Class BioTransformerDBBuilder


  • public class BioTransformerDBBuilder
    extends java.lang.Object
    • Constructor Detail

      • BioTransformerDBBuilder

        public BioTransformerDBBuilder()
    • Method Detail

      • 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
      • buildBiotransformationList

        public void buildBiotransformationList​(java.lang.String reactionOntologyFileName,
                                               java.lang.String biotransformationsFileName)
                                        throws java.lang.Exception
        Throws:
        java.lang.Exception
      • buildCYP450ReactionLibrary

        public void buildCYP450ReactionLibrary​(java.lang.String biotransformationsFileName)
                                        throws java.io.IOException
        Throws:
        java.io.IOException
      • 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
      • 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)
      • 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)
      • main

        public static void main​(java.lang.String[] args)
                         throws java.lang.Exception
        Throws:
        java.lang.Exception