public static Pattern controlsTransportOfChemical ( Blacklist blacklist ) { Pattern p = new Pattern ( SequenceEntityReference . class , "controller ER" ) ; p . add ( linkedER ( true ) , "controller ER" , "controller generic ER" ) ; p . add ( erToPE ( ) , "controller generic ER" , "controller simple PE" ) ; p . add ( linkToComplex ( ) , "controller simple PE" , "controller PE" ) ; p . add ( peToControl ( ) , "controller PE" , "Control" ) ; p . add ( controlToConv ( ) , "Control" , "Conversion" ) ; p . add ( new Participant ( RelType . INPUT , blacklist , true ) , "Control" , "Conversion" , "input PE" ) ; p . add ( linkToSimple ( blacklist ) , "input PE" , "input simple PE" ) ; p . add ( new Type ( SmallMolecule . class ) , "input simple PE" ) ; p . add ( notGeneric ( ) , "input simple PE" ) ; p . add ( peToER ( ) , "input simple PE" , "changed generic SMR" ) ; p . add ( new ConversionSide ( ConversionSide . Type . OTHER_SIDE , blacklist , RelType . OUTPUT ) , "input PE" , "Conversion" , "output PE" ) ; p . add ( equal ( false ) , "input PE" , "output PE" ) ; p . add ( linkToSimple ( blacklist ) , "output PE" , "output simple PE" ) ; p . add ( new Type ( SmallMolecule . class ) , "output simple PE" ) ; p . add ( notGeneric ( ) , "output simple PE" ) ; p . add ( peToER ( ) , "output simple PE" , "changed generic SMR" ) ; p . add ( linkedER ( false ) , "changed generic SMR" , "changed SMR" ) ; p . add ( new OR ( new MappedConst ( hasDifferentCompartments ( ) , 0 , 1 ) , new MappedConst ( hasDifferentCompartments ( ) , 2 , 3 ) ) , "input simple PE" , "output simple PE" , "input PE" , "output PE" ) ; return p ; }
Pattern for a ProteinReference has a member PhysicalEntity that is controlling a reaction that changes cellular location of a small molecule .