[Biojava-l] PDBFileParser and Atom element symbol

[Andreas Prlic]

Hi Andy

Questions:

> * Is this pattern documented in the PDB specification?
>

see here:
http://www.wwpdb.org/documentation/format23/sect9.html#ATOM


> * If this pattern can be relied on, why are columns 77-78 also dedicated to
> the element symbol?
>
That is the atom's element symbol (as given in the periodic table), in
contrast to the first name, which contains numbering information.

* Should reliance on the pattern be hidden behind a BioJava method?
>

If you think that is important we could probably provide an enum for all
atom types. There are two categories though: the periodic table symbol and
the one that is related to the position in an amino acid....

Andreas




>
>
>
>  ------------------------------
>
> *From:* andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] *On
> Behalf Of *Andreas Prlic
> *Sent:* Friday, April 23, 2010 6:52 PM
> *To:* Andy Thomas-Cramer
> *Cc:* biojava-l at lists.open-bio.org
> *Subject:* Re: [Biojava-l] PDBFileParser and Atom element symbol
>
>
>
> 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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>
>
>
> --
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------
>



-- 
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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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