1. JChem Base chemical database
Szilárd Dóránt
May, 2005

2. Contents Introduction Structural overview Compatibility Administration
JChem tables
Fingerprints
Structural search
Structure cache
Standardization
Search options
JSP example
API examples
Performance
Future plans

3. Introduction
JChem Base provides high performance Java based tools for the storage, search and retrieval of chemical structures and associated data.
These components can be integrated into web-based or standalone applications in association with other ChemAxon tools.

4. Structural overview Application Web application (JSP) JChem Base API:
Chemical logic
Structure cache
Web
browser
JDBC driver: Standard interface to the RDBMS
RDBMS (e.g. Oracle, MySQL, etc.) : Storage and security

5. Compatibility and integration
File formats:
SMILES
MDL molfile (v2000 and v3000)
MDL SDF
RXN
RDF
MRV
Integration:
100% Java
extensive API
JChem Cartridge for Oracle
Database engines:
Oracle
MySQL
MS SQL Server
PostgreSQL
MS Access
DB2
etc.
Operating systems:
Windows
Linux
Mac OS X
Solaris

6. Administration with JChemManager
User interface for
creating tables
import
export
deleting rows
dropping tables
Most functions are also available from command-line.

7. The property table
The property table stores information about JChem structure tables, including:
Fingerprint parameters
Custom standardization rules
Recent changes (to optimize cache updates)
Other table options and information
Database-related licence keys
More than one property table can be used, each property table represents a particular JChem environment.

8. The structure of JChem tables
Column name
Explanation
cd_id
unique numeric identifier in the table
cd_structure
the imported structure in the original format, without modifications (except for the removal of data fields)
cd_smiles
the standardized structure in ChemAxon Extended Smiles (cxsmiles) format, used by the search process
cd_formula
the formula of the standardized structure
cd_molweight
the molecular weight of the standardized structure
cd_hash
hash code used for duplicate filtering (PERFECT search)
cd_flags
can store row specific option, e.g. overriding the chiral flag
cd_timestamp
the date and time of the insertion of the row
cd_fp…
fingerprint columns
[user fields]
custom data fields can be added by the user

9. Chemical Hashed Fingerprints
Chemical Hashed Fingerprints encode structural patterns in bit strings
If structure A is a substructure of structure B, every bit in B’s fingerprint will be set that is set in structure A’s fingerprint:
Tanimoto similarity of hashed fingerprints can be used for diversity analysis and similarity search:

10. Structural search in database
Two stage method provides optimal performance:
Rapid pre-screening reduces the number of possible hit candidates
Chemical Hashed Fingerprints are used for substructure and superstructure searches
Hash code is used for duplicate filtering (usually during compound registration)
Graph search algorithm is used to determine the final hit list

11. Structure Cache
Contains Fingerprints for screening and ChemAxon Extended SMILES for ABAS
Instant access to the structures for the search process
Reduced load on the database server
Incremental update ensures minimum overhead after changes in the table
Small memory footprint due to
SMILES compression
Optimized storage technique
Approximately 100MB memory needed for 1 million typical drug-like structures (using 512 bit long fingerprints)

12. Standardization Default standardization includes: Hydrogen removal
Aromatization
Custom standardization can be specified for each table by specifying an XML configuration file at table creation or in the “Regenerate” dialog of JChem Manager (jcman)

13. Custom Standardization Example
before
after

14. Database search options
Maximum search time / number of hits
SQL SELECT statement for pre-filtering
Ordering of results
Result table
Inverse hit list
Chemical Terms filter constraint

15. JSP example application
Open source, customizable
Features:
Substructure, Superstructure, Exact and Similarity search
Molecular Descriptor similarity search with descriptor coloring
Substructure hit alignment and coloring, inverse hit list
Chemical Terms filter
Import / Export
Export of hits
Insert / Modify / Delete structures

16. API example : connecting to a database
ConnectionHandler ch = new chemaxon.jchem.db.ConnectionHandler();
ch.setDriver(“oracle.jdbc.driver.OracleDriver”);
ch.setPropertyTable(“JChemProperties”);
ch.setLoginName(“scott”);
ch.setPassword("tiger");
ch.connect();
// the java.sql.Connection object is available if needed:
Connection con=ch.getConnection(); …
// closing the connection:
ch.close();

