Doubt about extracting functional groups

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Doubt about extracting functional groups

David García Aristegui
Hello, newbie question: i would like to load in a database the structure
of some functional groups, but not "by hand". So, i think a way to do it
is to code a script invoking Open Babel, extracting from a .smi file the
structure of the existing functional groups.

I know how to use Obgrep to detect which structures have a certain
functional group in it (is very useful the SMARTS values provided in
patterns.txt file), but not how to extract the functional group itself
and his structure.

Is this possible? i mean, how could i use Open Babel to do the check of
the matching atoms (the functional group), and then extract functional
group structure and convert it to SMILES?

Thank you in advanced, best regards.


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Re: Doubt about extracting functional groups

Noel O'Boyle
Administrator
Dear David,

If you look at the Pybel code you will see how you can use a SMARTS
search to identify the matching atoms. The matching atoms will just be
a fragment of the structure, and so I don't know how/why you would
convert this to a SMILES.

HTH,
Noel

2008/10/22 David García Aristegui <[hidden email]>:

> Hello, newbie question: i would like to load in a database the structure
> of some functional groups, but not "by hand". So, i think a way to do it
> is to code a script invoking Open Babel, extracting from a .smi file the
> structure of the existing functional groups.
>
> I know how to use Obgrep to detect which structures have a certain
> functional group in it (is very useful the SMARTS values provided in
> patterns.txt file), but not how to extract the functional group itself
> and his structure.
>
> Is this possible? i mean, how could i use Open Babel to do the check of
> the matching atoms (the functional group), and then extract functional
> group structure and convert it to SMILES?
>
> Thank you in advanced, best regards.
>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________
> OpenBabel-discuss mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Doubt about extracting functional groups

David García Aristegui
Thank you for your response.  My goal is to load in a database the
structure (SMILES format) of the functional groups extracted from the
ligand structure. I don't know if is possible to de the "extraction"
with Open Babel.

Best regards.

El jue, 23-10-2008 a las 09:35 +0100, Noel O'Boyle escribió:

> Dear David,
>
> If you look at the Pybel code you will see how you can use a SMARTS
> search to identify the matching atoms. The matching atoms will just be
> a fragment of the structure, and so I don't know how/why you would
> convert this to a SMILES.
>
> HTH,
> Noel
>
> 2008/10/22 David García Aristegui <[hidden email]>:
> > Hello, newbie question: i would like to load in a database the structure
> > of some functional groups, but not "by hand". So, i think a way to do it
> > is to code a script invoking Open Babel, extracting from a .smi file the
> > structure of the existing functional groups.
> >
> > I know how to use Obgrep to detect which structures have a certain
> > functional group in it (is very useful the SMARTS values provided in
> > patterns.txt file), but not how to extract the functional group itself
> > and his structure.
> >
> > Is this possible? i mean, how could i use Open Babel to do the check of
> > the matching atoms (the functional group), and then extract functional
> > group structure and convert it to SMILES?
> >
> > Thank you in advanced, best regards.
> >
> >
> > -------------------------------------------------------------------------
> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> > Build the coolest Linux based applications with Moblin SDK & win great prizes
> > Grand prize is a trip for two to an Open Source event anywhere in the world
> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> > _______________________________________________
> > OpenBabel-discuss mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >


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Re: Doubt about extracting functional groups

Noel O'Boyle
Administrator
Can you give a complete example? I don't think you can represent a
fragment of a molecule with SMILES at least with OpenBabel.

