate_pathways.append(copied_pw.url)
+            predicted_pathways.append(pred_pw.url)
+
+    return intermediate_pathways, predicted_pathways

epdb/urls.py

@@ -196,7 +196,8 @@ urlpatterns = [
     re_path(r"^indigo/dearomatize$", v.dearomatize, name="indigo_dearomatize"),
     re_path(r"^indigo/layout$", v.layout, name="indigo_layout"),
     re_path(r"^depict$", v.depict, name="depict"),
-    re_path(r"^jobs", v.jobs, name="jobs"),
+    path("jobs", v.jobs, name="jobs"),
+    path("jobs/<uuid:job_uuid>", v.job, name="job detail"),
     # OAuth Stuff
     path("o/userinfo/", v.userinfo, name="oauth_userinfo"),
     # Static Pages

epdb/views.py

@@ -970,7 +970,7 @@ def package_model(request, package_uuid, model_uuid):
             if classify:
                 from epdb.tasks import dispatch_eager, predict_simple
 
-                pred_res = dispatch_eager(
+                _, pred_res = dispatch_eager(
                     current_user, predict_simple, current_model.pk, stand_smiles
                 )
 
@@ -2023,7 +2023,7 @@ def package_pathway(request, package_uuid, pathway_uuid):
             rule_package = PackageManager.get_package_by_url(
                 current_user, request.GET.get("rule-package")
             )
-            res = dispatch_eager(
+            _, res = dispatch_eager(
                 current_user, identify_missing_rules, [current_pathway.pk], rule_package.pk
             )
 
@@ -2927,6 +2927,75 @@ def jobs(request):
 
         return render(request, "collections/joblog.html", context)
 
+    elif request.method == "POST":
+        job_name = request.POST.get("job-name")
+
+        if job_name == "engineer-pathway":
+            pathway_to_engineer = request.POST.get("pathway-to-engineer")
+            engineer_setting = request.POST.get("engineer-setting")
+
+            if not all([pathway_to_engineer, engineer_setting]):
+                raise BadRequest(
+                    f"Unable to run {job_name} as it requires 'pathway-to-engineer' and 'engineer-setting' parameters."
+                )
+
+            pathway_package = PackageManager.get_package_by_url(current_user, pathway_to_engineer)
+            pathway_to_engineer = Pathway.objects.get(
+                url=pathway_to_engineer, package=pathway_package
+            )
+
+            engineer_setting = SettingManager.get_setting_by_url(current_user, engineer_setting)
+
+            target_package = PackageManager.create_package(
+                current_user,
+                f"Autogenerated Package for Pathway Engineering of {pathway_to_engineer.name}",
+                f"This Package was generated automatically for the engineering Task of {pathway_to_engineer.name}.",
+            )
+
+            from .tasks import dispatch, engineer_pathways
+
+            res = dispatch(
+                current_user,
+                engineer_pathways,
+                [pathway_to_engineer.pk],
+                engineer_setting.pk,
+                target_package.pk,
+            )
+
+            return redirect(f"{s.SERVER_URL}/jobs/{res.task_id}")
+        else:
+            raise BadRequest(f"Job {job_name} is not supported!")
+    else:
+        return HttpResponseNotAllowed(["GET", "POST"])
+
+
+def job(request, job_uuid):
+    current_user = _anonymous_or_real(request)
+    context = get_base_context(request)
+
+    if request.method == "GET":
+        if current_user.is_superuser:
+            job = JobLog.objects.get(task_id=job_uuid)
+        else:
+            job = JobLog.objects.get(task_id=job_uuid, user=current_user)
+
+        # No op if status is already in a terminal state
+        job.check_for_update()
+
+        context["object_type"] = "joblog"
+        context["breadcrumbs"] = [
+            {"Home": s.SERVER_URL},
+            {"Jobs": s.SERVER_URL + "/jobs"},
+            {job.job_name: f"{s.SERVER_URL}/jobs/{job.task_id}"},
+        ]
+
+        context["job"] = job
+
+        return render(request, "objects/joblog.html", context)
+
+    else:
+        return HttpResponseNotAllowed(["GET"])
+
 
