Interacting with Chemaxon dataset

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the jcman utility and its frontend can be used for viewing and modifying the aggregator database. This tutorial demonstrates how to use JCman UI from the local machine.

Using Jcman to connect to aggregator database

1. Establish a SSH link to the server machine

ssh -L 3306:localhost:3306

you will be prompted for password

2. run jcman

3. a confirguration windows will popup. JDBC driver: com.mysql.jdbc.Driver database url: jdbc:mysql://localhost/Aggregates username: mysqlusr password:

The database contains three tables: aggregators, non-aggregators, ambigous

you can load any .smi files tab delimeted, with reference string in the second field counting from one

To load any smiles,

1. in the user interface click import icon,

2. in the new window choose the database(e.g aggregators)

3. select the file to load (in .smi format), click ok

4. if a "Connecting Fields" window appears, in the third column for REFERENCE row select FIELD_0