Noel

2008/10/23 David García Aristegui <[hidden email]>:

> Thank you for your response.  My goal is to load in a database the
> structure (SMILES format) of the functional groups extracted from the
> ligand structure. I don't know if is possible to de the "extraction"
> with Open Babel.
>
> Best regards.
>
> El jue, 23-10-2008 a las 09:35 +0100, Noel O'Boyle escribió:
>> Dear David,
>>
>> If you look at the Pybel code you will see how you can use a SMARTS
>> search to identify the matching atoms. The matching atoms will just be
>> a fragment of the structure, and so I don't know how/why you would
>> convert this to a SMILES.
>>
>> HTH,
>> Noel
>>
>> 2008/10/22 David García Aristegui <[hidden email]>:
>> > Hello, newbie question: i would like to load in a database the structure
>> > of some functional groups, but not "by hand". So, i think a way to do it
>> > is to code a script invoking Open Babel, extracting from a .smi file the
>> > structure of the existing functional groups.
>> >
>> > I know how to use Obgrep to detect which structures have a certain
>> > functional group in it (is very useful the SMARTS values provided in
>> > patterns.txt file), but not how to extract the functional group itself
>> > and his structure.
>> >
>> > Is this possible? i mean, how could i use Open Babel to do the check of
>> > the matching atoms (the functional group), and then extract functional
>> > group structure and convert it to SMILES?
>> >
>> > Thank you in advanced, best regards.
>> >
>> >
>> > -------------------------------------------------------------------------
>> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> > Build the coolest Linux based applications with Moblin SDK & win great prizes
>> > Grand prize is a trip for two to an Open Source event anywhere in the world
>> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> > _______________________________________________
>> > OpenBabel-discuss mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>
>

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Re: Doubt about extracting functional groups

David García Aristegui
For example. i have a ligand with a formyl group in it. I would like to
detect the group, and "extract" the structure in SMILES format
([H]C([*])=O).

I have to load a database with functional groups structure, and if is
possible, i don't want to do it manually... I think a way to do it could
be to extract the functional groups from a representative set of
ligands.

Thankx!!!.

El jue, 23-10-2008 a las 10:37 +0100, Noel O'Boyle escribió:

> Can you give a complete example? I don't think you can represent a
> fragment of a molecule with SMILES at least with OpenBabel.
>
> Noel
>
> 2008/10/23 David García Aristegui <[hidden email]>:
> > Thank you for your response.  My goal is to load in a database the
> > structure (SMILES format) of the functional groups extracted from the
> > ligand structure. I don't know if is possible to de the "extraction"
> > with Open Babel.
> >
> > Best regards.
> >
> > El jue, 23-10-2008 a las 09:35 +0100, Noel O'Boyle escribió:
> >> Dear David,
> >>
> >> If you look at the Pybel code you will see how you can use a SMARTS
> >> search to identify the matching atoms. The matching atoms will just be
> >> a fragment of the structure, and so I don't know how/why you would
> >> convert this to a SMILES.
> >>
> >> HTH,
> >> Noel
> >>
> >> 2008/10/22 David García Aristegui <[hidden email]>:
> >> > Hello, newbie question: i would like to load in a database the structure
> >> > of some functional groups, but not "by hand". So, i think a way to do it
> >> > is to code a script invoking Open Babel, extracting from a .smi file the
> >> > structure of the existing functional groups.
> >> >
> >> > I know how to use Obgrep to detect which structures have a certain
> >> > functional group in it (is very useful the SMARTS values provided in
> >> > patterns.txt file), but not how to extract the functional group itself
> >> > and his structure.
> >> >
> >> > Is this possible? i mean, how could i use Open Babel to do the check of
> >> > the matching atoms (the functional group), and then extract functional
> >> > group structure and convert it to SMILES?
> >> >
> >> > Thank you in advanced, best regards.
> >> >
> >> >
> >> > -------------------------------------------------------------------------
> >> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> >> > Build the coolest Linux based applications with Moblin SDK & win great prizes
> >> > Grand prize is a trip for two to an Open Source event anywhere in the world
> >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> >> > _______________________________________________
> >> > OpenBabel-discuss mailing list
> >> > [hidden email]
> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >> >
> >
> >


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Re: Doubt about extracting functional groups

Noel O'Boyle
Administrator
The final structure you show is not a SMILES format, but is a SMARTS
substructure query. I think you should look at SMARTS_InteLigand.txt
which already contains a list of these.

