Class MetabolicReaction


  • public class MetabolicReaction
    extends java.lang.Object
    The first reactantsSMARTS is the main one, for which indices might be retrieved to apply position-specific transformations. The subsequent SMARTS (negativeReactantsSMARTS) will be checked just to match further constraints. For instance, long-chain fatty acids must NOT match the pattern of very-long-chain fatty acids. This combination of SMARTS patterns could be replaced in favor of MARKUSH formats. Because we are using CDK, we rather stick up the the combination of SMARTS
    • Field Detail

      • name

        public java.lang.String name
      • commonName

        public java.lang.String commonName
      • reactionsBTMRID

        public java.lang.String reactionsBTMRID
    • Constructor Detail

      • MetabolicReaction

        public MetabolicReaction​(MRPatterns.ReactionName r_name,
                                 java.lang.String commmonName,
                                 java.lang.String reactionsBTMRID,
                                 java.lang.String reactionSMIRKS,
                                 java.util.ArrayList<java.lang.String> reactantsSMARTS,
                                 java.util.ArrayList<java.lang.String> negativeReactantsSMARTS,
                                 ambit2.smarts.SMIRKSManager smrkMan)
      • MetabolicReaction

        public MetabolicReaction​(MRPatterns.ReactionName r_name,
                                 java.lang.String commmonName,
                                 java.lang.String reactionSMIRKS,
                                 java.util.ArrayList<java.lang.String> reactantsSMARTS,
                                 java.util.ArrayList<java.lang.String> negativeReactantsSMARTS,
                                 ambit2.smarts.SMIRKSManager smrkMan)
      • MetabolicReaction

        public MetabolicReaction​(MRPatterns.ReactionName r_name,
                                 java.lang.String reactionSMIRKS,
                                 java.util.ArrayList<java.lang.String> reactantsSMARTS,
                                 java.util.ArrayList<java.lang.String> negativeReactantsSMARTS,
                                 ambit2.smarts.SMIRKSManager smrkMan)
      • MetabolicReaction

        public MetabolicReaction​(java.lang.String smirks)
      • MetabolicReaction

        public MetabolicReaction​(MRPatterns.ReactionName r_name,
                                 ambit2.smarts.SMIRKSManager smrkMan)
      • MetabolicReaction

        public MetabolicReaction​(java.lang.String smirks,
                                 ambit2.smarts.SMIRKSManager smrkMan)
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
      • getReactantSMARTS

        public java.util.ArrayList<java.lang.String> getReactantSMARTS()
      • getNegativeReactantsSMARTS

        public java.util.ArrayList<java.lang.String> getNegativeReactantsSMARTS()
      • getBTRMID

        public java.lang.String getBTRMID()
      • getComonName

        public java.lang.String getComonName()
      • getReactionSMIRKS

        public java.lang.String getReactionSMIRKS()
      • getSmirksReaction

        public ambit2.smarts.SMIRKSReaction getSmirksReaction()
      • getReactionName

        public java.lang.String getReactionName()
      • getReactionEquation

        public java.lang.String getReactionEquation()
      • setReactionEquation

        public void setReactionEquation​(java.lang.String rEquation)
      • transformationDataToString

        public java.lang.String transformationDataToString()
      • display

        public void display()