How to use

setPath

method

in

org.biojava.nbio.structure.io.PDBFileReader

pdbr.setPath("/Users/andreas/WORK/PDB/");

reader.setPath(".");

public static void main(String[] args){
  try {
    PDBFileReader pdbr = new PDBFileReader();
    pdbr.setPath("/tmp/");
    String pdbCode = "5pti";
    Structure struc = pdbr.getStructureById(pdbCode);
    BiojavaJmol jmolPanel = new BiojavaJmol();
    jmolPanel.setStructure(struc);
    // send some RASMOL style commands to Jmol
    jmolPanel.evalString("select * ; color chain;");
    jmolPanel.evalString("select *; spacefill off; wireframe off; backbone 0.4;  ");
    jmolPanel.evalString("save STATE state_1");
  } catch (Exception e){
    e.printStackTrace();
  }
}

public static void main(String[] args){
  pdbr.setPath("/tmp/");

private void checkFile(String repre) throws IOException, StructureException {
  StructureName name = new StructureName(repre);
  PDBFileReader reader = new PDBFileReader();
  reader.setFetchBehavior(FetchBehavior.FETCH_REMEDIATED);
  reader.setPath(cache.getPath());
  reader.setFileParsingParameters(cache.getFileParsingParams());
  reader.prefetchStructure(name.getPdbId());
}