2008/10/23 David García Aristegui <[hidden email]>:

> For example. i have a ligand with a formyl group in it. I would like to
> detect the group, and "extract" the structure in SMILES format
> ([H]C([*])=O).
>
> I have to load a database with functional groups structure, and if is
> possible, i don't want to do it manually... I think a way to do it could
> be to extract the functional groups from a representative set of
> ligands.
>
> Thankx!!!.
>
> El jue, 23-10-2008 a las 10:37 +0100, Noel O'Boyle escribió:
>> Can you give a complete example? I don't think you can represent a
>> fragment of a molecule with SMILES at least with OpenBabel.
>>
>> Noel
>>
>> 2008/10/23 David García Aristegui <[hidden email]>:
>> > Thank you for your response.  My goal is to load in a database the
>> > structure (SMILES format) of the functional groups extracted from the
>> > ligand structure. I don't know if is possible to de the "extraction"
>> > with Open Babel.
>> >
>> > Best regards.
>> >
>> > El jue, 23-10-2008 a las 09:35 +0100, Noel O'Boyle escribió:
>> >> Dear David,
>> >>
>> >> If you look at the Pybel code you will see how you can use a SMARTS
>> >> search to identify the matching atoms. The matching atoms will just be
>> >> a fragment of the structure, and so I don't know how/why you would
>> >> convert this to a SMILES.
>> >>
>> >> HTH,
>> >> Noel
>> >>
>> >> 2008/10/22 David García Aristegui <[hidden email]>:
>> >> > Hello, newbie question: i would like to load in a database the structure
>> >> > of some functional groups, but not "by hand". So, i think a way to do it
>> >> > is to code a script invoking Open Babel, extracting from a .smi file the
>> >> > structure of the existing functional groups.
>> >> >
>> >> > I know how to use Obgrep to detect which structures have a certain
>> >> > functional group in it (is very useful the SMARTS values provided in
>> >> > patterns.txt file), but not how to extract the functional group itself
>> >> > and his structure.
>> >> >
>> >> > Is this possible? i mean, how could i use Open Babel to do the check of
>> >> > the matching atoms (the functional group), and then extract functional
>> >> > group structure and convert it to SMILES?
>> >> >
>> >> > Thank you in advanced, best regards.
>> >> >
>> >> >
>> >> > -------------------------------------------------------------------------
>> >> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> >> > Build the coolest Linux based applications with Moblin SDK & win great prizes
>> >> > Grand prize is a trip for two to an Open Source event anywhere in the world
>> >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> >> > _______________________________________________
>> >> > OpenBabel-discuss mailing list
>> >> > [hidden email]
>> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >> >
>> >
>> >
>
>

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Re: Doubt about extracting functional groups

David García Aristegui
I think is not the same: the SMILES format could use the wildcard (*):

"* is wildcard (any atom). The wildcard atom may also be written without
brackets"
http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html

The SMARTS pattern for an aldehyde is:
[#6][CX3](=O) 3 aldehyde or ketone

The SMILES representation for the funtional group is
([H]C([*])=O)

Thank you again. Best regards.

El jue, 23-10-2008 a las 11:15 +0100, Noel O'Boyle escribió:

