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[Fix] Stereochemistry prediction handling (#228 and #238) (#250)

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**This pull request will need a separate migration pull-request**

I have added an alert box in two places when the user tries to predict with stereo chemistry.

When a user predicts a pathway with stereo chemistry an alert box is shown in that node's hover.
To do this I added two new fields. Pathway now has a "predicted" BooleanField indicating whether it was predicted or not. It is set to True if the pathway mode for prediction is "predict" or "incremental" and False if it is "build". I think it is a flag that could be useful in the future, perhaps for analysing how many predicted pathways are in enviPath?
Node now has a `stereo_removed` BooleanField which is set to True if the Node's parent Pathways has "predicted" as true and the node SMILES has stereochemistry.
<img width="500" alt="{927AC9FF-DBC9-4A19-9E6E-0EDD3B08C7AC}.png" src="attachments/69ea29bc-c2d2-4cd2-8e98-aae5c5737f69">

When a user does a prediction on a model's page it shows at the top of the list. This did not require any new fields as the entered SMILES does not get saved anywhere.
<img width="500" alt="{BED66F12-5F07-419E-AAA6-FE1FE5B4F266}.png" src="attachments/5fcc3a9b-4d1a-4e48-acac-76b7571f6507">

I think the alert box is an alright solution but if you have a great idea for something that looks/fits better please change it or let me know.

Co-authored-by: Tim Lorsbach <tim@lorsba.ch>
Reviewed-on: enviPath/enviPy#250
Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
This commit is contained in:
Liam Brydon
2025-12-03 10:19:34 +13:00
committed by jebus
parent 69df139256
commit 901de4640c
23 changed files with 126 additions and 49 deletions
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2
.gitea/workflows/ci.yaml
View File

@ -41,7 +41,7 @@ jobs:
EP_DATA_DIR: /opt/enviPy/
ALLOWED_HOSTS: 127.0.0.1,localhost
DEBUG: True
LOG_LEVEL: DEBUG
LOG_LEVEL: INFO
MODEL_BUILDING_ENABLED: True
APPLICABILITY_DOMAIN_ENABLED: True
ENVIFORMER_PRESENT: True

22
epdb/migrations/0012_node_stereo_removed_pathway_predicted.py Normal file
View File

@ -0,0 +1,22 @@
# Generated by Django 5.2.7 on 2025-12-02 13:09
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
("epdb", "0011_auto_20251111_1413"),
]
operations = [
migrations.AddField(
model_name="node",
name="stereo_removed",
field=models.BooleanField(default=False),
),
migrations.AddField(
model_name="pathway",
name="predicted",
field=models.BooleanField(default=False),
),
]

10
epdb/models.py
View File

@ -1593,6 +1593,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
setting = models.ForeignKey(
"epdb.Setting", verbose_name="Setting", on_delete=models.CASCADE, null=True, blank=True
)
predicted = models.BooleanField(default=False, null=False)
@property
def root_nodes(self):
@ -1804,6 +1805,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
smiles: str,
name: Optional[str] = None,
description: Optional[str] = None,
predicted: bool = False,
):
pw = Pathway()
pw.package = package
@ -1816,6 +1818,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin):
pw.name = name
if description is not None and description.strip() != "":
pw.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip()
pw.predicted = predicted
pw.save()
try:
@ -1946,6 +1949,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
)
out_edges = models.ManyToManyField("epdb.Edge", verbose_name="Outgoing Edges")
depth = models.IntegerField(verbose_name="Node depth", null=False, blank=False)
stereo_removed = models.BooleanField(default=False, null=False)
def _url(self):
return "{}/node/{}".format(self.pathway.url, self.uuid)
@ -1955,6 +1959,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
return {
"depth": self.depth,
"stereo_removed": self.stereo_removed,
"url": self.url,
"node_label_id": self.default_node_label.url,
"image": f"{self.url}?image=svg",
@ -1980,12 +1985,17 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin):
name: Optional[str] = None,
description: Optional[str] = None,
):
stereo_removed = False
if pathway.predicted and FormatConverter.has_stereo(smiles):
smiles = FormatConverter.standardize(smiles, remove_stereo=True)
stereo_removed = True
c = Compound.create(pathway.package, smiles, name=name, description=description)
if Node.objects.filter(pathway=pathway, default_node_label=c.default_structure).exists():
return Node.objects.get(pathway=pathway, default_node_label=c.default_structure)
n = Node()
n.stereo_removed = stereo_removed
n.pathway = pathway
n.depth = depth

