Hi Phele, The mmcif parsing framework currently does not read some of the header information, yet. I'll file it as a feature request. In the meanwhile, you could use the PDB file parser to get that data loaded ...
Andreas On Tue, Jul 2, 2013 at 1:13 AM, Phelelani Mpangase <[email protected]>wrote: > Hi all > > I am using the MMCIFFileParser class to parse the mmCIF files, which I > understand should parse the mmCIF files into the same BioJava data > structure as the PDB files. However, it seems as if some of the data in the > mmCIF files is not loaded into the BioJava data structure. > > I was looking to obtain some information for each the chains in mmCIF files > (organism, expression system etc) but I noticed that when I use the class > getChains() on the structre parsed using the MMCIFFileParser, I always get > "null" results. Here is code below demonstrating the results of the same > PDB ID parsed with the PDBFileReader as well as the MMCIFFileReader: > > String pdbid = "4hhb"; > String dataDownload = "/tmp/"; > > //pdb parser > PDBFileReader pdbreader = new PDBFileReader(); > pdbreader.setAutoFetch(true); > pdbreader.setPath(dataDownload); > > //mmCIF parser > StructureIOFile cifreader = new MMCIFFileReader(); > cifreader.setAutoFetch(true); > cifreader.setPath(dataDownload); > > //Parse pdb and cif structures into BioJava data structure > Structure pdbstruc = pdbreader.getStructureById(pdbid); > Structure cifstruc = cifreader.getStructureById(pdbid); > > System.out.println("Chain information for PDB structure " + pdbid + > ":"); > > //Get the chain information > List<Chain> pdbChains = pdbstruc.getChains(); > for (Chain chain : pdbChains){ > System.out.println(chain.getHeader()); > } > > > System.out.println("----------------------------------------------------"); > System.out.println("\nChain information for mmCIF Structure " + > pdbid + ":"); > > //Get the chain information > List<Chain> cifChains = cifstruc.getChains(); > for (Chain chain : cifChains){ > System.out.println(chain.getHeader()); > } > > System.out.println("----------------------------------------------------"); > > > Are there additional classes I need to be using in order for the chain > information in mmCIF files to be parsed into the BioJava data structure at > the PDB files? > > Regards, > Phele > _______________________________________________ > 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
