Step 1

Before setting up Hadoop cluster, all nodes should be configured first. It can be done by following steps in given link: http://blog.puneethabm.in/hadoop-cloudera-cluster-set-up/

Step 2

Hadoop multi node cluster setup is done by following this link: http://tecadmin.net/set-up-hadoop-multi-node-cluster-on-centos-redhat/

Step 3

Install CDK on Master node.

Step 4

Download an active reference molecule in sdf format (say file 1) against which similar shaped compounds are to be searched.

Step 5

Download a chemical database of compounds in sdf format (say file 2) from which structurally similar shaped compounds are to be extracted.

Step 6

Make a directory ‘/data/cache/lib’ in Hadoop filesystem and copy following jar in this directory:
cdk-core.jar
cdk-data.jar
cdk-fingerprint.jar
cdk-interfaces.jar
cdk-io.jar
cdk-ioformats.jar
cdk-isomorphism.jar
cdk-nonotify.jar
cdk-qsar.jar
cdk-qsarmolecular.jar
cdk-standard.jar
cdk-valencycheck.jar
jgraph-0.5.3.jar
vectmath-1.3.1.jar

Step 7

Copy file1 and file2 to Hadoop filesystem.

Step 8

Download file ‘USR_n.jar’ and run following commands for DistMapVector (DMV) approach:
hadoop jar /path/to/USRn.jar USR.AggregateJob /path/to/file1 /path/to/file2 /path/to/output_file In this output_file is the required output.

Step 9

For running via DistMapVectorLibScreen (DMVLS):
    i) Download ‘lib_noreduce.jar’ and run following command for building library:
    hadoop jar /path/to/USR_library.jar USR_library.AggregateJob / path/to/file2 /path/to/output_file1

   ii) Download ‘screening.jar’ and run following command for final screening of compounds:
    hadoop jar /path/to/screening.jar lead_compounds.AggregateJob /path/to/file1 /path/to/output_file1 /path/to/final_output_file