18
epdb/views.py
View File

@ -961,9 +961,9 @@ def package_model(request, package_uuid, model_uuid):
# Check if smiles is non empty and valid
if smiles == "":
return JsonResponse({"error": "Received empty SMILES"}, status=400)
stereo = FormatConverter.has_stereo(smiles)
try:
stand_smiles = FormatConverter.standardize(smiles)
stand_smiles = FormatConverter.standardize(smiles, remove_stereo=True)
except ValueError:
return JsonResponse({"error": f'"{smiles}" is not a valid SMILES'}, status=400)
@ -974,7 +974,7 @@ def package_model(request, package_uuid, model_uuid):
current_user, predict_simple, current_model.pk, stand_smiles
)
res = []
res = {"pred": [], "stereo": stereo}
for pr in pred_res:
if len(pr) > 0:
@ -983,7 +983,7 @@ def package_model(request, package_uuid, model_uuid):
logger.debug(f"Checking {prod_set}")
products.append(tuple([x for x in prod_set]))
res.append(
res["pred"].append(
{
"products": list(set(products)),
"probability": pr.probability,
@ -1931,7 +1931,6 @@ def package_pathways(request, package_uuid):
"Pathway prediction failed!",
"Pathway prediction failed due to missing or empty SMILES",
)
try:
stand_smiles = FormatConverter.standardize(smiles)
except ValueError:
@ -1954,8 +1953,13 @@ def package_pathways(request, package_uuid):
prediction_setting = SettingManager.get_setting_by_url(current_user, prediction_setting)
else:
prediction_setting = current_user.prediction_settings()
pw = Pathway.create(current_package, stand_smiles, name=name, description=description)
pw = Pathway.create(
current_package,
stand_smiles,
name=name,
description=description,
predicted=pw_mode in {"predict", "incremental"},
)
# set mode
pw.kv.update({"mode": pw_mode})

BIN
fixtures/test_fixtures_incl_model.jsonl.gz
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Binary file not shown.

6
static/js/pw.js
View File

@ -360,7 +360,11 @@ function draw(pathway, elem) {
}
function node_popup(n) {
popupContent = "<a href='" + n.url + "'>" + n.name + "</a><br>";
popupContent = "";
if (n.stereo_removed) {
popupContent += "<span class='alert alert-warning alert-soft'>Removed stereochemistry for prediction</span>";
}
popupContent += "<a href='" + n.url + "'>" + n.name + "</a><br>";
popupContent += "Depth " + n.depth + "<br>"
if (appDomainViewEnabled) {

12
templates/objects/model.html
View File

@ -117,7 +117,9 @@
<!-- Predict Panel -->
<div class="collapse-arrow bg-base-200 collapse">
<input type="checkbox" checked />
<div class="collapse-title text-xl font-medium">Predict</div>
<div class="collapse-title text-xl font-medium" id="predictTitle">
Predict
</div>
<div class="collapse-content">
<div class="form-control">
<div class="join w-full">
@ -193,7 +195,13 @@
{# FIXME: This is a hack to get the precision recall curve data into the JavaScript code. #}
<script>
function handlePredictionResponse(data) {
let res = "<table class='table table-zebra'>"
let stereo = data["stereo"]
data = data["pred"]
let res = ""
if (stereo) {
res += "<span class='alert alert-warning alert-soft'>Removed stereochemistry for prediction</span><br>"
}
res += "<table class='table table-zebra'>"
res += "<thead>"
res += "<th scope='col'>#</th>"

