markush structures in openbabel

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markush structures in openbabel

Igor Filippov
Is there any way to set atomic labels in openbabel to non-existent
elements - i.e. X, Y, R1, R2, R3... ?

So far I see only SetAtomicNum to specify atom type, but nothing to set
the atomic label to something like "R1".

Thanks,
Igor


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Re: markush structures in openbabel

Tim Vandermeersch
On Mon, Jul 12, 2010 at 6:30 PM, Igor Filippov
<[hidden email]> wrote:
> Is there any way to set atomic labels in openbabel to non-existent
> elements - i.e. X, Y, R1, R2, R3... ?
>
> So far I see only SetAtomicNum to specify atom type, but nothing to set
> the atomic label to something like "R1".

You can use AliasData for this.

> Thanks,
> Igor
>
>
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Re: markush structures in openbabel

Geoffrey Hutchison

On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:

>> So far I see only SetAtomicNum to specify atom type, but nothing to set
>> the atomic label to something like "R1".
>
> You can use AliasData for this.

See src/formats/mdlformat.cpp for an exact example.

Hope that helps,
-Geoff

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Re: markush structures in openbabel

Igor Filippov
Tim, Geoff - thank you! Got it working for SDF, is there any way to have
it in SMILES?

Igor


On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:

> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
>
> >> So far I see only SetAtomicNum to specify atom type, but nothing to set
> >> the atomic label to something like "R1".
> >
> > You can use AliasData for this.
>
> See src/formats/mdlformat.cpp for an exact example.
>
> Hope that helps,
> -Geoff



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Re: markush structures in openbabel

Chris Morley-3
On 12/07/2010 18:38, Igor Filippov wrote:
> Tim, Geoff - thank you! Got it working for SDF, is there any way to have
> it in SMILES?

There is an SMILES extension described in
http://www.opensmiles.org/spec/open-smiles-6-extensions.html#6.1
but it looks as if the name of the group has to be specified
externally. Would that be sufficiently useful to be worth implementing?

Chris

>
> On Mon, 2010-07-12 at 13:07 -0400, Geoffrey Hutchison wrote:
>> On Jul 12, 2010, at 12:45 PM, Tim Vandermeersch wrote:
>>
>>>> So far I see only SetAtomicNum to specify atom type, but nothing to set
>>>> the atomic label to something like "R1".
>>>
>>> You can use AliasData for this.
>>
>> See src/formats/mdlformat.cpp for an exact example.
>>
>> Hope that helps,
>> -Geoff

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Re: markush structures in openbabel

Chris Morley-3
In reply to this post by Tim Vandermeersch
On 12/07/2010 17:45, Tim Vandermeersch wrote:
> On Mon, Jul 12, 2010 at 6:30 PM, Igor Filippov
> <[hidden email]>  wrote:
>> Is there any way to set atomic labels in openbabel to non-existent
>> elements - i.e. X, Y, R1, R2, R3... ?
>>
>> So far I see only SetAtomicNum to specify atom type, but nothing to set
>> the atomic label to something like "R1".
>
> You can use AliasData for this.

Currently AliasData is essentially an alternative representation of a
real structure, as defined by SMILES in superatoms.txt. There is the
occasional * representing an unspecified atom, but it does not extend
much further towards Markush structures.

It would be nice to take it further, but it requires some thought. For
instance, should molecules in OB should be required to have chemical
meaning, rather than being just being essentially images? Or would
descriptions like, "an electron withdrawing group" would be useful?.
Using SMARTS rather than SMILES in superatoms.txt goes a long way
towards Markush structures but is not completely general. I'm afraid I
am not familiar with the way other software handles this.

Chris

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