Fwd: atom naming for NMR assignments

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Fwd: atom naming for NMR assignments

Eiso AB-2

hi,

I'm looking for some convenient standard atom naming scheme that I
could use for assigning (1H) NMR resonances on a large set of compounds.

Preferably, atoms that are topologically similar and/or are chemically
and or magnetically equivalent would have similar names (or root names),
for example the protons of a single methylgroup, equivalent protons
of rotating aromatic groups (like PHE/TYR HD/HE).

My initial thoughts run in this direction:

* generate cansmi (to be independent of how the input format is specified)

* name heavy atoms numerically or alphabetically following the smiles string or
   molecular tree from the start, preferably taking symmetries in the molecule
   into account (but how?).

* name the hydrogens after the attached heavyatom.

First and last point are trivial I guess, but the middle point seems to
be quite tricky. I'm probably not the first with this problem, so if anyone
knows software that does something similar or has suggestions how to approach
this, I would be very grateful.

kind regards - Eiso











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Re: Fwd: atom naming for NMR assignments

Noel O'Boyle
Administrator
Try circular fingerprints. Open Babel has two: MolPrint2D and MNA. See
http://baoilleach.webfactional.com/site_media/ob-docs/FileFormats/Utility.html

NMRShiftDB uses circular fingerprints (HOSE codes to be exact) for
just this purpose. In fact, it might be worth while implementing HOSE
codes for Open Babel if you're interested in writing a new file
format.

- Noel

On 17 August 2010 12:16, Eiso AB <[hidden email]> wrote:

>
> hi,
>
> I'm looking for some convenient standard atom naming scheme that I
> could use for assigning (1H) NMR resonances on a large set of compounds.
>
> Preferably, atoms that are topologically similar and/or are chemically
> and or magnetically equivalent would have similar names (or root names),
> for example the protons of a single methylgroup, equivalent protons
> of rotating aromatic groups (like PHE/TYR HD/HE).
>
> My initial thoughts run in this direction:
>
> * generate cansmi (to be independent of how the input format is specified)
>
> * name heavy atoms numerically or alphabetically following the smiles string or
>   molecular tree from the start, preferably taking symmetries in the molecule
>   into account (but how?).
>
> * name the hydrogens after the attached heavyatom.
>
> First and last point are trivial I guess, but the middle point seems to
> be quite tricky. I'm probably not the first with this problem, so if anyone
> knows software that does something similar or has suggestions how to approach
> this, I would be very grateful.
>
> kind regards - Eiso
>
>
>
>
>
>
>
>
>
>
>
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>
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>

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Re: Fwd: atom naming for NMR assignments

Tim Vandermeersch
In reply to this post by Eiso AB-2
On Tue, Aug 17, 2010 at 1:16 PM, Eiso AB <[hidden email]> wrote:

>
> hi,
>
> I'm looking for some convenient standard atom naming scheme that I
> could use for assigning (1H) NMR resonances on a large set of compounds.
>
> Preferably, atoms that are topologically similar and/or are chemically
> and or magnetically equivalent would have similar names (or root names),
> for example the protons of a single methylgroup, equivalent protons
> of rotating aromatic groups (like PHE/TYR HD/HE).
>
> My initial thoughts run in this direction:
>
> * generate cansmi (to be independent of how the input format is specified)
>
> * name heavy atoms numerically or alphabetically following the smiles string or
>   molecular tree from the start, preferably taking symmetries in the molecule
>   into account (but how?).

OpenBabel has symmetry classes which might be an initial starting
point. See OBGraphSym and:

http://timvdm.blogspot.com/2009/09/symmetry-classes-how-to-get-them-and.html

> * name the hydrogens after the attached heavyatom.
>
> First and last point are trivial I guess, but the middle point seems to
> be quite tricky. I'm probably not the first with this problem, so if anyone
> knows software that does something similar or has suggestions how to approach
> this, I would be very grateful.
>
> kind regards - Eiso
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
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> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>

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Re: Fwd: atom naming for NMR assignments

Eiso AB-2

Tim and Noel thanks a lot for the info and links. Looks
very useful. I didn't know about HOSE codes. It seems hard
though to use those to generate a atoms label that you can
use in a pdb file (max 4 characters ; since I'm working with
3D structures that would be convenient)

Regarding the symmetry classes I had alreay run into
mol.OBMol.GetGIDVector yesterday but from the documentation in
http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBMol.shtml#de880e97f2bdf3c90e91375aec12aaf0
I can't figure out how to use it.

import pybel
smi='COC1=C(C(N)=O)C(C)=CC(C)=N1'
mol=pybel.readstring('smi',smi)
mol.OBMol.GetGIDVector(???)

what kind of argument does it expect? It seems some kind
of vector,but what? maybe I'm confusing the python/pybel and
c++ worlds.