 ###########
 # KETCHER #

static/js/pw.js

@@ -524,7 +524,7 @@ function draw(pathway, elem) {
     node.append("circle")
         // make radius "invisible" for pseudo nodes
         .attr("r", d => d.pseudo ? 0.01 : nodeRadius)
-        .style("fill", "#e8e8e8");
+        .style("fill", d => d.is_engineered_intermediate ? "#42eff5" : "#e8e8e8");
 
     // Add image only for non pseudo nodes
     node.filter(d => !d.pseudo).each(function (d, i) {

templates/actions/objects/pathway.html

@@ -41,6 +41,14 @@
     <i class="glyphicon glyphicon-floppy-save"></i> Download Pathway as Image</a
   >
 </li>
+<li>
+  <a
+    role="button"
+    onclick="document.getElementById('engineer_pathway_modal').showModal(); return false;"
+  >
+    <i class="glyphicon glyphicon-cog"></i> Engineer Pathway</a
+  >
+</li>
 {% if meta.can_edit %}
   <li>
     <a

templates/collections/joblog.html

@@ -20,6 +20,9 @@
           <table class="table-zebra table">
             <thead>
               <tr>
+                {% if meta.user.is_superuser %}
+                  <th>User</th>
+                {% endif %}
                 <th>ID</th>
                 <th>Name</th>
                 <th>Status</th>
@@ -36,7 +39,11 @@
                       <a href="{{ job.user.url }}">{{ job.user.username }}</a>
                     </td>
                   {% endif %}
-                  <td>{{ job.task_id }}</td>
+                  <td>
+                    <a href="{% url 'job detail' job.task_id %}"
+                      >{{ job.task_id }}</a
+                    >
+                  </td>
                   <td>{{ job.job_name }}</td>
                   <td>{{ job.status }}</td>
                   <td>{{ job.created }}</td>

templates/modals/objects/engineer_pathway_modal.html

@@ -0,0 +1,107 @@
+{% load static %}
+
+<dialog
+  id="engineer_pathway_modal"
+  class="modal"
+  x-data="modalForm()"
+  @close="reset()"
+>
+  <div class="modal-box max-w-2xl">
+    <!-- Header -->
+    <h3 class="font-bold text-lg">Engineer Pathway</h3>
+
+    <!-- Close button (X) -->
+    <form method="dialog">
+      <button
+        class="btn btn-sm btn-circle btn-ghost absolute right-2 top-2"
+        :disabled="isSubmitting"
+      >
+        ✕
+      </button>
+    </form>
+
+    <!-- Body -->
+    <div class="py-4">
+      <p class="mb-4">
+        Engineering Package is a process used to identify potential intermediate
+        transformation products. To achieve this, a pathway is predicted using
+        an existing setting. The threshold is temporarily set to zero to ensure
+        that even intermediates with very low probability are not filtered out.
+        <br /><br />
+        If any intermediates are found, two pathways will be saved in a
+        generated Package:
+        <br />
+        1. The engineered Pathway with the identified intermediates highlighted.
+        <br />
+        2. The fully predicted Pathway preserved for further analysis.
+        <br /><br />
+        Note: This is an asynchronous process and may take a few minutes to
+        complete. You will be redirected to a page containing details about the
+        task and its status.
+      </p>
+      <form
+        id="engineer-pathway-modal-form"
+        accept-charset="UTF-8"
+        action="{% url 'jobs' %}"
+        method="post"
+      >
+        {% csrf_token %}
+
+        <div class="form-control mb-3">
+          <label class="label" for="engineer-setting">
+            <span class="label-text">
+              Select the Setting you want to use for pathway engineering
+            </span>
+          </label>
+          <select
+            id="engineer-setting"
+            name="engineer-setting"
+            class="select select-bordered w-full"
+            required
+          >
+            <option value="" disabled selected>Select Setting</option>
+            {% for s in meta.available_settings %}
+              <option value="{{ s.url }}">{{ s.name|safe }}</option>
+            {% endfor %}
+          </select>
+          <input
+            type="hidden"
+            name="pathway-to-engineer"
+            value="{{ pathway.url }}"
+          />
+          <input type="hidden" name="job-name" value="engineer-pathway" />
+        </div>
+      </form>
+    </div>
+
+    <!-- Footer -->
+    <div class="modal-action">
+      <button
+        type="button"
+        class="btn"
+        onclick="this.closest('dialog').close()"
+        :disabled="isSubmitting"
+      >
+        Close
+      </button>
+      <button
+        type="button"
+        class="btn btn-primary"
+        @click="submit('engineer-pathway-modal-form')"
+        :disabled="isSubmitting"
+      >
+        <span x-show="!isSubmitting">Engineer</span>
+        <span
+          x-show="isSubmitting"
+          class="loading loading-spinner loading-sm"
+        ></span>
+        <span x-show="isSubmitting">Engineering...</span>
+      </button>
+    </div>
+  </div>
+
+  <!-- Backdrop -->
+  <form method="dialog" class="modal-backdrop">
+    <button :disabled="isSubmitting">close</button>
+  </form>
+</dialog>

