Re: [AMBER] NAB atom manipulation

From: David A. Case <>
Date: Thu, 18 Jul 2013 11:43:09 -0400

On Wed, Jul 17, 2013, Daniel Leclerc wrote:
> I am able to load in a .pdb file as a molecule, but how do I access the
> data of the individual atoms, such as the attributes in 15.3.2 of the
> manual (atomname, atomnum, etc)? I'm missing something like a "foreach" or
> "find atom" function that would allow me to work with individual atoms of
> the molecule. This seems like it should be fairly simple, am I missing
> something?

Typical pseudo-code looks like this:

m = getpdb(..)
for (a in m){
    if( a.fullname == "1:23:CA" ){
       // do something with the CA atom in residue 23 of strand 1

...hope this helps....dac

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Received on Thu Jul 18 2013 - 09:00:03 PDT
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