Are there any usage examples to be found on the web?


thanks ahead,

E


Tim Vandermeersch wrote:

> On Tue, Aug 17, 2010 at 1:16 PM, Eiso AB<[hidden email]>  wrote:
>>
>> hi,
>>
>> I'm looking for some convenient standard atom naming scheme that I
>> could use for assigning (1H) NMR resonances on a large set of compounds.
>>
>> Preferably, atoms that are topologically similar and/or are chemically
>> and or magnetically equivalent would have similar names (or root names),
>> for example the protons of a single methylgroup, equivalent protons
>> of rotating aromatic groups (like PHE/TYR HD/HE).
>>
>> My initial thoughts run in this direction:
>>
>> * generate cansmi (to be independent of how the input format is specified)
>>
>> * name heavy atoms numerically or alphabetically following the smiles string or
>>    molecular tree from the start, preferably taking symmetries in the molecule
>>    into account (but how?).
>
> OpenBabel has symmetry classes which might be an initial starting
> point. See OBGraphSym and:
>
> http://timvdm.blogspot.com/2009/09/symmetry-classes-how-to-get-them-and.html
>
>> * name the hydrogens after the attached heavyatom.
>>
>> First and last point are trivial I guess, but the middle point seems to
>> be quite tricky. I'm probably not the first with this problem, so if anyone
>> knows software that does something similar or has suggestions how to approach
>> this, I would be very grateful.
>>
>> kind regards - Eiso
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by
>>
>> Make an app they can't live without
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>> http://p.sf.net/sfu/RIM-dev2dev
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>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>
>


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Re: Fwd: atom naming for NMR assignments

Noel O'Boyle
Administrator
On 18 August 2010 15:47, Eiso AB <[hidden email]> wrote:
>
> Tim and Noel thanks a lot for the info and links. Looks
> very useful. I didn't know about HOSE codes. It seems hard
> though to use those to generate a atoms label that you can
> use in a pdb file (max 4 characters ; since I'm working with
> 3D structures that would be convenient)

Well, you could just create a one-to-one mapping between the HOSE code
and a 4-letter label. If you have more environments, then the 4
characters won't help in any case.

> Regarding the symmetry classes I had alreay run into
> mol.OBMol.GetGIDVector yesterday but from the documentation in
> http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBMol.shtml#de880e97f2bdf3c90e91375aec12aaf0
> I can't figure out how to use it.
>
> import pybel
> smi='COC1=C(C(N)=O)C(C)=CC(C)=N1'
> mol=pybel.readstring('smi',smi)
> mol.OBMol.GetGIDVector(???)
>
> what kind of argument does it expect? It seems some kind
> of vector,but what? maybe I'm confusing the python/pybel and
> c++ worlds.
>
>
> Are there any usage examples to be found on the web?

Hmmm...are you sure that's what you want to do? The symmetry labels
will not be the same between different molecules, whereas the circular
fingerprints would be.

Anyway, these are most easily used through a GraphSym object (see
http://openbabel.org/dev-api/classOpenBabel_1_1OBGraphSym.shtml). So
you need to pass in a vector unsigned int to GetSymmetry. In python,
try openbabel.vectorUnsignedInt().



