Re: [Rdkit-discuss] Question on chirality

[Jan Holst Jensen]

Hi Navid,






    >>> mol = Chem.MolFromMolBlock("""
   ...   BIOCHEMF09131911262D
   ...
   ...   7  6  0  0  1  0  0  0  0  0999 V2000
   ...     0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0 0  0  0  0  0
   ...     0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0 0  0  0  0  0
   ...     1.4290    0.0000    0.0000 C   0  0  0  0  0  0  0 0  0  0  0  0
   ...     1.4209   -0.8208    0.0000 O   0  0  0  0  0  0  0 0  0  0  0  0
   ...     0.7084    1.2417    0.0000 C   0  0  0  0  0  0  0 0  0  0  0  0
   ...    -1.0000    0.0000    0.0000 H   0  0  0  0  0  0  0 0  0  0  0  0
   ...     2.4290    0.0000    0.0000 O   0  0  0  0  0  0  0 0  0  0  0  0
   ...   2  3  1  0  0  0  0
   ...   1  2  1  0  0  0  0
   ...   3  4  2  0  0  0  0
   ...   2  5  1  1  0  0  0
   ...   1  6  1  0  0  0  0
   ...   3  7  1  0  0  0  0
   ... M  END
   ... """)
    >>> Chem.AssignAtomChiralTagsFromStructure(mol)
    >>> Chem.FindMolChiralCenters(mol)
   [(1, 'S')]
    >>> Chem.MolToSmiles(mol)
   'CC(N)C(=O)O'
    >>> mol = Chem.MolFromSmiles("CC(N)C(=O)O")
    >>> Chem.AssignAtomChiralTagsFromStructure(mol)
    >>> Chem.FindMolChiralCenters(mol)
   []
    >>>




    >>> from rdkit.Chem import AllChem
    >>> AllChem.EmbedMolecule(mol)
   0
    >>> Chem.AssignAtomChiralTagsFromStructure(mol)
    >>> Chem.FindMolChiralCenters(mol)
   [(1, 'S')]
    >>>




    >>> Chem.MolToSmiles(mol, isomericSmiles = True)
   'C[C*@*H](N)C(=O)O'
    >>> mol = Chem.MolFromSmiles("C[C@H](N)C(=O)O")
    >>> Chem.FindMolChiralCenters(mol)
   [(1, 'S')]
    >>>


Cheers
-- Jan Holst Jensen


On 2019-09-12 04:44, Navid Shervani-Tabar wrote:

I am not familiar with the paper you mention, but I believe that the problem is caused by non-isomeric input SMILES. Below is an Alanine read in from molfile, with coordinates. It has a chiral center with "S" configuration. When you output it as non-isomeric SMILES and read it back in, the chiral information is lost because the molecule no longer has a conformation: You can generate a conformation that produces chiral information by 3D embedding the molecule. Another way would be if you can get isomeric SMILES as input. Then the chiral information is right there.

Hello,

In the paper: "Graph Networks as a Universal Machine Learning


> Chirality: (categorical) R, S, or not a Chiral center (one-hot encoded).

The code I used is:

    from chainer_chemistry import datasets

    from rdkit import Chem
    import numpy as np



    for i in range(len(dataset_smiles)):
        mol = Chem.MolFromSmiles(dataset_smiles[i])
        Chem.AssignAtomChiralTagsFromStructure(mol)
        chiral_cc = Chem.FindMolChiralCenters(mol)

        if not len(chiral_cc) == 0:
            print(chiral_cc)



Sincerely,
Navid

Framework for Molecules and Crystals", authors introduce chirality as an atom feature input to analyze QM9 dataset. I was trying to recreate this atom feature as following     from chainer_chemistry.dataset.preprocessors.ggnn_preprocessor import GGNNPreprocessor     dataset, dataset_smiles = datasets.get_qm9(GGNNPreprocessor(), return_smiles=True) The output shows no Chiral centers for this dataset. When I use `includeUnassigned=True`, code gives a list of tuples, but instead of "R/S", I get "?". I was wondering if there is a mistake in my implementation. If this is expected, any thoughts on how chirality was assigned in the above paper? Thanks.

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