private HELM2Notation readNotation ( String notation ) throws ParserException , JDOMException , IOException , MonomerException , ChemistryException { /* xhelm notation */ if ( notation . contains ( "<Xhelm>" ) ) { LOG . info ( "xhelm is used as input" ) ; String xhelm = notation ; Element xHELMRootElement = getXHELMRootElement ( xhelm ) ; notation = xHelmNotationParser . getHELMNotationString ( xHELMRootElement ) ; MonomerStore store = xHelmNotationParser . getMonomerStore ( xHELMRootElement ) ; updateMonomerStore ( store ) ; } return HELM2NotationUtils . readNotation ( notation ) ; }
method to read the HELM string the HELM can be in version 1 or 2 or in Xhelm format