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:* [email protected] [mailto:[email protected]] *On > Behalf Of *Andreas Prlic > *Sent:* Friday, April 23, 2010 6:52 PM > *To:* Andy Thomas-Cramer > *Cc:* [email protected] > *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 < > [email protected]> 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 - [email protected] > 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 > ----------------------------------------------------------------------- > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
