The current prototype software classifies molecular descriptions extracted from the ChEBI ontology (http://www.ebi.ac.uk/chebi/) using the DLV deductive database system (http://www.dlvsystem.com/dlvsystem/index.php/Home). 

ORGANISATION OF THE FOLDER
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-A folder "ijcai-1182-implementation/input/testbed" which contains the descriptions of 500 molecular entities in molfile format as extracted from ChEBI.
-A folder "ijcai-1182-implementation/input/fungroups" which contains graph-based representations of 30 chemical classes that depend on containment of functional groups.
-A file "ijcai-1182-implementation/output/results-for-ijcai-submission-1182.xls" which contains an excel file with the superclasses of the abovementioned 500 molecules and 30 chemical classes that depend on functional groups after running ijcai-1182-implementation 
-A file "ijcai-1182-implementation/dlv/nonGroupRules" which contains rules representing generic chemical classes.
-A file "ijcai-1182-implementation/dlv/jMolecules500_500_strat" which contains the lower R-stratum of the constructed set of rules.
-A file "ijcai-1182-implementation/dlv/jMolecules500_500Model" which contains the stable model of the constructed set of rules.
-A file "ijcai-1182-implementation/dlv/jGroupsClasses" which contains the remaining upper R-strata of the constructed set of rules.
-A folder "ijcai-1182-implementation/src" that contains the java code of the prototype
-A folder "ijcai-1182-implementation/bin" that contains the .class files of the .java files in the folder "src"
-A folder "ijcai-1182-implementation/dlv" where the DLV engine should be placed
-A folder "ijcai-1182-implementation/libraries" where the cdk and poi .jar files can be placed.

HOW TO REPRODUCE THE EXPERIMENTS THROUGH ECLIPSE
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1.Create a java project by importing the folder "ijcai-1182-implementation/".
2.Add the cdk .jar files to the library of the said project:
	(i) Download the cdk and poi .jar files from http://sourceforge.net/projects/cdk/files/cdk/ and http://poi.apache.org/download.html.
	(ii) Save the files under "ijcai-1182-implementation/libraries".
	(iii) Right click on the name of the java project -> Properties -> Java Build Path -> Add external JARS... and select the two .jar files from "ijcai-1182-implementation/libraries".
2.Add the dlv file:
	(i) Download the DLV engine that suits your machine from http://www.dlvsystem.com/dlvsystem/index.php/DLV#Download.
	(ii) Place it under the folder "ijcai-1182-implementation/dlv".
	(iii)Either change the name of the DLV engine file to 'dlv' or change the name of the variable m_dlvEnginePath to the name of the DLV engine file. (for mac computers the .bin extension of the DLV engine file needs to be preserved)
	(iv)run the command 'chmod a+rx dlv_engine_file_name' to make the DLV engine file executable.
3.Right click on MolClassifier.java -> Run Java application.
4.An excel file with name "ijcai-1182-implementation/output/results" is created with the subclass/superclass pairs and time measurements. Please note that the aforementioned file contains results for 10 runs, each of which classifies 50xi (1 <= i <=10) molecules and 30 functional groups (the last two coluns contain the results for the experiments described in the paper).