> The final structure you show is not a SMILES format, but is a SMARTS
> substructure query. I think you should look at SMARTS_InteLigand.txt
> which already contains a list of these.
>
> 2008/10/23 David García Aristegui <[hidden email]>:
> > For example. i have a ligand with a formyl group in it. I would like to
> > detect the group, and "extract" the structure in SMILES format
> > ([H]C([*])=O).
> >
> > I have to load a database with functional groups structure, and if is
> > possible, i don't want to do it manually... I think a way to do it could
> > be to extract the functional groups from a representative set of
> > ligands.
> >
> > Thankx!!!.
> >
> > El jue, 23-10-2008 a las 10:37 +0100, Noel O'Boyle escribió:
> >> Can you give a complete example? I don't think you can represent a
> >> fragment of a molecule with SMILES at least with OpenBabel.
> >>
> >> Noel
> >>
> >> 2008/10/23 David García Aristegui <[hidden email]>:
> >> > Thank you for your response.  My goal is to load in a database the
> >> > structure (SMILES format) of the functional groups extracted from the
> >> > ligand structure. I don't know if is possible to de the "extraction"
> >> > with Open Babel.
> >> >
> >> > Best regards.
> >> >
> >> > El jue, 23-10-2008 a las 09:35 +0100, Noel O'Boyle escribió:
> >> >> Dear David,
> >> >>
> >> >> If you look at the Pybel code you will see how you can use a SMARTS
> >> >> search to identify the matching atoms. The matching atoms will just be
> >> >> a fragment of the structure, and so I don't know how/why you would
> >> >> convert this to a SMILES.
> >> >>
> >> >> HTH,
> >> >> Noel
> >> >>
> >> >> 2008/10/22 David García Aristegui <[hidden email]>:
> >> >> > Hello, newbie question: i would like to load in a database the structure
> >> >> > of some functional groups, but not "by hand". So, i think a way to do it
> >> >> > is to code a script invoking Open Babel, extracting from a .smi file the
> >> >> > structure of the existing functional groups.
> >> >> >
> >> >> > I know how to use Obgrep to detect which structures have a certain
> >> >> > functional group in it (is very useful the SMARTS values provided in
> >> >> > patterns.txt file), but not how to extract the functional group itself
> >> >> > and his structure.
> >> >> >
> >> >> > Is this possible? i mean, how could i use Open Babel to do the check of
> >> >> > the matching atoms (the functional group), and then extract functional
> >> >> > group structure and convert it to SMILES?
> >> >> >
> >> >> > Thank you in advanced, best regards.
> >> >> >
> >> >> >
> >> >> > -------------------------------------------------------------------------
> >> >> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> >> >> > Build the coolest Linux based applications with Moblin SDK & win great prizes
> >> >> > Grand prize is a trip for two to an Open Source event anywhere in the world
> >> >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
> >> >> > _______________________________________________
> >> >> > OpenBabel-discuss mailing list
> >> >> > [hidden email]
> >> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
> >> >> >
> >> >
> >> >
> >
> >


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Re: Doubt about extracting functional groups

Noel O'Boyle
Administrator
Apologies - you're correct - I didn't know that. I'm not sure though
whether OB will be able to create such SMILES for you.

2008/10/23 David García Aristegui <[hidden email]>:

