Re: [Rdkit-discuss] problem matching SMART pattern
Thank you very much Scott for pointing this issue, I did not noticed
that the problem was originated in the SMILES parsing,
kind regards
Alfredo
On 28/8/22 21:57, Scott Harrison wrote:
Hi Alfredo,
After parsing the SMILES strings of your molecules the RDKit considers all of
the atoms of your triazole to be aromatic, which you can see in the SMILES
string created from parsing your query molecule and regenerating its RDKit
SMILES string. I've included a simple template query that works below, which
you could be made more specific with additional SMARTS features as you like.
from rdkit import Chem
query = 'N1N=NC=C1'
mol = Chem.MolFromSmiles(query)
Chem.MolToSmiles(mol)
'c1c[nH]nn1'
template = 'n1nncc1'
mol.HasSubstructMatch(Chem.MolFromSmarts(template))
True
specific_template = '[n&D2]1[n&D2][n&D2][c][c]1'
mol.HasSubstructMatch(Chem.MolFromSmarts(specific_template))
True
Cheers,
Scott
-Original Message-
From: Alfredo Quevedo
Sent: Sunday, August 28, 2022 7:09 PM
To: RDKit Discuss
Subject: [Rdkit-discuss] problem matching SMART pattern
Dear users,
I am trying to math a triazole scaffold using SMARTS notation. My code is shown
below:
query = 'N1N=NC=C1'
template = '[NX3H1]1[N]=[N][C]=[C]1'
mol = Chem.MolFromSmiles(query)
mol.HasSubstructMatch(Chem.MolFromSmarts(template))
This results in 'False'. By depicting the structures I can see that the SMARTS
pattern is not including the explicit hydrogen in the structure.
However as long as I understand I am indicating the nitrogen atom to contain
the explicit hydrogen ('[NX3H1]'). However the structure is show as aromatic.
Can anyone suggest what is wrong with my code? the SMARTS pattern or some
keyword to make hydrogens explicit?
thanks in advance for the support,
regards
Alfredo
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*Dr. Alfredo Quevedo,*
Faculty of Chemical Sciences,
National University of Córdoba,
Argentina.
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Re: [Rdkit-discuss] problem matching SMART pattern
Hi Alfredo,
After parsing the SMILES strings of your molecules the RDKit considers all of
the atoms of your triazole to be aromatic, which you can see in the SMILES
string created from parsing your query molecule and regenerating its RDKit
SMILES string. I've included a simple template query that works below, which
you could be made more specific with additional SMARTS features as you like.
>>> from rdkit import Chem
>>> query = 'N1N=NC=C1'
>>> mol = Chem.MolFromSmiles(query)
>>> Chem.MolToSmiles(mol)
'c1c[nH]nn1'
>>> template = 'n1nncc1'
>>> mol.HasSubstructMatch(Chem.MolFromSmarts(template))
True
>>> specific_template = '[n&D2]1[n&D2][n&D2][c][c]1'
>>> mol.HasSubstructMatch(Chem.MolFromSmarts(specific_template))
True
Cheers,
Scott
-----Original Message-
From: Alfredo Quevedo
Sent: Sunday, August 28, 2022 7:09 PM
To: RDKit Discuss
Subject: [Rdkit-discuss] problem matching SMART pattern
Dear users,
I am trying to math a triazole scaffold using SMARTS notation. My code is shown
below:
query = 'N1N=NC=C1'
template = '[NX3H1]1[N]=[N][C]=[C]1'
mol = Chem.MolFromSmiles(query)
mol.HasSubstructMatch(Chem.MolFromSmarts(template))
This results in 'False'. By depicting the structures I can see that the SMARTS
pattern is not including the explicit hydrogen in the structure.
However as long as I understand I am indicating the nitrogen atom to contain
the explicit hydrogen ('[NX3H1]'). However the structure is show as aromatic.
Can anyone suggest what is wrong with my code? the SMARTS pattern or some
keyword to make hydrogens explicit?
thanks in advance for the support,
regards
Alfredo
___
Rdkit-discuss mailing list
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___
Rdkit-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] problem matching SMART pattern
Dear users,
I am trying to math a triazole scaffold using SMARTS notation. My code
is shown below:
query = 'N1N=NC=C1'
template = '[NX3H1]1[N]=[N][C]=[C]1'
mol = Chem.MolFromSmiles(query)
mol.HasSubstructMatch(Chem.MolFromSmarts(template))
This results in 'False'. By depicting the structures I can see that the
SMARTS pattern is not including the explicit hydrogen in the structure.
However as long as I understand I am indicating the nitrogen atom to
contain the explicit hydrogen ('[NX3H1]'). However the structure is show
as aromatic.
Can anyone suggest what is wrong with my code? the SMARTS pattern or
some keyword to make hydrogens explicit?
thanks in advance for the support,
regards
Alfredo
___
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[email protected]
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