public static HELM2Notation convertIntoAnalogSequence ( HELM2Notation helm2Notation ) throws FastaFormatException , AnalogSequenceException , ChemistryException , CTKException { initMapAminoAcid ( ) ; initMapNucleotides ( ) ; initMapNucleotidesNaturalAnalog ( ) ; initMapTransformNucleotides ( ) ; /* * transform/convert only the peptides + rnas into the analog sequence */ List < PolymerNotation > polymers = helm2Notation . getListOfPolymers ( ) ; for ( int i = 0 ; i < helm2Notation . getListOfPolymers ( ) . size ( ) ; i ++ ) { if ( helm2Notation . getListOfPolymers ( ) . get ( i ) . getPolymerID ( ) instanceof RNAEntity ) { helm2Notation . getListOfPolymers ( ) . set ( i , convertRNAIntoAnalogSequence ( polymers . get ( i ) ) ) ; } if ( helm2Notation . getListOfPolymers ( ) . get ( i ) . getPolymerID ( ) instanceof PeptideEntity ) { helm2Notation . getListOfPolymers ( ) . set ( i , convertPeptideIntoAnalogSequence ( polymers . get ( i ) ) ) ; } } return helm2Notation ; }
method to convert all Peptides and RNAs into the natural analogue sequence and generates HELM2Notation