Hi Devendra,
Your starting molecule is aromatic, as is your product; by default RDKit writes
aromatic SMILES.
If you wish to write your molecule as kekulized SMILES, do the following:
In [1]: from rdkit import Chem
In [2]: smi = "CN1C(NC2=NC=CC=C2)=CC=C1"
In [3]: mol = Chem.MolFromSmiles(smi)
In [4]: Chem.MolToSmiles(mol)
Out[4]: 'Cn1cccc1Nc1ccccn1'
In [6]: Chem.Kekulize(mol)
In [7]: Chem.MolToSmiles(mol, kekuleSmiles=True)
Out[7]: 'CN1C=CC=C1NC1=NC=CC=C1'
Cheers,
p.
> On 3 Jan 2020, at 23:26, Devendra Dhaked <devendra....@gmail.com> wrote:
>
>
> Hi,
>
> I have written SMIRKS for reaction transformation of reagent
> "CN1C(NC2=NC=CC=C2)=CC=C1" into product "CN1CC=CC1=NC2=NC=CC=C2".
>
> but after transformation in forward direction it showed lost bond order in
> product molecule Cn1cC=C[c]1=Nc1ccccn1.
> code for forward direction
> reactant1 = Chem.MolFromSmiles('CN1C(NC2=NC=CC=C2)=CC=C1')
> rxn =
> AllChem.ReactionFromSmarts('[O,NX3;H1:2][cX3z2;r5:3]:[c;r5:4][c;r5:5]:[cr5R{1-2}:6]>>[O,S,NX2:2]=[CX3;z2;r5:3][C;r5:4]=[C;r5:5][CX4;r5;!H0:6]')
> ps=rxn.RunReactants((reactant1,))
> print(len(ps))
> print(Chem.MolToSmiles(ps[0][0],True))
>
> Similarly in backward direction produced product(reactant) also lost its bond
> order
> CN1cccc1Nc1ccccn1.
> code for backward direction
> reactant1 = Chem.MolFromSmiles('CN1CC=CC1=NC2=NC=CC=C2')
> rxn =
> AllChem.ReactionFromSmarts('[O,S,NX2:2]=[CX3;z2;r5:3][C;r5:4]=[C;r5:5][CX4;r5;!H0:6]>>[O,NX3;H1:2][cX3z2;r5:3]:[c;r5:4][c;r5:5]:[cr5R{1-2}:6]')
> ps=rxn.RunReactants((reactant1,))
> print(len(ps))
> print(Chem.MolToSmiles(ps[0][0],True))
>
> Thanks.
>
> --
> Regards
>
> Devendra K Dhaked (Ph.D.)
> Center for Cancer Research
> Chemical Biology Laboratory
> National Cancer Institute (NIH)
> Boyles Street, Frederick, MD
> USA
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