{
// FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
- pdb = new JmolParser(pdbFile, sourceType);
-
+ pdb = new JmolParser(false, pdbFile, sourceType);
+ pdb.addSettings(parseSecStr && processSecondaryStructure,
+ parseSecStr && addTempFacAnnot,
+ parseSecStr && secStructServices);
+ pdb.doParse();
if (pdb.getId() != null && pdb.getId().trim().length() > 0
&& DataSourceType.FILE == sourceType)
{
{
System.err.println(e.getMessage());
}
+ catch (Exception e)
+ {
+ System.err
+ .println(
+ "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+ System.err.println(e.getMessage());
+ }
}
if (!foundSiftsMappings.isEmpty())
{