Package biotransformer.utils
Class BioTransformerDBBuilder
- java.lang.Object
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- biotransformer.utils.BioTransformerDBBuilder
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public class BioTransformerDBBuilder extends java.lang.Object
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Constructor Summary
Constructors Constructor Description BioTransformerDBBuilder()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
buildBiotransformationList(java.lang.String reactionOntologyFileName, java.lang.String biotransformationsFileName)
void
buildCYP450ReactionLibrary(java.lang.String biotransformationsFileName)
void
buildCYPspecificitySDFFileFromDB(java.lang.String inputFileName, java.lang.String outputFileName)
java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<java.lang.String>>
extendChildrenParentAssociations(java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<java.lang.String>> cpAssociations)
java.util.ArrayList<java.lang.String>
findAllAncestors(java.lang.String node, java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<java.lang.String>> cpPairs)
static void
main(java.lang.String[] args)
void
updateMetabolicReactions()
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Method Detail
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buildCYPspecificitySDFFileFromDB
public void buildCYPspecificitySDFFileFromDB(java.lang.String inputFileName, java.lang.String outputFileName) throws java.io.IOException, org.openscience.cdk.exception.CDKException
- Throws:
java.io.IOException
org.openscience.cdk.exception.CDKException
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buildBiotransformationList
public void buildBiotransformationList(java.lang.String reactionOntologyFileName, java.lang.String biotransformationsFileName) throws java.lang.Exception
- Throws:
java.lang.Exception
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buildCYP450ReactionLibrary
public void buildCYP450ReactionLibrary(java.lang.String biotransformationsFileName) throws java.io.IOException
- Throws:
java.io.IOException
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updateMetabolicReactions
public void updateMetabolicReactions() throws org.codehaus.jackson.JsonParseException, org.codehaus.jackson.map.JsonMappingException, java.io.IOException
- Throws:
org.codehaus.jackson.JsonParseException
org.codehaus.jackson.map.JsonMappingException
java.io.IOException
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findAllAncestors
public java.util.ArrayList<java.lang.String> findAllAncestors(java.lang.String node, java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<java.lang.String>> cpPairs)
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extendChildrenParentAssociations
public java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<java.lang.String>> extendChildrenParentAssociations(java.util.LinkedHashMap<java.lang.String,java.util.ArrayList<java.lang.String>> cpAssociations)
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main
public static void main(java.lang.String[] args) throws java.lang.Exception
- Throws:
java.lang.Exception
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