diff --git a/ippisite/ippidb/forms.py b/ippisite/ippidb/forms.py
index 45fd7a56747c5177228710cbbbc652c40061cd6a..d62f6debe2dc3a22c70a59b3a90cc670068e7bb8 100644
--- a/ippisite/ippidb/forms.py
+++ b/ippisite/ippidb/forms.py
@@ -844,7 +844,7 @@ class CompoundActivityResultForm(ModelForm):
activity_unit = forms.CharField(
label="Activity unit",
max_length=5,
- required=True,
+ required=False,
widget=widgets.Select(
choices=(
(None, "-----"),
@@ -855,6 +855,7 @@ class CompoundActivityResultForm(ModelForm):
("1e-12", "pmol"),
),
),
+ help_text="Only required if 'activity type' is not Kd ratio.",
)
class Meta:
@@ -896,20 +897,27 @@ class CompoundActivityResultForm(ModelForm):
return cleaned_data
if cleaned_data["activity_mol"] is None:
return cleaned_data
- if cleaned_data["activity_unit"] in (None, ""):
- self.add_error("activity_unit", "Unit must be provided")
+ if (
+ cleaned_data.get("activity_unit", "") == ""
+ and cleaned_data.get("activity_type", None) != "KdRat"
+ ):
+ self.add_error("activity_unit", "Unit is required if type is not Kd ratio")
return cleaned_data
try:
- d = Decimal(
- -log10(
- Decimal(self.cleaned_data["activity_mol"])
- * Decimal(self.cleaned_data["activity_unit"])
+ if self.cleaned_data["activity_type"] != "KdRat":
+ d = Decimal(
+ -log10(
+ Decimal(self.cleaned_data["activity_mol"])
+ * Decimal(self.cleaned_data["activity_unit"])
+ )
)
- )
- d = d.quantize(
- Decimal(10) ** -self.instance._meta.get_field("activity").decimal_places
- )
- self.cleaned_data["activity"] = d
+ d = d.quantize(
+ Decimal(10)
+ ** -self.instance._meta.get_field("activity").decimal_places
+ )
+ self.cleaned_data["activity"] = d
+ else:
+ self.cleaned_data["activity"] = self.cleaned_data["activity_mol"]
except Exception as e:
self.add_error(
"activity_mol",
@@ -945,6 +953,7 @@ class CompoundActivityResultBaseInlineNestedFormSet(BaseInlineNestedFormSet):
("pEC50", "EC50 (half maximal effective concentration)"),
("pKd", "Kd (dissociation constant)"),
("pKi", "Ki (inhibition constant)"),
+ ("KdRat", "Kd ratio (Kd w/o ligand / Kd with ligand"),
]
def add_fields(self, form, index):
diff --git a/ippisite/ippidb/migrations/0050_auto_20200420_2015.py b/ippisite/ippidb/migrations/0050_auto_20200420_2015.py
new file mode 100644
index 0000000000000000000000000000000000000000..1e8802eb65d8fd3e759a7b951a27ce54d13122db
--- /dev/null
+++ b/ippisite/ippidb/migrations/0050_auto_20200420_2015.py
@@ -0,0 +1,18 @@
+# Generated by Django 2.2.1 on 2020-04-20 20:15
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0049_auto_20200419_2005'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='compoundactivityresult',
+ name='activity_type',
+ field=models.CharField(choices=[('pIC50', 'pIC50 (half maximal inhibitory concentration, -log10)'), ('pEC50', 'pEC50 (half maximal effective concentration, -log10)'), ('pKd', 'pKd (dissociation constant, -log10)'), ('pKi', 'pKi (inhibition constant, -log10)'), ('KdRat', 'Kd ratio (Kd without/with ligand')], max_length=5, verbose_name='Activity type'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 8f01f1afa9841144ce999e6d4790943fd7a11a47..b510423fa334708310c3b879dec4fb922de2468c 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -1078,6 +1078,7 @@ class CompoundActivityResult(models.Model):
("pEC50", "pEC50 (half maximal effective concentration, -log10)"),
("pKd", "pKd (dissociation constant, -log10)"),
("pKi", "pKi (inhibition constant, -log10)"),
+ ("KdRat", "Kd ratio (Kd without/with ligand"),
)
compound = models.ForeignKey(Compound, models.CASCADE)
test_activity_description = models.ForeignKey(
diff --git a/ippisite/ippidb/tests/test_simple_heterodimer_208.yaml b/ippisite/ippidb/tests/test_simple_heterodimer_208.yaml
index 13859df89dc9adc196434a2d499cd82418d011a2..ca004f5a96001390d7a261a3b0edc49251282c5f 100644
--- a/ippisite/ippidb/tests/test_simple_heterodimer_208.yaml
+++ b/ippisite/ippidb/tests/test_simple_heterodimer_208.yaml
@@ -49,9 +49,8 @@ activity_tests:
cell_line_name: 'Human small-cell lung cancer'
protein_complex: '1'
compound_activity_results:
- - activity_mol: 61
- activity_type: pIC50
- activity_unit: 1e-9
+ - activity_mol: 20
+ activity_type: "KdRat"
compound_name: 'compound 12'
modulation_type: I
\ No newline at end of file
diff --git a/ippisite/ippidb/tests/tests_contribute_e2e.py b/ippisite/ippidb/tests/tests_contribute_e2e.py
index ce253eb0248d4f1e866a42c00981cdbfaf8dd605..610f92f8d756e1c1c8ae2ef5905aad9a6efe6310 100644
--- a/ippisite/ippidb/tests/tests_contribute_e2e.py
+++ b/ippisite/ippidb/tests/tests_contribute_e2e.py
@@ -149,10 +149,15 @@ class ContributionE2ETestCase(TestCase):
"activity_mol" in compound_activity_results
and compound_activity_results["activity_mol"] != ""
):
- compound_activity_results["activity"] = -math.log10(
- Decimal(str(compound_activity_results["activity_mol"]))
- * Decimal(str(compound_activity_results["activity_unit"]))
- )
+ if compound_activity_results["activity_type"] != "KdRat":
+ compound_activity_results["activity"] = -math.log10(
+ Decimal(str(compound_activity_results["activity_mol"]))
+ * Decimal(str(compound_activity_results["activity_unit"]))
+ )
+ else:
+ compound_activity_results["activity"] = Decimal(
+ str(compound_activity_results["activity_mol"])
+ )
self._process_contribution_wizard_without_sanity_check(entry_data)