Hello! I have a pdb block that I am working with, which is attached to this email. The ligand has aromatic ring structures in it; however, when it is read into RDKit and converted into a smiles string, the aromatic rings are converted into aliphatic rings. Any thoughts?
Here is the python code:
def extract_data( filename):
extracted_info = ""
with open(filename) as f:
for line in f.readlines():
if "HETATM" in line:
extracted_info += ( line)
return extracted_info
for index, filename in enumerate(solution_pdb_filenames):
row = extract_data( filename)
m = Chem.MolFromPDBBlock(row, sanitize=True, removeHs=False )
Chem.SetHybridization(m)
Chem.SetAromaticity(m)
Chem.SanitizeMol(m,
sanitizeOps=Chem.rdmolops.SanitizeFlags.SANITIZE_ALL) #not needed since
sanitizing during read in, but trying to figure out if it actually worked
print ("Parsing file " + str(index) + " of " +
str(len(solution_pdb_filenames)))
print (Chem.MolToSmiles(m, kekuleSmiles=True, allHsExplicit=True))
The output smile string is:
[H][O][CH]1[NH][CH]([C]([H])([H])[CH]([OH])[OH])[CH]([C]([H])([H])[C]([H])([H])[H])[CH]([CH]([OH])[CH]2[CH]([H])[CH]([H])[CH]([H])[CH]([N]([H])[H])[CH]2[H])[CH]1[N]([C]([H])([H])[H])[C]([H])([H])[H]
Steven Combs
test.pdb
Description: Protein Databank data
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