Overview

If you don't understand the default options and somehow use Chem.MolToSmiles, it's time to graduate. A memo summarized by that.

environment

RDkit 2020.03.5

Option description

option	Description
iosomericSmiles	Include information about stereochemistry in SMILES. The default is true
kekuleSmiles	Uses Kekule format (no aromatic bonds) with SMILES. Default is false
rootedAtAtom	If not negative, this forces SMILES to start at a particular atom. The default is-1
canonical	If false, it will not be normalized. The default is true.
allBondsExplicit	If true, all bond orders are explicitly printed in the output SMILES. The default is false.
allHsExplicit	If true, all H counts are explicitly output in the output SMILES. The default is false.

let's try it

Create such a method to check the operation other than rootedAtAtom.

def generate_smiles(old_smiles, isometric=True, kekule=False, allBondsExplicit=False, allHsExplicit=False, canonical=True):
    print(f"\n\ngenerate smiles {old_smiles}")
    print(f"prev smiles = {old_smiles}")
    old_mol = Chem.MolFromSmiles(old_smiles)
    new_smiles = Chem.MolToSmiles(old_mol, isomericSmiles=isometric, kekuleSmiles=kekule,
                                 allBondsExplicit=allBondsExplicit, allHsExplicit=allHsExplicit, canonical=canonical)

    print(f"new smiles = {new_smiles}")

SMILES to be tested

Let's check with this guy who has 3D information and aromatic ring information.

C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C

When changing isometicSmiles from the default true to flase

CC1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C

Oh, the 3D information has disappeared.

When canonical is changed from the default true to flaz

C[C@H]1COC2=C1C(=O)C(=O)c1c2ccc2c1CCCC2(C)C

No change. It is possible that the original SMILES was canonical.

When changing kekureSmiles from the default false to true

C[C@H]1COC2=C1C(=O)C(=O)C1:C2:C:C:C2:C:1CCCC2(C)C

c has been capitalized and colons have increased. -And = alternate, isn't it a pattern?

When allBondsExplicit is changed from the default false to true

C-[C@H]1-C-O-C2=C-1-C(=O)-C(=O)-c1:c-2:c:c:c2:c:1-C-C-C-C-2(-C)-C

The single bond has also come out properly. Well, it's noisy (laughs).

When allHsExplicit is changed from the default false to true

[CH3][C@H]1[CH2][O][C]2=[C]1[C](=[O])[C](=[O])[c]1[c]2[cH][cH][c]2[c]1[CH2][CH2][CH2][C]2([CH3])[CH3]

Implicit hydrogen has been revealed. Even more noisy (laughs)

Finally, set allBondsExplicit and allHsExplicit to true at the same time (bonus)

 [CH3]-[C@H]1-[CH2]-[O]-[C]2=[C]-1-[C](=[O])-[C](=[O])-[c]1:[c]-2:[cH]:[cH]:[c]2:[c]:1-[CH2]-[CH2]-[CH2]-[C]-2(-[CH3])-[CH3]

For people who cannot read between lines.

reference

https://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html

It's time to stop generating SMILES with RDKit