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: [email protected] [mailto:[email protected]] On Behalf Of Fico Sent: Wednesday, December 15, 2010 8:46 PM To: [email protected] 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. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
