[Biojava-l] PDBFileParser and Atom element symbol

Andreas Prlic andreas at sdsc.edu
Fri Apr 23 23:52:15 UTC 2010

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...


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?
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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

More information about the Biojava-l mailing list