[Biojava-l] sturcture.io

[Tamas Horvath]

Oh, I forgot I should instanciate a PDBFileParser, so the following codeworks fine:
public static Object parse_pdb(String pdb_datafile, String pdb_id) {       Structure structure = null;       pdb_inputstream = Utils.get_pdbinputstream(pdb_datafile,pdb_id);       PDBFileParser pdbfileparser = new PDBFileParser();       try {           if (pdb_inputstream != null)               structure = pdbfileparser.parsePDBFile(pdb_inputstream);       }       catch (IOException ioe) {System.out.println(ioe);}
       return structure;   }
On 11/30/05, Tamas Horvath <hotafin at gmail.com> wrote:>> In my case, I had a bunch of pdb files in a jar archive, so here's the> code I try to use:>>    public static InputStream get_pdbinputstream(String fileName,String> pdb_id) {>           System.out.println(fileName);>           InputStream returnstream = null;>           JarFile jarFile = null;>             try {>                jarFile = new JarFile(fileName);>                for (Enumeration e = jarFile.entries(); e.hasMoreElements();) {>>                    JarEntry jarEntry = (JarEntry) e.nextElement();>>                    if (jarEntry.isDirectory()) continue;>>                    String pdbid = jarEntry.getName();>                    pdbid = pdbid.substring(0, 4).toUpperCase();>                    System.out.println(pdbid);>                    if (pdbid.intern() != pdb_id) continue;>>                    returnstream = jarFile.getInputStream(jarEntry);>                }>             } catch (IOException ioe) {>                System.out.println("An IOException occurred: " +> ioe.getMessage());>             } finally {>                if (jarFile != null) {>                   try { jarFile.close(); } catch (IOException ioe) {}>                }>             }>             return returnstream;>    }>>    public static Object parse_pdb(String pdb_datafile, String pdb_id) {>        Structure structure = null;>        pdb_inputstream = Utils.get_pdbinputstream(pdb_datafile,pdb_id);>        if (pdb_inputstream != null) structure = org.biojava.bio.structure.io> .PDBFileParser.parsePDBFile(pdb_inputstream);>        return structure;>    }>> The 1st function is supposed to get the desired InputStream from the> specified archive file, while the second supposed to generate the structure.> However:>> "Utils.java": non-static method parsePDBFile(java.io.InputStream) cannot> be referenced from a static context at line 1132, column 92> as it kindly sais...>> Is there a solution of this problem?>>> On 11/30/05, Andreas Prlic < ap3 at sanger.ac.uk> wrote:>> > Hi Tamas,> >> > In case you are working with a PDB file that is located> > somewhere on  your hard disk, you could use the code from below> > to parse it in.> >> > Cheers,> > Andreas> >> >> > String filename =  "path/to/pdbfile.ent" ;> >> >   PDBFileReader pdbreader = new PDBFileReader();> >> >   try{> >         Structure struc = pdbreader.getStructure(filename);> >         System.out.println(struc);> >   } catch (Exception e) {> >         e.printStackTrace();> >   }> >> >> >> > On 29 Nov 2005, at 16:25, Tamas Horvath wrote:> >> > > I've got an ArrayList<String> object containing a PDB file's> > > information.How may I feed it to the structure parser? As far as I> > > could see, it onlyaccepts BufferdReader or imputStream...> >> >> > > ----------------------------------------------------------------------> >> > Andreas Prlic      Wellcome Trust Sanger Institute> >                                Hinxton, Cambridge CB10 1SA, UK> >                          +44 (0) 1223 49 6891> >> > _______________________________________________> > Biojava-l mailing list  -  Biojava-l at biojava.org> > http://biojava.org/mailman/listinfo/biojava-l> >>>