templates/objects/joblog.html

@@ -0,0 +1,123 @@
+{% extends "framework_modern.html" %}
+
+{% block content %}
+
+  {% block action_modals %}
+    {#    {% include "modals/objects/refresh_job_log.html" %}#}
+  {% endblock action_modals %}
+
+  <div class="space-y-2 p-4">
+    <!-- Header Section -->
+    <div class="card bg-base-100">
+      <div class="card-body">
+        <div class="flex items-center justify-between">
+          <h2 class="card-title text-2xl">Job Status for {{ job.job_name }}</h2>
+          <div id="actionsButton" class="dropdown dropdown-end hidden">
+            <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+              <svg
+                xmlns="http://www.w3.org/2000/svg"
+                width="16"
+                height="16"
+                viewBox="0 0 24 24"
+                fill="none"
+                stroke="currentColor"
+                stroke-width="2"
+                stroke-linecap="round"
+                stroke-linejoin="round"
+                class="lucide lucide-wrench"
+              >
+                <path
+                  d="M14.7 6.3a1 1 0 0 0 0 1.4l1.6 1.6a1 1 0 0 0 1.4 0l3.77-3.77a6 6 0 0 1-7.94 7.94l-6.91 6.91a2.12 2.12 0 0 1-3-3l6.91-6.91a6 6 0 0 1 7.94-7.94l-3.76 3.76z"
+                />
+              </svg>
+              Actions
+            </div>
+            <ul
+              tabindex="-1"
+              class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+            >
+              {% block actions %}
+                {% include "actions/objects/joblog.html" %}
+              {% endblock %}
+            </ul>
+          </div>
+        </div>
+      </div>
+    </div>
+
+    <!-- Description -->
+    <div class="collapse-arrow bg-base-200 collapse">
+      <input type="checkbox" checked />
+      <div class="collapse-title text-xl font-medium">Description</div>
+      <div class="collapse-content">
+        Status page for Task {{ job.job_name }}
+      </div>
+    </div>
+
+    <!-- Job Status -->
+    <div class="collapse-arrow bg-base-200 collapse">
+      <input type="checkbox" checked />
+      <div class="collapse-title text-xl font-medium">Task Status</div>
+      <div class="collapse-content">{{ job.status }}</div>
+    </div>
+
+    <!-- Job ID -->
+    <div class="collapse-arrow bg-base-200 collapse">
+      <input type="checkbox" checked />
+      <div class="collapse-title text-xl font-medium">Task ID</div>
+      <div class="collapse-content">{{ job.task_id }}</div>
+    </div>
+
+    <!-- Job Result -->
+    {% if job.is_in_terminal_state %}
+      <div class="collapse-arrow bg-base-200 collapse">
+        <input type="checkbox" checked />
+        <div class="collapse-title text-xl font-medium">Task Result</div>
+        <div class="collapse-content">
+          {% if job.job_name == 'engineer_pathways' %}
+            <div class="card bg-base-100">
+              <div class="card-body">
+                <p>Engineered Pathways:</p>
+                <ul class="menu bg-base-200 rounded-box w-full">
+                  {% for engineered_url in job.parsed_result.0 %}
+                    <li>
+                      <a href="{{ engineered_url }}" class="hover:bg-base-300"
+                        >{{ engineered_url }}</a
+                      >
+                    </li>
+                  {% endfor %}
+                </ul>
+              </div>
+            </div>
+            <div class="card bg-base-100">
+              <div class="card-body">
+                <p>Predicted Pathways:</p>
+                <ul class="menu bg-base-200 rounded-box w-full">
+                  {% for engineered_url in job.parsed_result.1 %}
+                    <li>
+                      <a href="{{ engineered_url }}" class="hover:bg-base-300"
+                        >{{ engineered_url }}</a
+                      >
+                    </li>
+                  {% endfor %}
+                </ul>
+              </div>
+            </div>
+          {% else %}
+            {{ job.parsed_result }}
+          {% endif %}
+        </div>
+      </div>
+    {% endif %}
+    <script>
+      // Show actions button if there are actions
+      document.addEventListener("DOMContentLoaded", function () {
+        const actionsButton = document.getElementById("actionsButton");
+        const actionsList = actionsButton?.querySelector("ul");
+        if (actionsList && actionsList.children.length > 0) {
+          actionsButton?.classList.remove("hidden");
+        }
+      });
+    </script>
+  </div>
+{% endblock content %}

