[Biojava-l] Working with mmCIF files

[Phelelani Mpangase]

Hi Andreas

That solved my problem. Thank you so much for the help.

-Phele


On Fri, Jun 14, 2013 at 2:34 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Phele,
>
> You are right that the PdbxEntityNonPoly class is the correct container
> for that cif-category. However, at the moment the SimpleMMcifConsumer does
> not do much with the PdbxEntityNonPoly data. This is because the same
> content is available via the chemical component dictionary which is used by
> biojava-structure as well.
>
> To explain this with an example:
>
> PDB ID 1A4W has the non-poly QWE
>
> You can access all the related information using the code below.
>
> Hope that makes sense and let us know if anything is unclear!
>
> Andreas
>
>
> String pdbId = "1A4W";
>
> StructureIOFile pdbreader = new MMCIFFileReader();
>
>  try {
>
>  pdbreader.setAutoFetch(true);
>
>  Structure s = pdbreader.getStructureById(pdbId);
>
>    Chain h = s.getChainByPDB("H");
>
>
>   List<Group> ligands = h.getAtomLigands();
>
>    System.out.println("These ligands have been found in chain " +
> h.getChainID());
>
>    for (Group l:ligands){
>
>   System.out.println(l);
>
>  }
>
>    System.out.println("Accessing QWE directly: ");
>
>  Group qwe = h.getGroupByPDB(new ResidueNumber("H",373,null));
>
>
>   System.out.println(qwe.getChemComp());
>
>    System.out.println(h.getSeqResSequence());
>
>  System.out.println(h.getAtomSequence());
>
>  System.out.println(h.getAtomGroups(GroupType.HETATM));
>
>      } catch (Exception e) {
>
>  e.printStackTrace();
>
>  }
>
>
>
>
> On Thu, Jun 13, 2013 at 1:11 AM, Phelelani Mpangase <pmpangase at gmail.com>wrote:
>
>> Hello
>>
>> I am new to the Java progrmming language, and I am currently working on a
>> project where I have to find information about a protein structure from
>> the
>> mmCIF file. I would like to extract information about non-polymers in
>> structures (_pdbx_entity_nonpoly table) using BioJava. How do I go about
>> achieving this?
>>
>> I have been able to parse the structure using the SimpleMMcifConsumer, but
>> I am unclear as to the steps I need to follow from there. Is the
>> PdbxEntityNonPoly the right class to use? How do I use this class to
>> achieve to get the data from the "_pdbx_entity_nonpoly"?
>>
>> Regards,
>> Phele
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
>
>
>
>