7
tests/test_compound_model.py
View File

@ -1,11 +1,12 @@
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from epdb.logic import PackageManager
from epdb.models import Compound, User, CompoundStructure
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class CompoundTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
def setUp(self):
pass

6
tests/test_copy_objects.py
View File

@ -1,12 +1,14 @@
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from epdb.logic import PackageManager
from epdb.models import Compound, User, Reaction
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class CopyTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

10
tests/test_dataset.py
View File

@ -1,14 +1,16 @@
import os.path
from tempfile import TemporaryDirectory
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from epdb.logic import PackageManager
from epdb.models import Reaction, Compound, User, Rule, Package
from utilities.chem import FormatConverter
from utilities.ml import RuleBasedDataset, EnviFormerDataset
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class DatasetTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
def setUp(self):
self.cs1 = Compound.create(
@ -106,7 +108,9 @@ class DatasetTest(TestCase):
def test_extra_features(self):
reactions = [r for r in Reaction.objects.filter(package=self.BBD_SUBSET)]
applicable_rules = [r for r in Rule.objects.filter(package=self.BBD_SUBSET)]
ds = RuleBasedDataset.generate_dataset(reactions, applicable_rules, feat_funcs=[FormatConverter.maccs, FormatConverter.morgan])
ds = RuleBasedDataset.generate_dataset(
reactions, applicable_rules, feat_funcs=[FormatConverter.maccs, FormatConverter.morgan]
)
print(ds.shape)
def test_to_arff(self):

6
tests/test_enviformer.py
View File

@ -3,7 +3,8 @@ from datetime import datetime
from tempfile import TemporaryDirectory
from django.conf import settings as s
from django.test import TestCase, tag
from django.test import TestCase, override_settings, tag
from epdb.logic import PackageManager
from epdb.models import EnviFormer, Setting, User
@ -30,8 +31,9 @@ def measure_predict(mod, pathway_pk=None):
@tag("slow")
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class EnviFormerTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

7
tests/test_model.py
View File

@ -2,7 +2,7 @@ from tempfile import TemporaryDirectory
import numpy as np
from django.conf import settings as s
from django.test import TestCase
from django.test import TestCase, override_settings
from epdb.logic import PackageManager
from epdb.models import MLRelativeReasoning, RuleBasedRelativeReasoning, User
@ -10,8 +10,9 @@ from epdb.models import MLRelativeReasoning, RuleBasedRelativeReasoning, User
Package = s.GET_PACKAGE_MODEL()
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class ModelTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):
@ -52,7 +53,7 @@ class ModelTest(TestCase):
expected = {
("CC=O", "CCNC(=O)C1=CC(C)=CC=C1"): (
"bt0243-4301",
np.float64(0.33333333333333337),
np.float64(0.5),
),
("CC1=CC=CC(C(=O)O)=C1", "CCNCC"): ("bt0430-4011", np.float64(0.25)),
}

5
tests/test_multigen_eval.py
View File

@ -1,5 +1,5 @@
from django.conf import settings as s
from django.test import TestCase
from django.test import TestCase, override_settings
from networkx.utils.misc import graphs_equal
from epdb.logic import PackageManager, SPathway
@ -9,8 +9,9 @@ from utilities.ml import graph_from_pathway, multigen_eval, pathway_edit_eval
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.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

6
tests/test_reaction_model.py
View File

@ -1,11 +1,13 @@
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from epdb.logic import PackageManager
from epdb.models import Compound, User, Reaction, Rule
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class ReactionTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

7
tests/test_rule_model.py
View File

@ -1,11 +1,12 @@
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from epdb.logic import PackageManager
from epdb.models import Rule, User
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class RuleTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