templates/objects/pathway.html

@@ -81,6 +81,7 @@
     {% include "modals/objects/delete_pathway_node_modal.html" %}
     {% include "modals/objects/delete_pathway_edge_modal.html" %}
     {% include "modals/objects/generic_delete_modal.html" %}
+    {% include "modals/objects/engineer_pathway_modal.html" %}
   {% endblock action_modals %}
 
   <div class="space-y-2 p-4">
@@ -103,38 +104,36 @@
         <div class="bg-base-100 mb-2 rounded-lg p-2">
           <div class="navbar bg-base-100 rounded-lg">
             <div class="flex-1">
-              {% if meta.can_edit %}
-                <div class="dropdown">
-                  <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
-                    <svg
-                      xmlns="http://www.w3.org/2000/svg"
-                      width="16"
-                      height="16"
-                      viewBox="0 0 24 24"
-                      fill="none"
-                      stroke="currentColor"
-                      stroke-width="2"
-                      stroke-linecap="round"
-                      stroke-linejoin="round"
-                      class="lucide lucide-edit"
-                    >
-                      <path
-                        d="M11 4H4a2 2 0 0 0-2 2v14a2 2 0 0 0 2 2h14a2 2 0 0 0 2-2v-7"
-                      />
-                      <path
-                        d="M18.5 2.5a2.121 2.121 0 0 1 3 3L12 15l-4 1 1-4 9.5-9.5z"
-                      />
-                    </svg>
-                    Edit
-                  </div>
-                  <ul
-                    tabindex="0"
-                    class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+              <div class="dropdown">
+                <div tabindex="0" role="button" class="btn btn-ghost btn-sm">
+                  <svg
+                    xmlns="http://www.w3.org/2000/svg"
+                    width="16"
+                    height="16"
+                    viewBox="0 0 24 24"
+                    fill="none"
+                    stroke="currentColor"
+                    stroke-width="2"
+                    stroke-linecap="round"
+                    stroke-linejoin="round"
+                    class="lucide lucide-edit"
                   >
-                    {% include "actions/objects/pathway.html" %}
-                  </ul>
+                    <path
+                      d="M11 4H4a2 2 0 0 0-2 2v14a2 2 0 0 0 2 2h14a2 2 0 0 0 2-2v-7"
+                    />
+                    <path
+                      d="M18.5 2.5a2.121 2.121 0 0 1 3 3L12 15l-4 1 1-4 9.5-9.5z"
+                    />
+                  </svg>
+                  Actions
                 </div>
-              {% endif %}
+                <ul
+                  tabindex="0"
+                  class="dropdown-content menu bg-base-100 rounded-box z-50 w-52 p-2"
+                >
+                  {% include "actions/objects/pathway.html" %}
+                </ul>
+              </div>
               {% if pathway.setting.model.app_domain %}
                 <div class="dropdown">
                   <div tabindex="0" role="button" class="btn btn-ghost btn-sm">

