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 <[email protected]> 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 > <[email protected]>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 - [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
