From c3e6a5f5e9dfc2ad50f03891340c1d9bff4f4565 Mon Sep 17 00:00:00 2001
From: Kohulan <kohulan.rajan@uni-jena.de>
Date: Fri, 22 Mar 2024 16:04:33 +0100
Subject: [PATCH] fix: add Molecular formula

---
 app/modules/coconut/descriptors.py  |  7 +++++--
 app/modules/toolkits/cdk_wrapper.py | 10 +++++++---
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/app/modules/coconut/descriptors.py b/app/modules/coconut/descriptors.py
index dfde6ed..0362692 100644
--- 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
index 23f4660..6f2e9ba 100644
--- 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.