Update app.py

app.py

@@ -24,12 +24,10 @@ import gradio as gr
 import hydra
 import pandas as pd
 import requests
-from markdown import markdown
-from rdkit.Chem.PandasTools import _MolPlusFingerprint
-from rdkit.Chem.rdMolDescriptors import CalcNumRotatableBonds, CalcNumHeavyAtoms, CalcNumAtoms, CalcTPSA
 from requests.adapters import HTTPAdapter, Retry
+from markdown import markdown
 from rdkit import Chem
-from rdkit.Chem import RDConfig, Descriptors, Draw, Lipinski, Crippen, PandasTools
+from rdkit.Chem import Draw, RDConfig, PandasTools, Descriptors, rdMolDescriptors, rdmolops, Lipinski, Crippen
 from rdkit.Chem.Scaffolds import MurckoScaffold
 import seaborn as sns
 
@@ -283,46 +281,6 @@ scheduler.add_job(check_expiry, 'interval', hours=1)
 scheduler.start()
 
 
-def sa_score(mol):
-    return sascorer.calculateScore(mol)
-
-
-def mw(mol):
-    return Chem.Descriptors.MolWt(mol)
-
-
-def mr(mol):
-    return Crippen.MolMR(mol)
-
-
-def hbd(mol):
-    return Lipinski.NumHDonors(mol)
-
-
-def hba(mol):
-    return Lipinski.NumHAcceptors(mol)
-
-
-def logp(mol):
-    return Crippen.MolLogP(mol)
-
-
-def atom(mol):
-    return CalcNumAtoms(mol)
-
-
-def heavy_atom(mol):
-    return CalcNumHeavyAtoms(mol)
-
-
-def rotatable_bond(mol):
-    return CalcNumRotatableBonds(mol)
-
-
-def tpsa(mol):
-    return CalcTPSA(mol)
-
-
 def lipinski(mol):
     """
     Lipinski's rules:
@@ -331,16 +289,12 @@ def lipinski(mol):
     Molecular weight <= 500 daltons
     logP <= 5
     """
-    if hbd(mol) > 5:
-        return False
-    elif hba(mol) > 10:
-        return False
-    elif mw(mol) > 500:
-        return False
-    elif logp(mol) > 5:
-        return False
-    else:
-        return True
+    return (
+            Lipinski.NumHDonors(mol) <= 5 and
+            Lipinski.NumHAcceptors(mol) <= 10 and
+            Descriptors.MolWt(mol) <= 500 and
+            Crippen.MolLogP(mol) <= 5
+    )
 
 
 def reos(mol):
@@ -354,20 +308,15 @@ def reos(mol):
     Rotatable bond count between 0 and 8
     Heavy atom count between 15 and 50
     """
-    if not 200 < mw(mol) < 500:
-        return False
-    elif not -5.0 < logp(mol) < 5.0:
-        return False
-    elif not 0 < hbd(mol) < 5:
-        return False
-    elif not 0 < hba(mol) < 10:
-        return False
-    elif not 0 < rotatable_bond(mol) < 8:
-        return False
-    elif not 15 < heavy_atom(mol) < 50:
-        return False
-    else:
-        return True
+    return (
+            200 <= Descriptors.MolWt(mol) <= 500 and
+            -5.0 <= Crippen.MolLogP(mol) <= 5.0 and
+            0 <= Lipinski.NumHDonors(mol) <= 5 and
+            0 <= Lipinski.NumHAcceptors(mol) <= 10 and
+            -2 <= rdmolops.GetFormalCharge(mol) <= 2 and
+            0 <= rdMolDescriptors.CalcNumRotatableBonds(mol) <= 8 and
+            15 <= rdMolDescriptors.CalcNumHeavyAtoms(mol) <= 50
+    )
 
 
 def ghose(mol):
@@ -378,16 +327,12 @@ def ghose(mol):
     Atom count between 20 and 70
     Molar refractivity between 40 and 130
     """
-    if not 160 < mw(mol) < 480:
-        return False
-    elif not -0.4 < logp(mol) < 5.6:
-        return False
-    elif not 20 < atom(mol) < 70:
-        return False
-    elif not 40 < mr(mol) < 130:
-        return False
-    else:
-        return True
+    return (
+            160 <= Descriptors.MolWt(mol) <= 480 and
+            -0.4 <= Crippen.MolLogP(mol) <= 5.6 and
+            20 <= rdMolDescriptors.CalcNumAtoms(mol) <= 70 and
+            40 <= Crippen.MolMR(mol) <= 130
+    )
 
