public static Pattern usedToProduce ( Blacklist blacklist ) { Pattern p = new Pattern ( SmallMoleculeReference . class , "SMR1" ) ; p . add ( erToPE ( ) , "SMR1" , "SPE1" ) ; p . add ( notGeneric ( ) , "SPE1" ) ; p . add ( linkToComplex ( blacklist ) , "SPE1" , "PE1" ) ; p . add ( new ParticipatesInConv ( RelType . INPUT , blacklist ) , "PE1" , "Conv" ) ; p . add ( type ( BiochemicalReaction . class ) , "Conv" ) ; p . add ( new InterToPartER ( InterToPartER . Direction . ONESIDERS ) , "Conv" , "SMR1" ) ; p . add ( new ConversionSide ( ConversionSide . Type . OTHER_SIDE , blacklist , RelType . OUTPUT ) , "PE1" , "Conv" , "PE2" ) ; p . add ( type ( SmallMolecule . class ) , "PE2" ) ; p . add ( linkToSimple ( blacklist ) , "PE2" , "SPE2" ) ; p . add ( notGeneric ( ) , "SPE2" ) ; p . add ( equal ( false ) , "SPE1" , "SPE2" ) ; p . add ( peToER ( ) , "SPE2" , "SMR2" ) ; p . add ( equal ( false ) , "SMR1" , "SMR2" ) ; p . add ( new InterToPartER ( InterToPartER . Direction . ONESIDERS ) , "Conv" , "SMR2" ) ; return p ; }
Constructs a pattern where first small molecule is an input a biochemical reaction that produces the second small molecule . biochemical reaction .