[Biojava-l] PDBFileReader vs MMCIFFileReader - Parsing chain data into BioJava data structure

[Andreas Prlic]

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 <pmpangase at gmail.com>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
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