 
 def veber(mol):
@@ -397,12 +342,10 @@ def veber(mol):
     Rotatable bonds <= 10
     Topological polar surface area <= 140
     """
-    if not rotatable_bond(mol) <= 10:
-        return False
-    elif not tpsa(mol) <= 140:
-        return False
-    else:
-        return True
+    return (
+            rdMolDescriptors.CalcNumRotatableBonds(mol) <= 10 and
+            rdMolDescriptors.CalcTPSA(mol) <= 140
+    )
 
 
 def rule_of_three(mol):
@@ -414,18 +357,13 @@ def rule_of_three(mol):
     H-bond acceptor count <= 3
     Rotatable bond count <= 3
     """
-    if not mw(mol) <= 300:
-        return False
-    elif not logp(mol) <= 3:
-        return False
-    elif not hbd(mol) <= 3:
-        return False
-    elif not hba(mol) <= 3:
-        return False
-    elif not rotatable_bond(mol) <= 3:
-        return False
-    else:
-        return True
+    return (
+            Descriptors.MolWt(mol) <= 300 and
+            Crippen.MolLogP(mol) <= 3 and
+            Lipinski.NumHDonors(mol) <= 3 and
+            Lipinski.NumHAcceptors(mol) <= 3 and
+            rdMolDescriptors.CalcNumRotatableBonds(mol) <= 3
+    )
 
 
 @cache
@@ -470,15 +408,16 @@ def bms(mol):
 
 
 SCORE_MAP = {
-    'SAscore': sa_score,
-    'LogP': logp,
-    'Molecular Weight': mw,
-    'Number of Heavy Atoms': heavy_atom,
-    'Molar Refractivity': mr,
-    'H-Bond Donor Count': hbd,
-    'H-Bond Acceptor Count': hba,
-    'Rotatable Bond Count': rotatable_bond,
-    'Topological Polar Surface Area': tpsa,
+    'SAscore': sascorer.calculateScore,
+    'LogP': Crippen.MolLogP,
+    'Molecular Weight': Descriptors.MolWt,
+    'Number of Atoms': rdMolDescriptors.CalcNumAtoms,
+    'Number of Heavy Atoms': rdMolDescriptors.CalcNumHeavyAtoms,
+    'Molar Refractivity': Crippen.MolMR,
+    'H-Bond Donor Count': Lipinski.NumHDonors,
+    'H-Bond Acceptor Count': Lipinski.NumHAcceptors,
+    'Rotatable Bond Count': rdMolDescriptors.CalcNumRotatableBonds,
+    'Topological Polar Surface Area': rdMolDescriptors.CalcTPSA,
 }
 
 FILTER_MAP = {
@@ -618,7 +557,7 @@ def ts_to_str(timestamp, timezone):
     localized_dt = dt.astimezone(target_timezone)
 
     # Format the datetime object to the specified string format
-    return localized_dt.strftime('%Y-%m-%d %H:%M:%S (%Z)')
+    return localized_dt.strftime('%Y-%m-%d %H:%M:%S (%Z%z)')
 
 
 def lookup_job(job_id):
@@ -783,12 +722,12 @@ def update_df(file, progress=gr.Progress(track_tqdm=True)):
                 desc=f"Calculating scaffold...").apply(MurckoScaffold.MurckoScaffoldSmilesFromSmiles)
             df['Scaffold'] = df['Scaffold SMILES'].swifter.progress_bar(
                 desc='Generating scaffold graphs...').apply(
-                lambda smiles: _MolPlusFingerprint(Chem.MolFromSmiles(smiles)))
+                lambda smiles: PandasTools._MolPlusFingerprint(Chem.MolFromSmiles(smiles)))
             # Add a new column with RDKit molecule objects
             if 'Compound' not in df.columns or df['Compound'].dtype != 'object':
                 df['Compound'] = df['X1'].swifter.progress_bar(
                     desc='Generating molecular graphs...').apply(
-                    lambda smiles: _MolPlusFingerprint(Chem.MolFromSmiles(smiles)))
+                    lambda smiles: PandasTools._MolPlusFingerprint(Chem.MolFromSmiles(smiles)))
 
         # DF_FOR_REPORT = df.copy()