tests/test_copy_objects.py

@@ -3,7 +3,7 @@ from django.test import TestCase, override_settings
 
 
 from epdb.logic import PackageManager
-from epdb.models import Compound, User, Reaction
+from epdb.models import Compound, User, Reaction, Rule, SimpleAmbitRule, ParallelRule
 
 
 @override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
@@ -48,11 +48,38 @@ class CopyTest(TestCase):
             description="Eawag BBD compound c0005",
         ).default_structure
 
+        cls.SIMPLE_RULE = Rule.create(
+            rule_type="SimpleAmbitRule",
+            package=cls.package,
+            name="bt0022-2833",
+            description="Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative",
+            smirks="[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]",
+        )
+
+        cls.SIMPLE_RULE_2 = Rule.create(
+            rule_type="SimpleAmbitRule",
+            package=cls.package,
+            name="Crap",
+            description=None,
+            smirks="CC>>CCC",
+        )
+
+        cls.PARALLEL_RULE = Rule.create(
+            rule_type="ParallelRule",
+            package=cls.package,
+            simple_rules=[cls.SIMPLE_RULE, cls.SIMPLE_RULE_2],
+            name="Par Rule",
+            description=None,
+            reactant_filter_smarts=None,
+            product_filter_smarts=None,
+        )
+
         cls.REACTION = Reaction.create(
             package=cls.package,
             name="Eawag BBD reaction r0001",
             educts=[cls.reaction_educt],
             products=[cls.reaction_product],
+            rules=[cls.SIMPLE_RULE],
             multi_step=False,
         )
 
@@ -188,3 +215,76 @@ class CopyTest(TestCase):
             self.assertEqual(copy_product.compound.package, self.target_package)
             self.assertEqual(orig_product.compound.package, self.package)
             self.assertEqual(orig_product.smiles, copy_product.smiles)
+
+    def test_copy_compound_deduplication(self):
+        mapping = dict()
+        first_copy = self.AFOXOLANER.copy(self.target_package, mapping)
+
+        # If we copy it again, we should get the exact same mapping and the number of
+        # Compounds should not increase
+        second_mapping = dict()
+        second_copy = self.AFOXOLANER.copy(self.target_package, second_mapping)
+
+        self.assertEqual(self.target_package.compounds.count(), 1)
+        self.assertEqual(first_copy, second_copy)
+
+        # Create a Compound where the initial SMILES is already normalized
+        # The Compound will only have a CompoundStructure
+        c = Compound.create(
+            package=self.target_package,
+            smiles="O=C(O)C1=CC=C([N+](=O)[O-])C=C1",
+            name="Compound with single structure",
+            description="Compound with single structure",
+        )
+
+        self.assertEqual(c.structures.count(), 1)
+
+        # Now we copy a Compound that share the same normalized structure but has
+        # a non normalized. We expect them to be merged
+        third_mapping = dict()
+        third_copy = self.FOUR_NITROBENZOIC_ACID.copy(self.target_package, third_mapping)
+
+        self.assertEqual(third_copy, c)
+        self.assertEqual(c.structures.count(), 2)
+
+    def test_copy_rule_deduplication(self):
+        mapping = dict()
+        first_copy = self.SIMPLE_RULE.copy(self.target_package, mapping)
+
+        # If we copy it again, we should get the exact same mapping and the number of
+        # Rule should not increase
+        second_mapping = dict()
+        second_copy = self.SIMPLE_RULE.copy(self.target_package, second_mapping)
+
+        self.assertEqual(self.target_package.rules.count(), 1)
+        self.assertEqual(first_copy, second_copy)
+
+        third_mapping = dict()
+        first_par_copy = self.PARALLEL_RULE.copy(self.target_package, third_mapping)
+        # 1 ParallelRule, 2 SimpleRules
+        self.assertEqual(self.target_package.rules.count(), 3)
+        self.assertEqual(SimpleAmbitRule.objects.filter(package=self.target_package).count(), 2)
+        self.assertEqual(ParallelRule.objects.filter(package=self.target_package).count(), 1)
+
+        fourth_mapping = dict()
+        second_par_copy = self.PARALLEL_RULE.copy(self.target_package, fourth_mapping)
+
+        # Counts should remain...
+        self.assertEqual(self.target_package.rules.count(), 3)
+        self.assertEqual(SimpleAmbitRule.objects.filter(package=self.target_package).count(), 2)
+        self.assertEqual(ParallelRule.objects.filter(package=self.target_package).count(), 1)
+
+        # Mapping should be identical
+        self.assertEqual(first_par_copy, second_par_copy)
+
+    def test_copy_reaction_deduplication(self):
+        mapping = dict()
+        first_copy = self.REACTION.copy(self.target_package, mapping)
+
+        # If we copy it again, we should get the exact same mapping and the number of
+        # Reaction should not increase
+        second_mapping = dict()
+        second_copy = self.REACTION.copy(self.target_package, second_mapping)
+
+        self.assertEqual(self.target_package.reactions.count(), 1)
+        self.assertEqual(first_copy, second_copy)

