Hello all:
I am trying to use the brics algorithm to fragment my compounds, filter the
fragments and try to group the original compounds by selected fragments.
As test I used the cdk2 data set provided by rdkit.
Here is a sample code partly cannibalizing Greg's and others' example code:
This part creates and displays the fragments:
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from rdkit.Chem import BRICS
df = PandasTools.LoadSDF('cdk2.sdf')
df.describe()
allfrags=set()
for i,rows in df.iterrows():
mol = rows['ROMol']
pieces = BRICS.BRICSDecompose(mol)
allfrags.update(pieces)
from rdkit.Chem import Descriptors
from rdkit.Chem import rdMolDescriptors
fragList = list(allfrags)
df1 = pd.Series(fragList)
df2 = df1.to_frame()
df2.columns = ['smiles']
PandasTools.AddMoleculeColumnToFrame(df2,smilesCol='smiles', molCol='ROMol')
df2['NumRings'] = df2['ROMol'].map(rdMolDescriptors.CalcNumRings)
df2['RingAroms'] = df2['ROMol'].apply(lambda x:
Descriptors.NumAromaticRings(x))
df2['HeavyAtoms'] = df2['ROMol'].apply(lambda x:
Descriptors.HeavyAtomCount(x))
df3 = df2[df2['HeavyAtoms']>6]
df4 = df3[df3['RingAroms'] > 0]
df5 = df4[df4['NumRings'] > 1]
PandasTools.FrameToGridImage(df5, column='ROMol')
This part removes the dummy atoms from smiles and tries to regenerate mol
objects:
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import re
resultsList = pd.DataFrame()
with open('my_csv.csv', 'a') as f:
for smi in df5['ROMol']:
smi = Chem.MolToSmiles(smi)
smi = re.sub(r"(\(\[\*\]\))", "", smi)
smi = re.sub(r"(\[\*\])", "", smi)
pattern = Chem.MolFromSmiles(smi)
-----------------------------------------------------------------------------------------------------------------------
This throws me here an error saying:
RDKIT Error: Can't kekulize mol
Do you know what is going on?
Many thanks in advance,
Markus
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