fix: add Molecular formula

Steinbeck-Lab · Mar 22, 2024 · c3e6a5f · c3e6a5f
1 parent 40e66f3
commit c3e6a5f
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Showing 2 changed files with 12 additions and 5 deletions.
diff --git a/app/modules/coconut/descriptors.py b/app/modules/coconut/descriptors.py
@@ -6,7 +6,10 @@
 from app.modules.all_descriptors import get_cdk_rdkit_combined_descriptors
 from app.modules.npscorer import get_np_score
 from app.modules.toolkits.cdk_wrapper import get_CDK_descriptors
-from app.modules.toolkits.cdk_wrapper import get_murko_framework, get_CDK_MolecularFormula
+from app.modules.toolkits.cdk_wrapper import (
+    get_murko_framework,
+    get_CDK_MolecularFormula,
+)
 from app.modules.toolkits.helpers import parse_input
 from app.modules.toolkits.rdkit_wrapper import get_rdkit_descriptors
 from app.modules.tools.sugar_removal import get_sugar_info
@@ -63,7 +66,7 @@ def get_COCONUT_descriptors(smiles: str, toolkit: str) -> Union[Dict[str, float]
 
         CombinedDescriptors = list(Descriptors)
         CombinedDescriptors.extend(
-            [hasLinearSugar, hasCircularSugars, framework, nplikeliness,molFormula],
+            [hasLinearSugar, hasCircularSugars, framework, nplikeliness, molFormula],
         )
 
         DescriptorList = (

diff --git a/app/modules/toolkits/cdk_wrapper.py b/app/modules/toolkits/cdk_wrapper.py
@@ -179,8 +179,9 @@ def get_vander_waals_volume(molecule: any) -> float:
         cdk_base + ".geometry.volume.VABCVolume",
     )().calculate(molecule)
     return VABCVolume
-
-def get_CDK_MolecularFormula(molecule: any)->str:
+
+
+def get_CDK_MolecularFormula(molecule: any) -> str:
     """This function takes the input SMILES and creates a CDK IAtomContainer.
 
     Args:
@@ -189,11 +190,14 @@ def get_CDK_MolecularFormula(molecule: any)->str:
     Returns:
         str : MolecularFormula generated using CDK.
     """
-    MolecularFormulaManipulator = JClass(cdk_base + ".tools.manipulator.MolecularFormulaManipulator")
+    MolecularFormulaManipulator = JClass(
+        cdk_base + ".tools.manipulator.MolecularFormulaManipulator"
+    )
 
     MolecularFormula = MolecularFormulaManipulator.getMolecularFormula(molecule)
     return MolecularFormulaManipulator.getString(MolecularFormula)
 
+
 def get_CDK_descriptors(molecule: any) -> Union[tuple, str]:
     """Take an input SMILES and generate a selected set of molecular.