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[Fix] AppDomain Leftovers (#161)

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Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#161
This commit is contained in:
jebus
2025-10-16 08:17:39 +13:00
parent 93dd811e39
commit d5ebb23622
4 changed files with 70 additions and 10 deletions
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51
epdb/views.py
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@ -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."
)
smirks = f"{stand_smiles}>>{'.'.join(sorted(res[0]))}"
# Some Rules are touching unrelated areas which might result in ~ indicating
# 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)