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 <pmpang...@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@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - Biojava-l@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l