Hi all,

Forgive me for my slight ignorance.  I searched the forum for the JAVA version of this method (not the Perl one) and found no matches, so I assumed

this' the right place to start.

Whenever I use this method when looping through a BondSet, I get the following exception thrown in Pipeline Pilot:

fromIndex < 0: -1
java.lang.IndexOutOfBoundsException: fromIndex < 0: -1

    at java.util.BitSet.nextSetBit(BitSet.java:526)

    at com.scitegic.pilot.chem.BondSet.hasMoreBonds(BondSet.java:402)

    at com.scitegic.pilot.chem.BondSet\$BondIterator.hasNext(BondSet.java:552)

    at ....

in this code, when looping through SGMap objects (from an SGMapper, after calling the init() method, setting query molecules & target molecule):

          StringBuilder bInds = new StringBuilder( 50 );

         for( Bond b : bonds ) {
                if( bonds.hasMoreBonds() )    bInds.append( b.getIndex() + "," );
                else                                    bInds.append( b.getIndex() );
                bondIndex++;
            }

It's interesting to note that when replacing that with this code, I don't get the exception thrown:

         int bondIndex = 0;

            for( Bond b : bonds ) {
                if(  bondIndex < bonds.getNumBonds() - 1 )    bInds.append( b.getIndex() + pairSeparator );
                else                                    bInds.append( b.getIndex() );
                bondIndex++;
            }

So, has anyone else found this occur?  It baffles me as I do exactly the same thing with AtomSet objects from the same SGMap objects -

using the AtomSet.hasMoreAtoms() method, and don't get this error!

Thanks in advance,

Ed.