[Biojava-l] PDBFileParser and identifying atoms in ligands

[Andreas Prlic]

Hi Andy,

I have updated the BioJava structure data model to support the PDB
chemical component dictionary. This has the benefit that now

* Chemically modified amino acids can be detected (and treated as
amino acids, rather than Hetatom groups)
* It is possible to get a  component type for each Group, which allows
to identify ligands.

As a consequence the nr. of amino acids in a chain can change compared
to the previous data representation. As such the loading of chem.
comps is set to "false" by default. It can be configure by the
"loadChemCompInfo" flag in the PDB/mmCIF file parsers.

You can get the code either from SVN, or I also uploaded it to the
(slightly experimental) Maven repository at
http://www.biojava.org/download/maven/ .

Andreas