[Biojava-l] PDBFileParser and Atom element symbol

[Andy Thomas-Cramer]

Thank you. I had not noticed the pattern that columns 13-14 at least
sometimes contain the element symbol, whether one- or two-character.

 

Questions:

* Is this pattern documented in the PDB specification? 

* If this pattern can be relied on, why are columns 77-78 also dedicated
to the element symbol?

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

 

 

________________________________

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
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