Daylight Summer School 2000, June 7-9, Santa Fe, NM

Daylight Chemistry Cartridge Worksheet

The Daylight Chemistry Cartridge provides chemical intelligence to an Oracle server. The interface is PL/SQL and the cartridge includes both functions as well as indexes. Two different interfaces are given for this lab. The first is sqlplus which is an Oracle application which allows pl/sql commands. The second is a JDBC interface which uses a Java Servlet. NOTE: The JDBC interface does not require a ";" at the end of the SQL statements . The Oracle cartridge has already been installed and tables created for you. This exercise is one to "try out" its usage rather than its installation and administration.

Decide which interface you would like to use to access the Oracle Cartrdige and follow the connection instructions

Oracle Searching Functions

  1. Lookup a Dopamine (NCCc1ccc(O)c(O)c1) in the Oracle table "small"
  2. Do a similarity search for Dopamine imposing a tanimoto/euclidean filter of 0.7
  3. Count the number of compounds in the small table which have phenol as a substructure

      The function utilized for a substructre search is:
        function ddpackage.fcontains (smiles1 IN VARCHAR2, smiles2 IN VARCHAR2) => NUMBER
        operator contains (smiles1 IN VARCHAR2, smiles2 IN VARCHAR2) => NUMBER

      The SQL command is:
        Select count(1) from small where contains(smiles,'c1ccccc1O') = 1;

  4. Perform a SMARTS query on the small table
  5. Find all the reactions from the reaction table "rxn" which used phenol as a reagent. Do the same except look for phenol as a product.

Oracle Molecule/Reaction Functions

  1. Find all compounds in the small table which have a molecular weight greater than that of dopamine.
  2. Find all compounds who share the same molecular formula with Dopamine.

    Oracle Cartridge Administration - For Advanced users only who want to play some more

    1. Create your own table and try out the administration features of the cartridge, like indexing, etc.

      The SQL command to generate a new table is:

        Create table tablename as
        select * from small where rownum < 1000;

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