> I think is not the same: the SMILES format could use the wildcard (*):
>
> "* is wildcard (any atom). The wildcard atom may also be written without
> brackets"
> http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html
>
> The SMARTS pattern for an aldehyde is:
> [#6][CX3](=O)   3 aldehyde or ketone
>
> The SMILES representation for the funtional group is
> ([H]C([*])=O)
>
> Thank you again. Best regards.
>
> El jue, 23-10-2008 a las 11:15 +0100, Noel O'Boyle escribió:
>> The final structure you show is not a SMILES format, but is a SMARTS
>> substructure query. I think you should look at SMARTS_InteLigand.txt
>> which already contains a list of these.
>>
>> 2008/10/23 David García Aristegui <[hidden email]>:
>> > For example. i have a ligand with a formyl group in it. I would like to
>> > detect the group, and "extract" the structure in SMILES format
>> > ([H]C([*])=O).
>> >
>> > I have to load a database with functional groups structure, and if is
>> > possible, i don't want to do it manually... I think a way to do it could
>> > be to extract the functional groups from a representative set of
>> > ligands.
>> >
>> > Thankx!!!.
>> >
>> > El jue, 23-10-2008 a las 10:37 +0100, Noel O'Boyle escribió:
>> >> Can you give a complete example? I don't think you can represent a
>> >> fragment of a molecule with SMILES at least with OpenBabel.
>> >>
>> >> Noel
>> >>
>> >> 2008/10/23 David García Aristegui <[hidden email]>:
>> >> > Thank you for your response.  My goal is to load in a database the
>> >> > structure (SMILES format) of the functional groups extracted from the
>> >> > ligand structure. I don't know if is possible to de the "extraction"
>> >> > with Open Babel.
>> >> >
>> >> > Best regards.
>> >> >
>> >> > El jue, 23-10-2008 a las 09:35 +0100, Noel O'Boyle escribió:
>> >> >> Dear David,
>> >> >>
>> >> >> If you look at the Pybel code you will see how you can use a SMARTS
>> >> >> search to identify the matching atoms. The matching atoms will just be
>> >> >> a fragment of the structure, and so I don't know how/why you would
>> >> >> convert this to a SMILES.
>> >> >>
>> >> >> HTH,
>> >> >> Noel
>> >> >>
>> >> >> 2008/10/22 David García Aristegui <[hidden email]>:
>> >> >> > Hello, newbie question: i would like to load in a database the structure
>> >> >> > of some functional groups, but not "by hand". So, i think a way to do it
>> >> >> > is to code a script invoking Open Babel, extracting from a .smi file the
>> >> >> > structure of the existing functional groups.
>> >> >> >
>> >> >> > I know how to use Obgrep to detect which structures have a certain
>> >> >> > functional group in it (is very useful the SMARTS values provided in
>> >> >> > patterns.txt file), but not how to extract the functional group itself
>> >> >> > and his structure.
>> >> >> >
>> >> >> > Is this possible? i mean, how could i use Open Babel to do the check of
>> >> >> > the matching atoms (the functional group), and then extract functional
>> >> >> > group structure and convert it to SMILES?
>> >> >> >
>> >> >> > Thank you in advanced, best regards.
>> >> >> >
>> >> >> >
>> >> >> > -------------------------------------------------------------------------
>> >> >> > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
>> >> >> > Build the coolest Linux based applications with Moblin SDK & win great prizes
>> >> >> > Grand prize is a trip for two to an Open Source event anywhere in the world
>> >> >> > http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> >> >> > _______________________________________________
>> >> >> > OpenBabel-discuss mailing list
>> >> >> > [hidden email]
>> >> >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >> >> >
>> >> >
>> >> >
>> >
>> >
>
>

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Re: Doubt about extracting functional groups

peter murray-rust
In reply to this post by David García Aristegui

David García Aristegui wrote:

> I think is not the same: the SMILES format could use the wildcard (*):
>
> "* is wildcard (any atom). The wildcard atom may also be written without
> brackets"
> http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html
>
> The SMARTS pattern for an aldehyde is:
> [#6][CX3](=O) 3 aldehyde or ketone
>
> The SMILES representation for the funtional group is
> ([H]C([*])=O)
>
> Thank you again. Best regards.

I agree with David's interpretation. Like a number of things in the SMILES
spec it is not sufficiently. There are cases where it is reasonable to say
"I know this compound has an atom here but I don't know what it is". That
represents uncertainty, which is not necessarily the same as a query. What
the intention of Weininger was when he wrote this we may never know.

In JUMBO I translate this to an atom of elementType "R" in CML. Whether
that is a single atom or potentially a group is left undefined.

P.--
Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069 Fax: +44 1223 763076



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Re: Doubt about extracting functional groups

Chris Morley-3
Dr P. Murray-Rust wrote:

> David García Aristegui wrote:
>> I think is not the same: the SMILES format could use the wildcard (*):
>>
>> "* is wildcard (any atom). The wildcard atom may also be written without
>> brackets"
>> http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html
>>
>> The SMARTS pattern for an aldehyde is:
>> [#6][CX3](=O) 3 aldehyde or ketone
>>
>> The SMILES representation for the funtional group is
>> ([H]C([*])=O)
>>
>> Thank you again. Best regards.
>
> I agree with David's interpretation. Like a number of things in the SMILES
> spec it is not sufficiently. There are cases where it is reasonable to say
> "I know this compound has an atom here but I don't know what it is". That
> represents uncertainty, which is not necessarily the same as a query. What
> the intention of Weininger was when he wrote this we may never know.
>
> In JUMBO I translate this to an atom of elementType "R" in CML. Whether
> that is a single atom or potentially a group is left undefined.

