[Biojava-l] Access chain letter and residue number from Atom object

[Jose Duarte]

All you need is to get the group (residue) and then the chain:

atom.getGroup().getChain().getChainID(); // gives you the author chain id
(biojava 4+)

In biojava 5 (currently in development, but some alpha versions have been
released) it would be slightly different:

atom.getGroup().getChain().getName(); // for the author chain id

atom.getGroup().getChain().getId(); // for the asym_id (internal chain
identifier in mmcif files)


For the residue number you can do:

atom.getGroup().getResidueNumber();

Hope that helps

Jose



On Fri, May 12, 2017 at 3:07 AM, Enrico Morelli <morelli at cerm.unifi.it>
wrote:

> Dear,
>
> I'm using BioJava for a project. After some filtering operations I've
> an Atom list, but I've to know the chain and the residue number for
> each atom.
>
> My PDB has the following format:
>
> HETATM 1661 MG    MG A 580      69.222  44.815  33.339  1.00
> 61.74          MG
>
> Through an Atom object seems that should not possible to access to the
> chain (A) and residue number (580). There is a way to do that?
>
> Thanks
>
> --
> -------------------------------------------------------------
>   Enrico Morelli
>   System Administrator | Programmer | Web Developer
>
>   CERM - Polo Scientifico
>   Via Sacconi, 6 - 50019 Sesto Fiorentino (FI) - ITALY
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