17. API example : database import
Importer importer = new chemaxon.jchem.db.Importer();
importer.setConnectionHandler(conh);
importer.setInput(“sample.sdf”);
// importer.setInput(is); // alternatively a stream can also be specified
importer.setTableName(“SCOTT.STRUCTURES”);
importer.setHaltOnError(false);
importer.setDuplicateImportAllowed(false); //can filter duplicates
// specifying SDFile field - table field pairs:
String fieldPairs = “DB_Field1=SDF_Field1; DB_Field2=SDF_Field2”;
importer.setFieldConnections(fieldPairs);
int importedCount = importer.importMols();
System.out.println( “Imported” + importedCount + “structures” );

18. API example : database export
Exporter exporter = new chemaxon.jchem.db.Exporter();
exporter.setConnectionHandler(conh);
exporter.setTableName(“structures”);
//data fields to be exported with the structure:
exporter.setFieldList(“cd_id cd_formula name comments”);
String fileName=“output.sdf”;
OutputStream os=new FileOutputStream(fileName);
exporter.setOutputStream(os);
exporter.setFormat(“sdf”);
int exportedCount = exporter.writeAll();
System.out.println(“Exported ” + exportedCount + “structures”);

19. API example : database search
JChemSearch searcher = new chemaxon.jchem.db.JChemSearch();
searcher.setConnectionHandler(ch);
searcher.setSearchType(JChemSearch.SUBSTRUCTURE)
searcher.setQueryStructure(“c1ccccc1”);
searcher.setStructureTable(“SCOTT.STRUCTURES”);
// a query that returns cd_id values can be used for prefiltering:
Searcher.setFilterQuery(
“SELECT cd_id FROM structures, biodata WHERE ”
+ “structures.cd_id = biodata.cd_id AND biodata.toxicity < 0.3” );
searcher.setWaitingForResult(true); // otherwise runs in a separate thread
searcher.setStructureCaching(true); // caching speeds up the search
searcher.run();
// getting the results as cd_id values:
int[] results=searcher.getResults();

20. API example : inserting a structure
// ConnectionHandler, mode, table name and data field names:
UpdateHandler uh = new chemaxon.jchem.db.UpdateHandler(
ch, UpdateHandler.INSERT, “structures”, “comment, stock”);
uh.setValueForFixColumns(“c1ccccc1”); // the structure
// specifying data field values:
uh.setStructureValueForAdditionalColumn(1, “some text”);
uh.setStructureValueForAdditionalColumn(2, new Double(8.5));
uh.setDuplicateFiltering(true); // filtering duplicate structures
int id=uh.execute(true); // getting back the cd_id of the inserted structure
if ( id > 0 ) {
System.out.println(“Inserted, cd_id value : ” + id);
} else {
System.out.println(“Already exists with cd_id value : ” + (-id)); }
// storing update information, the database connection remains open :
uh.close();

21. Performance (1) Compound registration:
Substructure search in a table of 3 million compounds:
Server parameters: Windows XP; 1 CPU: Intel P4 3.0GHz; 2GB RAM; Oracle 9i
12min 26s
8min 17s
200,000
6min 20s
4min 11s
100,000
45s
32s
10,000
Duplicates checked
Duplicates not checked
Elapsed time
Number of compounds
10.7
49740
1.2
0.9
936
0.1 12
Search time (s)
Number of hits
Query
Latest speed benchmarks:

22. Performance (2) Similarity search: Tanimoto >0.8
Server parameters: Windows XP; 1 CPU: Intel P4 3.0GHz; 2GB RAM; Oracle 9i
1.3
336
156
1.5 24
Search time (s)
Number of hits
Query
Latest speed benchmarks:

23. Future plans Additional layer: JChem Server (later also as grid)
Structural keys as optional extension to current fingerprints
Tables for storing query structures
Tables for storing general (Markush) structures
Partial clean option for hit alignment
Installer
etc.

24. Summary
ChemAxon’s JChem Base toolkit provides sophisticated methods to deal with chemical structures and associated data.
The usage of fingerprints and structure cache provide high search performance.

25. Links JChem home page: Live demos: API documentation: Brochure:
Live demos:
API documentation:
Brochure:

26. Thank you for your attention
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