tests/test_jobs.py

@@ -0,0 +1,95 @@
+from django.conf import settings as s
+from django.test import TestCase, override_settings
+
+from epdb.logic import PackageManager
+from epdb.models import Pathway, User
+
+Package = s.GET_PACKAGE_MODEL()
+
+
+@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
+class MultiGenTest(TestCase):
+    fixtures = ["test_fixtures_incl_model.jsonl.gz"]
+
+    @classmethod
+    def setUpClass(cls):
+        super(MultiGenTest, cls).setUpClass()
+        cls.user: "User" = User.objects.get(username="anonymous")
+        cls.package: "Package" = PackageManager.create_package(
+            cls.user, "Anon Test Package", "No Desc"
+        )
+        cls.BBD_SUBSET: "Package" = Package.objects.get(name="Fixtures")
+        # 1,1,1-Trichloroethane (an/aerobic)
+        cls.PW_WITH_INTERMEDIATE_NAME = "1,1,1-Trichloroethane (an/aerobic)"
+        cls.PW_WITHOUT_INTERMEDIATE_NAME = "Caffeine"
+
+    def test_engineer_pathway(self):
+        from epdb.tasks import engineer_pathways
+
+        pw_to_engineer = Pathway.objects.get(name=self.PW_WITH_INTERMEDIATE_NAME)
+        engineered, predicted = engineer_pathways(
+            [pw_to_engineer.pk], self.user.prediction_settings().pk, self.package.pk
+        )
+
+        self.assertEqual(len(engineered), 1)
+        self.assertEqual(len(predicted), 1)
+        eng_pw = Pathway.objects.get(url=engineered[0])
+
+        for n in eng_pw.nodes:
+            if n.kv.get("is_engineered_intermediate"):
+                self.assertEqual(n.default_node_label.smiles, "CCO")
+
+        pw_to_engineer = Pathway.objects.get(name=self.PW_WITHOUT_INTERMEDIATE_NAME)
+        engineered, predicted = engineer_pathways(
+            [pw_to_engineer.pk], self.user.prediction_settings().pk, self.package.pk
+        )
+
+        self.assertEqual(len(engineered), 0)
+        self.assertEqual(len(predicted), 0)
+
+        # Test pathway deduplication in eng pathway process
+        pw1 = Pathway.objects.get(name=self.PW_WITH_INTERMEDIATE_NAME)
+
+        # Add pw1 twice
+        engineered, predicted = engineer_pathways(
+            [pw1.pk, pw1.pk], self.user.prediction_settings().pk, self.package.pk
+        )
+
+        self.assertEqual(len(engineered), 1)
+        self.assertEqual(len(predicted), 1)
+
+        # Check that both pathways contain the intermediate
+        num_intermediates_found = 0
+        for eng in engineered:
+            eng_pw = Pathway.objects.get(url=eng)
+
+            for n in eng_pw.nodes:
+                if n.kv.get("is_engineered_intermediate"):
+                    self.assertEqual(n.default_node_label.smiles, "CCO")
+                    num_intermediates_found += 1
+
+        self.assertEqual(num_intermediates_found, 1)
+
+        # Get a copy to have two pathways with potential intermediates as the fixture
+        # only contains one
+        mapping = {}
+        pw2 = pw1.copy(self.package, mapping=mapping)
+
+        engineered, predicted = engineer_pathways(
+            [pw1.pk, pw2.pk], self.user.prediction_settings().pk, self.package.pk
+        )
+
+        self.assertEqual(len(engineered), 2)
+        self.assertEqual(len(predicted), 2)
+
+        # Check that both pathways contain the intermediate
+        num_intermediates_found = 0
+        for eng in engineered:
+            eng_pw = Pathway.objects.get(url=eng)
+
+            for n in eng_pw.nodes:
+                if n.kv.get("is_engineered_intermediate"):
+                    self.assertEqual(n.default_node_label.smiles, "CCO")
+                    num_intermediates_found += 1
+
+        self.assertEqual(num_intermediates_found, 2)

