JChem Release Information

• Content of the JChem Package
• Licensing Issues
• History of Changes

Content of the JChem Package

After decompressing the appropriate archive file in a directory, the jchem subdirectory is created, which contains the files of the JChem system. Since JChem is 100% Java, it runs in practically all modern operating systems. See the software requirements and the details on preparing and running the scripts and batch files.

1. JChem Class Library, a library of Java classes for
   • substructure and similarity searching
   • inserting and modifying data in structure tables
   • manipulating structures
   • Marvin Beans:
     • MarvinSketch JavaBean for structure input and modification.
     • MarvinView JavaBean for displaying structures.
     Java applets with the same functionality are available at the Marvin download page
2. JChemManager, a Java application with a graphical interface (Some operations are also available in command line). Main features:
   • Creation and removal of structure tables
   • SDfile, Molfile, SMILES import/export.
   Usage of GUI program: run jcman.
   Usage of command line program: run jcman -h for help.
   
3. MarvinSketch application for drawing structures.
   Run msketch -h for help.
4. MarvinView application for displaying structure files.
   Run mview -h for help.
5. MarvinSpace application for high performance 3D visualization.
   Run mspace -h for help.
6. MolConverter application for interconverting structure files in different formats.
   Run molconvert -h for help.
7. JChemSearch application for substructure searching in structure files from command line.
   Run jcsearch -h for help.
8. JKlustor is an add-on module for clustering. It includes
   • GenerFP is an application for generating fingerprints that can be applied for
     • similarity/diversity analysis.
     • fine tuning substructure/similarity search in databases.
     Run generfp -h for help.
   • Compr is an application for diversity/dissimilarity calculations between compound libraries.
     Run compr -h for help.
   • Jarp is an application for Jarvis-Patrick clustering.
     Run jarp -h and/or nneib -h for help.
   • Ward clusters molecules using Ward's hierarchic method.
     Run ward -h for help.
   • CreateView composes a new SDfile from an SDfile and a data table. It is useful for viewing the results of clustering.
     Run crview -h for help.
9. Screen is a collection of tools for virtual screening. It includes
   • PMapper perceives pharmacophoric points in molecular structures and assigns pharmacophore types to atoms.
     Run pmapper -h for help.
   • GenerateMD generates Molecular Descriptors for molecular structures. Such descriptors are suitable for virtual screening.
     Run generatemd -h for help.
   • ScreenMD performs virtual screening of large compound databases using molecular descriptors. The screening procedure is based on the comparison of molecular descriptors using various dissimilarity metrics.
     Run screenmd -h for help.
   • OptimizeMetrics optimizes parameters of dissimilarity metrics in order to achieve the best hit ratio (highest enrichment factor) in screening.
     Run optimizemetrics -h for help.
   • HitStatistics evaluates the performance of the optimized metrics.
     Run hitstatistics -h for help.
   • ScreeningOptimizer integrates OptimizeMetrics and HitStatistics in one tool for easier use.
     Run screeningoptimizer -h for help.
10. Molecular Transformations
    • Standardizer is a structure canonicalization tool converting molecules from different sources into standard representations. The standardization process helps to automate the identification of mesomers and tautomers and can be used for counter ion removal.
      Run standardize -h for help.
11. Reaction Processing
    • Reactor performs chemical reactions by processing reactants to products according to generic reaction equations. The tool evaluates Chemical Terms containing complex expressions built from structural and reactivity conditions.
      Run react -h for help.
12. Drug Design
    • Fragmenter cleaves input molecules into fragments by opening chemical bonds along configurable cleavage reactions. Additional cleavage rules can be added (e.g. never cut a bond connecting a hetero atom and a ring carbon, never cut ring-bonds) to the base cleavage mechanism. The current release defines one such cleavage rule set: the RECAP method.
      Run fragment -h for help.
13. XML Configuration Editor provides a graphical environment in which you can edit configuration files needed for JChem programs such as ScreenMD or OptimizeMetrics.
    Run config -h for help.
14. Example JSP and ASP scripts showing how to write custom web applications that search, display, modify and insert mixed chemical and corporate data.
15. JChem license file

For information on versions, see the list of changes.

Licensing Issues

If you have not received a license key from ChemAxon yet, then please contact us Without a license key for JChem, the system is in demo mode that allows one structure search per minute. Without a license key for JKlustor, clustering database structures is limited to 1000 rows. In demo mode the components of the JChem package may only be used

• for testing
• within one month after installation.