private void writeAtomContainerSet ( IAtomContainerSet som ) throws IOException , CDKException { for ( int i = 0 ; i < som . getAtomContainerCount ( ) ; i ++ ) { IAtomContainer mol = som . getAtomContainer ( i ) ; for ( int j = 0 ; j < som . getMultiplier ( i ) ; j ++ ) { StringWriter sw = new StringWriter ( ) ; writer . write ( "$MOL" ) ; writer . write ( ' ' ) ; MDLV2000Writer mdlwriter = null ; try { mdlwriter = new MDLV2000Writer ( sw ) ; } catch ( Exception ex ) { logger . error ( ex . getMessage ( ) ) ; logger . debug ( ex ) ; throw new CDKException ( "Exception while creating MDLWriter: " + ex . getMessage ( ) , ex ) ; } mdlwriter . write ( mol ) ; mdlwriter . close ( ) ; writer . write ( sw . toString ( ) ) ; } } }
Writes a MoleculeSet to an OutputStream for the reaction .