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All commands need to come from a shell where the working directory is the directory where the chemsearchindex.zip file had been unzipped

Running Benchmarking from the Command Line
==========================================
1. Download the sdf file to index from ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/latest/chembl_14.sdf.gz  

2. Create an index (or add to an existing index)
Important: The last parameter specifies a list of Primary Keys to ignore. The specified ID would currently crash RDKit and the Indexing
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.benchmarking.LuceneBenchmark -index index chembl_14.sdf.gz chembl_id CHEMBL1973569

3. Run the benchmarking
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.benchmarking.LuceneBenchmark -benchmark index benchmarking/benchmark-zinc.leads-1thread.ini
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.benchmarking.LuceneBenchmark -benchmark index benchmarking/benchmark-zinc.leads-6threads.ini
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.benchmarking.LuceneBenchmark -benchmark index benchmarking/benchmark-zinc.frags-1thread.ini
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.benchmarking.LuceneBenchmark -benchmark index benchmarking/benchmark-zinc.frags-6threads.ini
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.benchmarking.LuceneBenchmark -benchmark index benchmarking/benchmark-fragqueries-1thread.ini
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.benchmarking.LuceneBenchmark -benchmark index benchmarking/benchmark-fragqueries-6threads.ini

4. For further information print the usage info
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.benchmarking.LuceneBenchmark

Exploring ChemIndex with a Demo GUI
===================================
The optional index directory parameter can be the same directory that was used to create an index with the LuceneBenchmark application
java -cp ".;chemsearchindex.jar" org.rdkit.lucene.demo.LuceneDemo [<Index directory>]

The GUI offers the possibility to add files to an index and to search an existing index. "Free Search" does not work properly yet.
The current demo code uses the Avalon Fingerprint. This can be changed in the main() method of the LuceneDemo class.