Re: [Rdkit-discuss] From MW to structure

[Peter S. Shenkin]

Are you starting with an integral molecular weight or an experimentally
determined value, perhaps even a set of values from mass spec?

If it's an integral value then, if you are willing to settle for known
compounds, it might not be too hard. You could derive a bunch of empirical
formulas consistent with that molecular weight, given a list you would
supply of allowed elements. Then you could simply look up known compounds
with those formulas.

Actually, you could probably just look up the known compounds with the
specified molecular weight.

If it's a high-precision experimentally determined average molecular
weight, you could rule out some empirical formulas because many empirical
formulas would be inconsistent with the elements' known isotopic ratios.

If you are looking at high-res mass spec data, you could be even more
precise.

If you are actually trying to propose structures de-novo, that is a much
harder problem, per the Rdkit discussion thread cited by Nils. It probably
still makes sense to proceed via empirical formulas as an intermediate
result, but that would be a small fraction of the work it would take to get
you there. Going from empirical formulas to all consistent structures is
the hard part, and if you insist on stable structures or readily
synthesizable structures, that makes it harder.

-P.

On Thu, Jan 7, 2021 at 2:06 PM BOURG Stephane 
wrote:

> Dear all,
>
>
>
> I'm looking for a tool that can generate chemical structures from the
> molecular weight of the compound.
>
> Do you know RDKit functions or other tools able to offer that service ?
>
>
>
> Best regards,
>
>
>
>
>
>
>
> Stéphane BOURG, Ph. D.
>
> Equipe Bioinformatique Structurale et Chémoinformatique (SBC)
>
>
>
> Institut de Chimie Organique et Analytique (ICOA)
>
> UMR CNRS-Université d’Orléans 7311
>
> Pôle de Chimie
>
> Rue de Chartres – BP 6759
>
> 45 067 Orléans Cedex 2
>
>
>
> Tél : +33 (0)2 38 49 45 89
>
> E-mail : stephane.bo...@cnrs.fr
>
>
>
>
>
>
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Re: [Rdkit-discuss] From MW to structure

[Nils Weskamp]

Dear Stephane,

you may want to take a look at this older thread:

https://sourceforge.net/p/rdkit/mailman/rdkit-discuss/thread/8b455d6f-7817-5046-1f72-449954132621%40gmx.net/#msg37036275

Starting from just a molecular weight instead of a sum formula is 
probably not making things easier.


Hope this helps,
Nils

Am 07.01.2021 um 19:45 schrieb BOURG Stephane:

Dear all,

I'm looking for a tool that can generate chemical structures from the 
molecular weight of the compound.


Do you know RDKit functions or other tools able to offer that service ?

Best regards,

Stéphane BOURG, Ph. D.

Equipe Bioinformatique Structurale et Chémoinformatique (SBC)

Institut de Chimie Organique et Analytique (ICOA)

UMR CNRS-Université d’Orléans 7311

Pôle de Chimie

Rue de Chartres – BP 6759

45 067 Orléans Cedex 2

Tél : +33 (0)2 38 49 45 89

E-mail : stephane.bo...@cnrs.fr 



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[Rdkit-discuss] From MW to structure

[BOURG Stephane]

Dear all,

I'm looking for a tool that can generate chemical structures from the molecular 
weight of the compound.
Do you know RDKit functions or other tools able to offer that service ?

Best regards,



Stéphane BOURG, Ph. D.
Equipe Bioinformatique Structurale et Chémoinformatique (SBC)

Institut de Chimie Organique et Analytique (ICOA)
UMR CNRS-Université d’Orléans 7311
Pôle de Chimie
Rue de Chartres – BP 6759
45 067 Orléans Cedex 2

Tél : +33 (0)2 38 49 45 89
E-mail : stephane.bo...@cnrs.fr



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