utilities/chem.py

@@ -2,12 +2,13 @@ import logging
 import re
 from abc import ABC
 from collections import defaultdict
-from typing import List, Optional, Dict, TYPE_CHECKING
+from typing import List, Optional, Dict, TYPE_CHECKING, Union
 
 from indigo import Indigo, IndigoException, IndigoObject
 from indigo.renderer import IndigoRenderer
 from rdkit import Chem, rdBase
 from rdkit.Chem import MACCSkeys, Descriptors, rdFingerprintGenerator
+from rdkit.Chem import rdchem
 from rdkit.Chem import rdChemReactions
 from rdkit.Chem.Draw import rdMolDraw2D
 from rdkit.Chem.MolStandardize import rdMolStandardize
@@ -94,8 +95,15 @@ class FormatConverter(object):
         return Chem.MolToSmiles(mol, canonical=canonical)
 
     @staticmethod
-    def InChIKey(smiles):
-        return Chem.MolToInchiKey(FormatConverter.from_smiles(smiles))
+    def InChIKey(mol_or_smiles: Union[rdchem.Mol | str]):
+        if isinstance(mol_or_smiles, str):
+            mol_or_smiles = mol_or_smiles.replace("~", "")
+            mol_or_smiles = FormatConverter.from_smiles(mol_or_smiles)
+
+        if mol_or_smiles is None:
+            return None
+
+        return Chem.MolToInchiKey(mol_or_smiles)
 
     @staticmethod
     def InChI(smiles):
@@ -352,7 +360,8 @@ class FormatConverter(object):
                             product = GetMolFrags(product, asMols=True)
                             for p in product:
                                 p = FormatConverter.standardize(
-                                    Chem.MolToSmiles(p), remove_stereo=remove_stereo
+                                    Chem.MolToSmiles(p).replace("~", ""),
+                                    remove_stereo=remove_stereo,
                                 )
 
                                 if product_filter_smarts and FormatConverter.smarts_matches(

utilities/misc.py

@@ -9,7 +9,7 @@ from collections import defaultdict
 from datetime import datetime
 from enum import Enum
 from types import NoneType
-from typing import Any, Dict, List
+from typing import Any, Dict, List, TYPE_CHECKING
 
 from django.conf import settings as s
 from django.db import transaction
@@ -35,6 +35,7 @@ from epdb.models import (
     RuleBasedRelativeReasoning,
     Scenario,
     SequentialRule,
+    Setting,
     SimpleAmbitRule,
     SimpleRDKitRule,
     SimpleRule,
@@ -44,6 +45,9 @@ from utilities.chem import FormatConverter
 logger = logging.getLogger(__name__)
 Package = s.GET_PACKAGE_MODEL()
 