The SMILES atom * is handled ok by OpenBabel. In OBMol it is an atom
with zero atomic number. It is output as * in MDL mol , as *(without
the brackets)in SMILES and as R in CML.

What you seem to be looking for is a SMARTS to SMILES converter,
which, as far as I know OpenBabel doesn't have, and I wonder whether
such a thing is possible. While SMILES ([H]C([*])=O) will match (as
SMARTS) all aldehydes, it will also match formic acid and its esters.
You could probably devise a SMARTS pattern to exclude these, but
SMILES isn't subtle enough. So why do you want to store functional
groups in you database as SMILES rather than SMARTS?

By the way, don't use patterns.txt because it is too incomplete. Use
SMARTS_InteLigand.txt instead.

Chris

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Re: Doubt about extracting functional groups

Craig James-2
Chris Morley wrote:

> Dr P. Murray-Rust wrote:
>> David García Aristegui wrote:
>>> I think is not the same: the SMILES format could use the wildcard (*):
>>>
>>> "* is wildcard (any atom). The wildcard atom may also be written without
>>> brackets"
>>> http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html
>>>
>>> The SMARTS pattern for an aldehyde is:
>>> [#6][CX3](=O) 3 aldehyde or ketone
>>>
>>> The SMILES representation for the funtional group is
>>> ([H]C([*])=O)

Watch out for the brackets.  [H]C([*])=O is not the same as [H]C(*)=O.  Inside brackets, '*' specifically means "an atom with a hydrogen count of zero".

>>> Thank you again. Best regards.
>> I agree with David's interpretation. Like a number of things in the SMILES
>> spec it is not sufficiently. There are cases where it is reasonable to say
>> "I know this compound has an atom here but I don't know what it is". That
>> represents uncertainty, which is not necessarily the same as a query. What
>> the intention of Weininger was when he wrote this we may never know.

The '*' is not unique in this regard.  As an analogy, if you write, "ClC=CCl", does it mean "unknown" or "racimic mixture" of the cis/trans forms? This is identical to the uncertainty of the meaning of '*'.  It could be an atom, or a functional group -- the SMILES doesn't say, because that's outside of the scope of the SMILES spec.

This is the domain of chemical registry systems, not cheminformatics systems.  There's a brief example of the difference in my "cheminformatics 101" article: http://www.emolecules.com/doc/cheminformatics-101.htm#A5

Craig



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Re: Doubt about extracting functional groups

David García Aristegui
Very interesting your article!!! So, a quick question: we are using a
program to do a combinatorial enumeration, but it only works with
strcutures in SMILES format.

We are downloading the functional groups from a public database, and all
groups in have an  asterisk in in them indicating where the group would
be attached. This is the default annotation prescribed by IUPAC for
drawing structures. For example:

acetyl group
 
  Marvin  03150713092D          

  4  3  0  0  0  0            999 V2000
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
M  END

How could convert and store the fg structure in SMILES format, is this
possible?. Thank you in advanced, best regards.

El jue, 23-10-2008 a las 09:23 -0700, Craig A. James escribió:

> Chris Morley wrote:
> > Dr P. Murray-Rust wrote:
> >> David García Aristegui wrote:
> >>> I think is not the same: the SMILES format could use the wildcard (*):
> >>>
> >>> "* is wildcard (any atom). The wildcard atom may also be written without
> >>> brackets"
> >>> http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html
> >>>
> >>> The SMARTS pattern for an aldehyde is:
> >>> [#6][CX3](=O) 3 aldehyde or ketone
> >>>
> >>> The SMILES representation for the funtional group is
> >>> ([H]C([*])=O)
>
> Watch out for the brackets.  [H]C([*])=O is not the same as [H]C(*)=O.  Inside brackets, '*' specifically means "an atom with a hydrogen count of zero".
>
> >>> Thank you again. Best regards.
> >> I agree with David's interpretation. Like a number of things in the SMILES
> >> spec it is not sufficiently. There are cases where it is reasonable to say
> >> "I know this compound has an atom here but I don't know what it is". That
> >> represents uncertainty, which is not necessarily the same as a query. What
> >> the intention of Weininger was when he wrote this we may never know.
>
> The '*' is not unique in this regard.  As an analogy, if you write, "ClC=CCl", does it mean "unknown" or "racimic mixture" of the cis/trans forms? This is identical to the uncertainty of the meaning of '*'.  It could be an atom, or a functional group -- the SMILES doesn't say, because that's outside of the scope of the SMILES spec.
>
> This is the domain of chemical registry systems, not cheminformatics systems.  There's a brief example of the difference in my "cheminformatics 101" article: http://www.emolecules.com/doc/cheminformatics-101.htm#A5
>
> Craig
>
>
>
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Other conversors

David García Aristegui
In reply to this post by Craig James-2
The conversion can be done with other programs...

acetyl group
 
  Marvin  03150713092D          

  4  3  0  0  0  0            999 V2000
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
M  END

babel -imol acetyl.mol -osmi acetyl.smi
0 molecules converted
3 audit log messages

http://www.molecular-networks.com/online_demos/convert_demo.html
C(=O)([*])[C]

http://cactus.nci.nih.gov/services/translate/
CC(=O)[*]

Best regards.
El jue, 23-10-2008 a las 09:23 -0700, Craig A. James escribió:

> Chris Morley wrote:
> > Dr P. Murray-Rust wrote:
> >> David García Aristegui wrote:
> >>> I think is not the same: the SMILES format could use the wildcard (*):
> >>>
> >>> "* is wildcard (any atom). The wildcard atom may also be written without
> >>> brackets"
> >>> http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html
> >>>
> >>> The SMARTS pattern for an aldehyde is:
> >>> [#6][CX3](=O) 3 aldehyde or ketone
> >>>
> >>> The SMILES representation for the funtional group is
> >>> ([H]C([*])=O)
>
> Watch out for the brackets.  [H]C([*])=O is not the same as [H]C(*)=O.  Inside brackets, '*' specifically means "an atom with a hydrogen count of zero".
>
> >>> Thank you again. Best regards.
> >> I agree with David's interpretation. Like a number of things in the SMILES
> >> spec it is not sufficiently. There are cases where it is reasonable to say
> >> "I know this compound has an atom here but I don't know what it is". That
> >> represents uncertainty, which is not necessarily the same as a query. What
> >> the intention of Weininger was when he wrote this we may never know.
>
> The '*' is not unique in this regard.  As an analogy, if you write, "ClC=CCl", does it mean "unknown" or "racimic mixture" of the cis/trans forms? This is identical to the uncertainty of the meaning of '*'.  It could be an atom, or a functional group -- the SMILES doesn't say, because that's outside of the scope of the SMILES spec.
>
> This is the domain of chemical registry systems, not cheminformatics systems.  There's a brief example of the difference in my "cheminformatics 101" article: http://www.emolecules.com/doc/cheminformatics-101.htm#A5
>
> Craig
>
>
>
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> Build the coolest Linux based applications with Moblin SDK & win great prizes
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Re: Doubt about extracting functional groups

cristallino
In reply to this post by David García Aristegui
Hi
i've a similar (if not identical) problem... Just to make an example, i want to extract from a ATP molecule (in PDB format) the ribose atoms.
I know how to use obgrep to test if an ATP molecule has the ribose inside (for example a simple SMARTS 'CC1OCCC1' ), but then i do not know how to extract the ATP atoms forming that 'CC1OCCC1' SMARTS.

Can anyone help me (us)? (thanks a lot)