How to use

getStructureById

method

in

org.biojava.nbio.structure.io.PDBFileReader

Structure s1 = pdbr.getStructureById(pdb1);
Structure s2 = pdbr.getStructureById(pdb2);

Structure s1 = pdbr.getStructureById(pdb1);
Structure s2 = pdbr.getStructureById(pdb2);

protected Structure loadStructureFromPdbByPdbId(String pdbId) throws IOException, StructureException {
  logger.debug("Loading structure {} from PDB file {}.", pdbId, path);
  Structure s;
  flagLoading(pdbId);
  try {
    PDBFileReader reader = new PDBFileReader(path);
    reader.setFetchBehavior(fetchBehavior);
    reader.setObsoleteBehavior(obsoleteBehavior);
    reader.setFileParsingParameters(params);
    s = reader.getStructureById(pdbId.toLowerCase());
  } finally {
    flagLoadingFinished(pdbId);
  }
  return s;
}

Structure structure1 = reader.getStructureById(pdb);

Structure structure1 = reader.getStructureById(pdb);

Structure s1 = pdbr.getStructureById(pdb1);
Structure s2 = pdbr.getStructureById(pdb2);

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();
  }
}