Hello,
Maybe you can use this:
Chem.MolToSmiles(mol, allHsExplicit=True)
This will place each heavy atom between '[' and ']' and give you the
number
of hydrogens for each.
It get easier to work with SMILES strings after this (you don't need
anymore
a full blown SMILES parser).
Regards,
F.
On 09/05/2023 14:55, Haijun Feng wrote:
[1]
Hi All,
I am trying to add atom numbers in smiles as belows,
from rdkit import Chem
mol=Chem.MolFromSmiles('c1ccccc(C(N)=O)1')
for i, atom in enumerate(mol.GetAtoms()):
atom.SetProp('molAtomMapNumber',str(i))
smi=Chem.MolToSmiles(mol)
print(smi)
the output is: [cH:0]1[cH:1][cH:2][cH:3][cH:4][c:5]1C:6=[O:8]
then I want to split the smiles into atoms, I did it like this:
from rdkit import Chem
mol=Chem.MolFromSmiles('c1ccccc(C(N)=O)1')
for i, atom in enumerate(mol.GetAtoms()):
atom.SetProp('molAtomMapNumber',str(i))
print(i,atom.GetSymbol())
the output is:
0 C
1 C
2 C
3 C
4 C
5 C
6 C
7 N
8 O
But what I do want is something like this (with fragments instead of
atoms):
0 cH
1 CH
...
7 NH2
8 O
Can anyone help me figure out how to get each atom with H from the
smiles as above. Thanks so much!
best,
Hal
Links:
------
[1] https://stackoverflow.com/posts/76197437/timeline
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