import binding model

meyer-lab · Jun 4, 2024 · 3db9b0c · 3db9b0c
1 parent b9eee24
commit 3db9b0c
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Showing 5 changed files with 353 additions and 227 deletions.
diff --git a/bicytok/BindingMod.py b/bicytok/BindingMod.py
diff --git a/bicytok/MBmodel.py b/bicytok/MBmodel.py
@@ -3,8 +3,7 @@
 """
 
 import numpy as np
-
-from .BindingMod import polyc
+from valentbind import polyc
 
 
 def getKxStar():
@@ -14,6 +13,7 @@ def getKxStar():
 def cytBindingModel(
     recCount: np.ndarray, recXaffs: np.ndarray, dose: float, vals: np.ndarray
 ):
+    # Armaan: update this docstring, particularly the Return section
     """Runs binding model for a given mutein, valency, dose, and cell type
     Args:
         recCount: total count of signaling and targeting receptors
@@ -26,6 +26,13 @@ def cytBindingModel(
     Kx = getKxStar()
     ligandConc = dose / (vals[0][0] * 1e9)
 
-    output = polyc(ligandConc, Kx, recCount, vals, recXaffs)[0]
+    output = polyc(
+        ligandConc,
+        Kx,
+        recCount,
+        vals,
+        np.array([1]),
+        recXaffs,
+    )[1][0, 0]
 
     return output
diff --git a/bicytok/test/test_model.py b/bicytok/test/test_model.py
@@ -5,12 +5,12 @@
 import numpy as np
 import pandas as pd
 
+from bicytok.MBmodel import cytBindingModel
 from bicytok.selectivityFuncs import (
     calcReceptorAbundances,
-    optimizeSelectivityAffs,
     get_affs,
+    optimizeSelectivityAffs,
 )
-from bicytok.MBmodel import cytBindingModel
 
 
 def test_optimize_design():
@@ -35,30 +35,30 @@ def test_optimize_design():
 
 
 def test_binding_model():
-    assert (
+    assert np.isclose(
         cytBindingModel(
             recCount=np.array([4000.0, 3400.0]),
             recXaffs=get_affs(np.array([8.0, 8.0])),
             dose=0.1,
             vals=np.array([[1, 1]]),
-        )
-        == 4.070165414304938e-5
+        ),
+        4.070165414304938e-5,
     )
-    assert (
+    assert np.isclose(
         cytBindingModel(
             recCount=np.array([6000.0, 2100.0]),
             recXaffs=get_affs(np.array([7.6, 8.2])),
             dose=1.0,
             vals=np.array([[4, 4]]),
-        )
-        == 0.0009870173680610606
+        ),
+        0.0009870173680610606,
     )
-    assert (
+    assert np.isclose(
         cytBindingModel(
             recCount=np.array([4000.0, 3400.0, 5700.0, 33800.0]),
             recXaffs=get_affs(np.array([8.9, 7.0, 8.0, 8.0])),
             dose=0.1,
             vals=np.array([[1, 4, 4, 4]]),
-        )
-        == 0.017104443169046135
+        ),
+        0.017104443169046135,
     )