[Biojava-l] PDBFileParser and Atom element symbol

[Andreas Prlic]

Hi Andy,

you could check with  Atom.getFullname(), which contains the space
characters from the PDB file:
e.g Calpha: " CA ", Calcium "CA  "

in addition the parent group of a Calpha atom is usually an AminoAcid and
for Calciums it is a Hetatom group...

Andreas

On Fri, Apr 23, 2010 at 3:58 PM, Andy Thomas-Cramer <
thomascramera at dnastar.com> wrote:

>
>
> Is there an easy way to identify the type of atom referenced by an Atom
> object?
>
> For example, if Atom.getName() is "CA", is the element calcium or the
> atom carbon alpha?
>
> If not, would it be feasible to add a method providing this in Atom,
> AtomImpl, and parsing it in PDBFileParser, using the columns defined at
> http://www.wwpdb.org/documentation/format32/sect9.html#ATOM?
>
>
>
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>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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