Re: [Rdkit-discuss] SMARTS for an amide in an aromatic ring
Hi James,
what about '[nX3]c=O'?
p.
On 09/19/2017 12:26 AM, James T. Metz via Rdkit-discuss wrote:
Hello,
Given the following aromatic structure
m = Chem.MolFromSmiles("CN1C=CC(N)=NC1=O")
I would like to construct a SMARTS pattern to
recognize the aromatic amide (nitrogen attached to
the exocyclic methyl group) and not recognize the other
NCO group of atoms.
I have tried
pattern = Chem.MolFromSmarts('[N,n]-,:[C,c](=[O])')
but, this matches */both/* NCO groups of atoms which
I do not want.
The completely "aliphatic version"
pattern = Chem.MolFromSmarts('[N]-[C](=[O])')
does not match either NCO group of atoms.
I am stumped. I have also tried several recursive
SMARTS expressions, but I can't get the syntax
right.
I would appreciate any suggestions. Thank you.
Regards,
Jim Metz
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Re: [Rdkit-discuss] SMARTS for an amide in an aromatic ring
Try either of these:
[N,n](C)-,:[C,c](=[O])
C[N,n]-,:[C,c](=[O])
TJ O'Donnell
On Mon, Sep 18, 2017 at 4:26 PM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Hello,
>
> Given the following aromatic structure
>
> m = Chem.MolFromSmiles("CN1C=CC(N)=NC1=O")
>
> I would like to construct a SMARTS pattern to
> recognize the aromatic amide (nitrogen attached to
> the exocyclic methyl group) and not recognize the other
> NCO group of atoms.
>
>
> I have tried
>
> pattern = Chem.MolFromSmarts('[N,n]-,:[C,c](=[O])')
>
> but, this matches *both* NCO groups of atoms which
> I do not want.
>
>
> The completely "aliphatic version"
>
> pattern = Chem.MolFromSmarts('[N]-[C](=[O])')
>
> does not match either NCO group of atoms.
>
> I am stumped. I have also tried several recursive
> SMARTS expressions, but I can't get the syntax
> right.
>
> I would appreciate any suggestions. Thank you.
>
>
> Regards,
> Jim Metz
>
>
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
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[Rdkit-discuss] SMARTS for an amide in an aromatic ring
Hello,
Given the following aromatic structure
m = Chem.MolFromSmiles("CN1C=CC(N)=NC1=O")
I would like to construct a SMARTS pattern to
recognize the aromatic amide (nitrogen attached to
the exocyclic methyl group) and not recognize the other
NCO group of atoms.
I have tried
pattern = Chem.MolFromSmarts('[N,n]-,:[C,c](=[O])')
but, this matches both NCO groups of atoms which
I do not want.
The completely "aliphatic version"
pattern = Chem.MolFromSmarts('[N]-[C](=[O])')
does not match either NCO group of atoms.
I am stumped. I have also tried several recursive
SMARTS expressions, but I can't get the syntax
right.
I would appreciate any suggestions. Thank you.
Regards,
Jim Metz
--
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[Rdkit-discuss] chemfp 1.3 released
Hi all, I have just released chemfp 1.3. It is available from http://dalkescientific.com/releases/chemfp-1.3.tar.gz . Chemfp is a set of command-line tools and a Python library for working with cheminformatics fingerprints. It can use OEChem/OEGraphSim, RDKit, or Open Babel to create fingerprints in the FPS format, and it implements a high-speed Tanimoto search. The software is available under the MIT license. For more information see http://chemfp.com/ . Documentation is available from http://chemfp.readthedocs.io/en/chemfp-1.3/ . There are many changes over chemfp 1.1, which was the last release of the public/no-cost version of chemfp. The biggest ones are: - Tested against the current version of all of the toolkits - Added support for the Avalon and pattern fingerprints in RDKit - In-memory Tanimoto searches for 166-bit MACCS keys on computers with the POPCNT instruction is about 30% faster. - FPS loading is about 40% faster. As a result, file-based searches are about 25% faster. - The in-memory search algorithms in version 1.1 were parallelized with OpenMP, but the NxM k-nearest search was left out. That case is now also parallelized. - Some of the APIs from the commercial version were backported to 1.3, including the fingerprint writer API and functions for substructure fingerprint screening. - Added and improved docstrings This release support Python 2.7 but it no longer supports Python 2.5 or Python 2.6. The commercial version supports Python 2.7 and Python 3.5+, handles more than 4GB of fingerprint data, and has a binary fingerprint format for fast loading. I'll be at the RDKit Users Group meeting if people want to ask me questions about chemfp in person. Cheers, Andrew da...@dalkescientific.com -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
