Re: [Rdkit-discuss] postgres cartridge not parsing a SMILES

[Rajarshi Guha]

Ah, should have checked in the shell first! Thanks for the pointer

On Sat, Jan 13, 2018 at 5:07 PM, Andrew Dalke 
wrote:

> Hi Rajarshi,
>
> Here's what RDKit says from the interactive shell:
>
> >>> from rdkit import Chem
> >>> Chem.MolFromSmiles("C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=
> C4)C5=CC=CN=C5)N=C3")
> [23:02:36] Explicit valence for atom # 6 N, 4, is greater than permitted
>
> RDKit is pretty strict about accepting chemically reasonable structures,
> and will reject a lot of structures which other programs accept.
>
> This warning about a too-high valence on a nitrogen is probably the most
> common failure message I get from RDKit's SMILES parser.
>
> Cheers,
>
>
> Andrew
> da...@dalkescientific.com
>
>
> > On Jan 13, 2018, at 22:52, Rajarshi Guha 
> wrote:
> >
> > Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query
> is failing when the query SMILES is
> >
> > C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3
> >
> > The error reported from Postgres is
> >
> > PSQLException: ERROR: could not create molecule from SMILES
> 'C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3'
> >   Position: 81
> >
> >
> > The SMILES is parsed by CDK and JChem and I can't see why this should
> fail.
> >
> > I must be missing something obvious (?)
> > --
> > Rajarshi Guha | http://blog.rguha.net
> > NIH Center for Advancing Translational Science
>
>
>
> 
> --
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Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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Re: [Rdkit-discuss] postgres cartridge not parsing a SMILES

[Paul Emsley]

On 13/01/2018 18:52, Rajarshi Guha wrote:

Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query is 
failing when the query SMILES is

C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3



Within [] the formal charge must be specified:

C1=CC=C(C=C1)[N+]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3

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Re: [Rdkit-discuss] postgres cartridge not parsing a SMILES

[Andrew Dalke]

Hi Rajarshi,

Here's what RDKit says from the interactive shell:

>>> from rdkit import Chem
>>> Chem.MolFromSmiles("C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3")
[23:02:36] Explicit valence for atom # 6 N, 4, is greater than permitted

RDKit is pretty strict about accepting chemically reasonable structures, and 
will reject a lot of structures which other programs accept.

This warning about a too-high valence on a nitrogen is probably the most common 
failure message I get from RDKit's SMILES parser.

Cheers,


Andrew
da...@dalkescientific.com


> On Jan 13, 2018, at 22:52, Rajarshi Guha  wrote:
> 
> Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query is 
> failing when the query SMILES is
> 
> C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3
> 
> The error reported from Postgres is
> 
> PSQLException: ERROR: could not create molecule from SMILES 
> 'C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3'
>   Position: 81
> 
> 
> The SMILES is parsed by CDK and JChem and I can't see why this should fail.
> 
> I must be missing something obvious (?)
> -- 
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science



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[Rdkit-discuss] postgres cartridge not parsing a SMILES

[Rajarshi Guha]

Hi, I'm using RDKit 2017.09 with Postgres 9.5 and a substructure query is
failing when the query SMILES is

C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3

The error reported from Postgres is

PSQLException: ERROR: could not create molecule from SMILES
'C1=CC=C(C=C1)[N]2=CC=CC3=C2C4=C(C=CC(=C4)C5=CC=CN=C5)N=C3'

  Position: 81



The SMILES is parsed by CDK and JChem and I can't see why this should fail.

I must be missing something obvious (?)
-- 
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
--
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