[Biojava-l] how to cancel download chemcomp when parser a PDB file

[Andreas Prlic]

ok that behavior is fixed in SVN now. Now you can have setAlignSeqRes
set to true and it will not download chemical components if
loadChemComp is false. The drawback is that the data representation
will not be as precise.

Andreas



On Thu, Dec 16, 2010 at 8:26 AM, Steve Darnell <darnells at dnastar.com> wrote:
> The SeqRes to Atom record alignment forces the use of chemical
> components to translate non-standard residues to their closest standard
> counterpart for the sequence alignment.  I have to disable
> setLoadChemCompInfo and setAlignSeqRes when I don't want to download
> chemical component files from RCSB when parsing a PDB file.
>
> Regards,
> Steve
>
> -----Original Message-----
> From: biojava-l-bounces at lists.open-bio.org
> [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Fico
> Sent: Wednesday, December 15, 2010 8:46 PM
> To: Biojava-l at lists.open-bio.org
> Subject: [Biojava-l] how to cancel download chemcomp when parser a PDB
> file
>
> Hi, dear all:
>
> I use biojava3 beta1 to parse the PDB files recently, my program is:
>
>            PDBFileReader pdbreader = new PDBFileReader();
>            pdbreader.setAutoFetch(false);
>            pdbreader.setPath(pdbDirPath);
>
>            FileParsingParameters params = new FileParsingParameters();
>            params.setLoadChemCompInfo(*false*);
>            params.setHeaderOnly(*false*);
>            params.setAlignSeqRes(*true*);
>            params.setParseSecStruc(*false*);
>            pdbreader.setFileParsingParameters(params);
>
>            Structure structure = null;
>            try {
>                structure = pdbreader.getStructure(pdbDirPath + "\\" +
> file);
>            } catch (IOException e) {
>                e.printStackTrace();
>            }
>
> when I execute this program, it will download something such as:
>
> *creating directory D:\MyWorkspace\TestFiles\pdbFiles\chemcomp
> downloading http://www.rcsb.org/pdb/files/ligand/35G.cif
> downloading http://www.rcsb.org/pdb/files/ligand/GDP.cif*
>
> but I do not want to lownload those stuff, How can I cancel it?
> Thanks.
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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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