Package biotransformer.transformation
Class MetabolicReaction
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- biotransformer.transformation.MetabolicReaction
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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
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Field Summary
Fields Modifier and Type Field Description java.lang.String
commonName
java.lang.String
name
java.lang.String
reactionsBTMRID
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Constructor Summary
Constructors Constructor Description MetabolicReaction(MRPatterns.ReactionName r_name)
MetabolicReaction(MRPatterns.ReactionName r_name, ambit2.smarts.SMIRKSManager smrkMan)
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(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(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(java.lang.String smirks)
MetabolicReaction(java.lang.String smirks, ambit2.smarts.SMIRKSManager smrkMan)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
display()
java.lang.String
getBTRMID()
java.lang.String
getComonName()
java.util.ArrayList<java.lang.String>
getNegativeReactantsSMARTS()
java.util.ArrayList<java.lang.String>
getReactantSMARTS()
java.lang.String
getReactionEquation()
java.lang.String
getReactionName()
java.lang.String
getReactionSMIRKS()
ambit2.smarts.SMIRKSReaction
getSmirksReaction()
static void
main(java.lang.String[] args)
void
setReactionEquation(java.lang.String rEquation)
java.lang.String
transformationDataToString()
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Constructor Detail
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MetabolicReaction
public MetabolicReaction(MRPatterns.ReactionName r_name)
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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)
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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)
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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)
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MetabolicReaction
public MetabolicReaction(java.lang.String smirks)
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MetabolicReaction
public MetabolicReaction(MRPatterns.ReactionName r_name, ambit2.smarts.SMIRKSManager smrkMan)
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MetabolicReaction
public MetabolicReaction(java.lang.String smirks, ambit2.smarts.SMIRKSManager smrkMan)
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Method Detail
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main
public static void main(java.lang.String[] args)
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getReactantSMARTS
public java.util.ArrayList<java.lang.String> getReactantSMARTS()
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getNegativeReactantsSMARTS
public java.util.ArrayList<java.lang.String> getNegativeReactantsSMARTS()
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getBTRMID
public java.lang.String getBTRMID()
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getComonName
public java.lang.String getComonName()
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getReactionSMIRKS
public java.lang.String getReactionSMIRKS()
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getSmirksReaction
public ambit2.smarts.SMIRKSReaction getSmirksReaction()
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getReactionName
public java.lang.String getReactionName()
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getReactionEquation
public java.lang.String getReactionEquation()
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setReactionEquation
public void setReactionEquation(java.lang.String rEquation)
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transformationDataToString
public java.lang.String transformationDataToString()
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display
public void display()
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