5
tests/test_simpleambitrule.py
View File

@ -1,15 +1,16 @@
from unittest.mock import MagicMock, PropertyMock, patch
from django.conf import settings as s
from django.test import TestCase
from django.test import TestCase, override_settings
from epdb.logic import PackageManager
from epdb.models import SimpleAmbitRule, User
from utilities.chem import FormatConverter
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class SimpleAmbitRuleTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

6
tests/views/test_compound_views.py
View File

@ -1,4 +1,5 @@
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from django.urls import reverse
from envipy_additional_information import Temperature, Interval
@ -6,8 +7,9 @@ from epdb.logic import UserManager, PackageManager
from epdb.models import Compound, Scenario, ExternalDatabase
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class CompoundViewTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

6
tests/views/test_model_views.py
View File

@ -9,12 +9,12 @@ Package = s.GET_PACKAGE_MODEL()
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class PathwayViewTest(TestCase):
class ModelViewTest(TestCase):
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):
super(PathwayViewTest, cls).setUpClass()
super(ModelViewTest, cls).setUpClass()
cls.user1 = UserManager.create_user(
"user1",
"user1@envipath.com",
@ -72,7 +72,7 @@ class PathwayViewTest(TestCase):
},
]
actual = response.json()
actual = response.json()["pred"]
self.assertEqual(actual, expected)
response = self.client.get(

5
tests/views/test_package_views.py
View File

@ -1,6 +1,6 @@
from django.conf import settings as s
from django.core.files.uploadedfile import SimpleUploadedFile
from django.test import TestCase, tag
from django.test import TestCase, override_settings, tag
from django.urls import reverse
from epdb.logic import UserManager
@ -15,8 +15,9 @@ from epdb.models import (
Package = s.GET_PACKAGE_MODEL()
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class PackageViewTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

6
tests/views/test_reaction_views.py
View File

@ -1,4 +1,5 @@
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from django.urls import reverse
from envipy_additional_information import Temperature, Interval
@ -6,8 +7,9 @@ from epdb.logic import UserManager, PackageManager
from epdb.models import Reaction, Scenario, ExternalDatabase
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class ReactionViewTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

6
tests/views/test_rule_views.py
View File

@ -1,4 +1,5 @@
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from django.urls import reverse
from envipy_additional_information import Temperature, Interval
@ -6,8 +7,9 @@ from epdb.logic import UserManager, PackageManager
from epdb.models import Rule, Scenario
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class RuleViewTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):

13
tests/views/test_user_views.py
View File

@ -1,12 +1,14 @@
from django.test import TestCase
from django.conf import settings as s
from django.test import TestCase, override_settings
from django.urls import reverse
from epdb.logic import PackageManager
from epdb.models import Package, User
from django.urls import reverse
@override_settings(MODEL_DIR=s.FIXTURE_DIRS[0] / "models", CELERY_TASK_ALWAYS_EAGER=True)
class UserViewTest(TestCase):
fixtures = ["test_fixtures.jsonl.gz"]
fixtures = ["test_fixtures_incl_model.jsonl.gz"]
@classmethod
def setUpClass(cls):
@ -48,8 +50,9 @@ class UserViewTest(TestCase):
},
)
self.assertEqual(response.status_code, 200)
# TODO currently fails as the fixture does not provide a global setting...
self.assertContains(response, "Registration failed!")
self.assertContains(
response, "Your account has been created! An admin will activate it soon!"
)
def test_register_password_mismatch(self):
response = self.client.post(

4
utilities/chem.py
View File

@ -81,6 +81,10 @@ class FormatConverter(object):
def formula(smiles):
return Chem.rdMolDescriptors.CalcMolFormula(FormatConverter.from_smiles(smiles))
@staticmethod
def has_stereo(smiles):
return "@" in smiles or "/" in smiles or "\\" in smiles
@staticmethod
def from_smiles(smiles):
return Chem.MolFromSmiles(smiles)