Dear All RDKiters,
I have a simple question about generating all possible smiles of a given
molecule:
RDKit provides only 4 differents smiles for my molecule “CCC1CC1“:
C1C(CC)C1
CCC1CC1
C1(CC)CC1
C(C)C1CC1
While by hand we can write those 7 smiles:
CCC1CC1
C(C)C1CC1
C(C1CC1)C
C1CC(CC)1
C1C(CC)C1
C1CC1CC
C(CC)1CC1
I use this function for the enumeration:
def allsmiles(smil):
m = Chem.MolFromSmiles(smil) # Construct a molecule from a SMILES string.
if m is None:
return smil
N = m.GetNumAtoms()
if N==0:
return smil
try:
n= np.random.randint(0,high=N)
t= Chem.MolToSmiles(m, rootedAtAtom=n, canonical=False)
except :
return smil
return t
n= 50
SMILES = [“CCC1CC1”]
SMILES_mult = [allsmiles(S) for S in SMILES for i in range(n)]
Why we cannot generate all the 7 smiles ?
Thanks guys,
Best regards,
Guillaume
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