+if TYPE_CHECKING:
+    from epdb.logic import SPathway
+
 
 class HTMLGenerator:
     registry = {x.__name__: x for x in NAME_MAPPING.values()}
@@ -1260,3 +1264,122 @@ class PathwayUtils:
                 res[edge.url] = rule_chain
 
         return res
+
+    def engineer(self, setting: "Setting"):
+        from epdb.logic import SPathway
+        from utilities.chem import FormatConverter
+        from utilities.ml import graph_from_pathway, get_shortest_path
+
+        # get a fresh copy
+        pw = Pathway.objects.get(id=self.pathway.pk)
+
+        root_nodes = [n.default_node_label.smiles for n in pw.root_nodes]
+
+        if len(root_nodes) != 1:
+            logger.warning(f"Pathway {pw.name} has {len(root_nodes)} root nodes")
+            # spw, mapping, intermediates
+            return None, {}, []
+
+        # Predict the Pathway in memory
+        spw = SPathway(root_nodes[0], None, setting)
+
+        level = 0
+        while not spw.done:
+            spw.predict_step(from_depth=level)
+            level += 1
+
+        # Generate SNode -> Node mapping
+        node_mapping = {}
+
+        for node in pw.nodes:
+            for snode in spw.smiles_to_node.values():
+                data_smiles = node.default_node_label.smiles
+                pred_smiles = snode.smiles
+
+                # "~" denotes any bond remove and use implicit single bond for comparison
+                data_key = FormatConverter.InChIKey(data_smiles.replace("~", ""))
+                pred_key = FormatConverter.InChIKey(pred_smiles.replace("~", ""))
+
+                if data_key == pred_key:
+                    node_mapping[snode] = node
+
+        reverse_mapping = {v: k for k, v in node_mapping.items()}
+
+        graph = graph_from_pathway(spw)
+
+        intermediate_mapping = []
+
+        # loop through each edge and each reactant <-> product pair
+        # and compute the shortest path on the predicted pathway
+        for e in pw.edges:
+            for start in e.start_nodes.all():
+                if start not in reverse_mapping:
+                    continue
+
+                start_snode = reverse_mapping[start]
+
+                for end in e.end_nodes.all():
+                    if end not in reverse_mapping:
+                        continue
+
+                    end_snode = reverse_mapping[end]
+
+                    # If res is non-empty, we've found intermediates
+                    intermediate_smiles = get_shortest_path(
+                        graph,
+                        FormatConverter.standardize(start_snode.smiles, remove_stereo=True),
+                        FormatConverter.standardize(end_snode.smiles, remove_stereo=True),
+                    )
+
+                    if intermediate_smiles:
+                        intermediates = []
+
+                        prev = start_snode.smiles
+
+                        for smi in intermediate_smiles + [end_snode.smiles]:
+                            for e in spw.get_edge_for_educt_smiles(prev):
+                                if smi in e.product_smiles():
+                                    intermediates.append(e)
+
+                            prev = smi
+
+                        intermediate_mapping.append(
+                            (start, end, start_snode, end_snode, intermediates)
+                        )
+
+        return spw, reverse_mapping, intermediate_mapping
+
+    @staticmethod
+    def spathway_to_pathway(
+        package: "Package", spw: "SPathway", name: str = None, description: str = None
+    ):
+        snode_to_node_mapping = dict()
+
+        root_nodes = spw.root_nodes
+
+        pw = Pathway.create(
+            package=package,
+            smiles=root_nodes[0].smiles,
+            name=name,
+            description=description,
+            predicted=True,
+        )
+
+        pw.setting = spw.prediction_setting
+        pw.save()
+
+        snode_to_node_mapping[root_nodes[0]] = pw.root_nodes[0]
+
+        if len(root_nodes) > 1:
+            for rn in root_nodes[1:]:
+                n = Node.create(pw, rn.smiles, depth=0)
+                snode_to_node_mapping[rn] = n
+
+        for snode, node in snode_to_node_mapping.items():
+            spw.snode_persist_lookup[snode] = node
+
+        spw.persist = pw
+
+        spw._sync_to_pathway()
+
+        return pw