I mean the starting position of the first Atom for e.g.
I import the Molecule from a SDFile so I thought there is a ordering of the
atoms. So I need to get a position for each fragment I can order them.
Example: I have a Molecule and have 5 fragments which are created out of the
molecule. Now I want to build a fragment graph which represents the molecule on
a abstracted way that I only have the ids of the fragments. Here it is very
important that the fragments are ordered correctly.
So I need to get the information of each fragment where it is integrated in the
molecule.
I think it is enough to get the position of a specific atom of every fragment.
As I remember an AtomContainer provides a method to get the id of a given atom.
Maybe this is enough but I thought if there is a more elegant way to handle
with this problem.
I am new in the field and not very familiar working with molecules so I need
some advices how to work on this problem.
Thanks for you’re advices!
Cheers,
Niko
> On 30 Mar 2017, at 14:41, Christoph Steinbeck <[email protected]>
> wrote:
>
> Not sure what you mean by 'position', as opposed to 'presence'.
> You can indeed get a sub graph matching and then find, for example, the
> neighbouring atoms.
>
> Cheers,
>
> Chris
>
> --
> Prof. Dr. Christoph Steinbeck
> Analytical Chemistry - Cheminformatics and Chemometrics
> Institute for Inorganic and Analytical Chemistry
> Friedrich-Schiller-University
> Lessingstr. 8, D-07743 Jena, Germany <x-apple-data-detectors://2/0>
> Phone Secretariat: +49-3641-948171 <tel:+49-3641-948171>
> Email: [email protected]
> <mailto:[email protected]>
> http://orcid.org/0000-0001-6966-0814 <http://orcid.org/0000-0001-6966-0814>
>
> Am 30.03.2017 um 13:37 schrieb Nikolas Glaser <[email protected]
> <mailto:[email protected]>>:
>
>> Hello guys,
>>
>> is there a class provided which helps to detect a position of a fragment
>> e.g. a ring in a given molecule?
>>
>> Thanks for your help.
>>
>> NG
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