>
> thanks ahead,
>
> E
>
>
> Tim Vandermeersch wrote:
>> On Tue, Aug 17, 2010 at 1:16 PM, Eiso AB<[hidden email]>  wrote:
>>>
>>> hi,
>>>
>>> I'm looking for some convenient standard atom naming scheme that I
>>> could use for assigning (1H) NMR resonances on a large set of compounds.
>>>
>>> Preferably, atoms that are topologically similar and/or are chemically
>>> and or magnetically equivalent would have similar names (or root names),
>>> for example the protons of a single methylgroup, equivalent protons
>>> of rotating aromatic groups (like PHE/TYR HD/HE).
>>>
>>> My initial thoughts run in this direction:
>>>
>>> * generate cansmi (to be independent of how the input format is specified)
>>>
>>> * name heavy atoms numerically or alphabetically following the smiles string or
>>>    molecular tree from the start, preferably taking symmetries in the molecule
>>>    into account (but how?).
>>
>> OpenBabel has symmetry classes which might be an initial starting
>> point. See OBGraphSym and:
>>
>> http://timvdm.blogspot.com/2009/09/symmetry-classes-how-to-get-them-and.html
>>
>>> * name the hydrogens after the attached heavyatom.
>>>
>>> First and last point are trivial I guess, but the middle point seems to
>>> be quite tricky. I'm probably not the first with this problem, so if anyone
>>> knows software that does something similar or has suggestions how to approach
>>> this, I would be very grateful.
>>>
>>> kind regards - Eiso
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> This SF.net email is sponsored by
>>>
>>> Make an app they can't live without
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>>> http://p.sf.net/sfu/RIM-dev2dev
>>> _______________________________________________
>>> OpenBabel-discuss mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>
>>
>
>
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Re: Fwd: atom naming for NMR assignments

Eiso AB-2
Noel O'Boyle wrote:

> On 18 August 2010 15:47, Eiso AB<[hidden email]>  wrote:
>>
>> Tim and Noel thanks a lot for the info and links. Looks
>> very useful. I didn't know about HOSE codes. It seems hard
>> though to use those to generate a atoms label that you can
>> use in a pdb file (max 4 characters ; since I'm working with
>> 3D structures that would be convenient)
>
> Well, you could just create a one-to-one mapping between the HOSE code
> and a 4-letter label. If you have more environments, then the 4
> characters won't help in any case.
>
>> Regarding the symmetry classes I had alreay run into
>> mol.OBMol.GetGIDVector yesterday but from the documentation in
>> http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBMol.shtml#de880e97f2bdf3c90e91375aec12aaf0
>> I can't figure out how to use it.
>>
>> import pybel
>> smi='COC1=C(C(N)=O)C(C)=CC(C)=N1'
>> mol=pybel.readstring('smi',smi)
>> mol.OBMol.GetGIDVector(???)
>>
>> what kind of argument does it expect? It seems some kind
>> of vector,but what? maybe I'm confusing the python/pybel and
>> c++ worlds.
>>
>>
>> Are there any usage examples to be found on the web?
>
> Hmmm...are you sure that's what you want to do? The symmetry labels
> will not be the same between different molecules, whereas the circular
> fingerprints would be.

not sure at all, just trying to figure out what is available
and what it all means.

>
> Anyway, these are most easily used through a GraphSym object (see
> http://openbabel.org/dev-api/classOpenBabel_1_1OBGraphSym.shtml). So
> you need to pass in a vector unsigned int to GetSymmetry. In python,
> try openbabel.vectorUnsignedInt().

thanks. E

>
>
>
>>
>> thanks ahead,
>>
>> E
>>
>>
>> Tim Vandermeersch wrote:
>>> On Tue, Aug 17, 2010 at 1:16 PM, Eiso AB<[hidden email]>    wrote:
>>>>
>>>> hi,
>>>>
>>>> I'm looking for some convenient standard atom naming scheme that I
>>>> could use for assigning (1H) NMR resonances on a large set of compounds.
>>>>
>>>> Preferably, atoms that are topologically similar and/or are chemically
>>>> and or magnetically equivalent would have similar names (or root names),
>>>> for example the protons of a single methylgroup, equivalent protons
>>>> of rotating aromatic groups (like PHE/TYR HD/HE).
>>>>
>>>> My initial thoughts run in this direction:
>>>>
>>>> * generate cansmi (to be independent of how the input format is specified)
>>>>
>>>> * name heavy atoms numerically or alphabetically following the smiles string or
>>>>     molecular tree from the start, preferably taking symmetries in the molecule
>>>>     into account (but how?).
>>>
>>> OpenBabel has symmetry classes which might be an initial starting
>>> point. See OBGraphSym and:
>>>
>>> http://timvdm.blogspot.com/2009/09/symmetry-classes-how-to-get-them-and.html
>>>
>>>> * name the hydrogens after the attached heavyatom.
>>>>
>>>> First and last point are trivial I guess, but the middle point seems to
>>>> be quite tricky. I'm probably not the first with this problem, so if anyone
>>>> knows software that does something similar or has suggestions how to approach
>>>> this, I would be very grateful.
>>>>
>>>> kind regards - Eiso
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> This SF.net email is sponsored by
>>>>
>>>> Make an app they can't live without
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>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>
>>>
>>
>>
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>


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