Re: [Rdkit-discuss] Question on chirality
Thank you very much Jan, this in fact fixed the issue. I just had to add "
AllChem.EmbedMolecule(mol)".
Best,
Navid
On Fri, Sep 13, 2019 at 5:49 AM Jan Holst Jensen
wrote:
> Hi Navid,
>
> 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:
>
> >>> mol = Chem.MolFromMolBlock("""
> ... BIOCHEMF09131911262D
> ...
> ... 7 6 0 0 1 0 0 0 0 0999 V2000
> ... 0.0.0. N 0 0 0 0 0 0 0 0 0 0 0 0
> ... 0.71450.41250. C 0 0 0 0 0 0 0 0 0 0 0 0
> ... 1.42900.0. C 0 0 0 0 0 0 0 0 0 0 0 0
> ... 1.4209 -0.82080. O 0 0 0 0 0 0 0 0 0 0 0 0
> ... 0.70841.24170. C 0 0 0 0 0 0 0 0 0 0 0 0
> ...-1.0.0. H 0 0 0 0 0 0 0 0 0 0 0 0
> ... 2.42900.0. 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)
> []
> >>>
>
>
> You can generate a conformation that produces chiral information by 3D
> embedding the molecule.
>
> >>> from rdkit.Chem import AllChem
> >>> AllChem.EmbedMolecule(mol)
> 0
> >>> Chem.AssignAtomChiralTagsFromStructure(mol)
> >>> Chem.FindMolChiralCenters(mol)
> [(1, 'S')]
> >>>
>
>
> Another way would be if you can get isomeric SMILES as input. Then the
> chiral information is right there.
>
> >>> 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:
>
> Hello,
>
> In the paper: "Graph Networks as a Universal Machine Learning
> 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
>
> > Chirality: (categorical) R, S, or not a Chiral center (one-hot encoded).
>
> The code I used is:
>
> from chainer_chemistry import datasets
> from chainer_chemistry.dataset.preprocessors.ggnn_preprocessor import
> GGNNPreprocessor
> from rdkit import Chem
> import numpy as np
>
> dataset, dataset_smiles = datasets.get_qm9(GGNNPreprocessor(),
> return_smiles=True)
>
> 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)
>
> 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.
>
> Sincerely,
> Navid
>
>
>
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Re: [Rdkit-discuss] Question on chirality
Hi Navid,
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:
>>> mol = Chem.MolFromMolBlock("""
... BIOCHEMF09131911262D
...
... 7 6 0 0 1 0 0 0 0 0999 V2000
... 0. 0. 0. N 0 0 0 0 0 0 0 0 0 0 0 0
... 0.7145 0.4125 0. C 0 0 0 0 0 0 0 0 0 0 0 0
... 1.4290 0. 0. C 0 0 0 0 0 0 0 0 0 0 0 0
... 1.4209 -0.8208 0. O 0 0 0 0 0 0 0 0 0 0 0 0
... 0.7084 1.2417 0. C 0 0 0 0 0 0 0 0 0 0 0 0
... -1. 0. 0. H 0 0 0 0 0 0 0 0 0 0 0 0
... 2.4290 0. 0. 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)
[]
>>>
You can generate a conformation that produces chiral information by 3D
embedding the molecule.
>>> from rdkit.Chem import AllChem
>>> AllChem.EmbedMolecule(mol)
0
>>> Chem.AssignAtomChiralTagsFromStructure(mol)
>>> Chem.FindMolChiralCenters(mol)
[(1, 'S')]
>>>
Another way would be if you can get isomeric SMILES as input. Then the
chiral information is right there.
>>> 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:
Hello,
In the paper: "Graph Networks as a Universal Machine Learning
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
> Chirality: (categorical) R, S, or not a Chiral center (one-hot encoded).
The code I used is:
from chainer_chemistry import datasets
from chainer_chemistry.dataset.preprocessors.ggnn_preprocessor
import GGNNPreprocessor
from rdkit import Chem
import numpy as np
dataset, dataset_smiles = datasets.get_qm9(GGNNPreprocessor(),
return_smiles=True)
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)
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.
Sincerely,
Navid
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[Rdkit-discuss] Question on chirality
Hello, In the paper: "Graph Networks as a Universal Machine Learning 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 > Chirality: (categorical) R, S, or not a Chiral center (one-hot encoded). The code I used is: from chainer_chemistry import datasets from chainer_chemistry.dataset.preprocessors.ggnn_preprocessor import GGNNPreprocessor from rdkit import Chem import numpy as np dataset, dataset_smiles = datasets.get_qm9(GGNNPreprocessor(), return_smiles=True) 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) 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. Sincerely, Navid ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
