/oct.java

Ojus Chemistry Toolkit (OCT) is an open-source chemistry toolkit with primary emphasis on organic synthesis problems.

Primary LanguageJavaOtherNOASSERTION

OCT

Ojus Chemistry Toolkit (OCT) is a toolkit intended to aid in solving a variety of cheminformatics problems. Its primary focus shall be on problems pertaining to organic synthesis.

OCT is created and maintained by Ojus Software Labs Private Limited. It is available under Apache License 2.0 to both encourage its use and participation of a wider community. See the file LICENSE for more details.

PROPOSED STRUCTURE

  • The package oct.cmd contains some useful stand-alone programs that can be run from the command line. [This is empty currently.]

  • The package oct.common contains common definitions utilized across the toolkit.

    • PeriodicTable, which defines a chemical periodic table.
    • Constants enumerating various chemical properties and configurations.
    • ... .

  • The package oct.data contains the essential classes, including:

    • Atom,
    • Bond,
    • Ring,
    • Molecule,
    • FunctionalGroup,
    • LeavingGroup,
    • Reaction,
    • Route,
    • RouteNode,
    • ... .

  • The package oct.lib contains the algorithmic code. Property calculators, molecule analyzers, reaction retro-synthesizers, etc., reside here. Examples include:

    • FunctionalGroups,
    • DefaultRingDetector,
    • ... .

  • The package oct.util contains general utility classes and functions that are useful across the toolkit.

  • The package oct.xlate contains the code to convert molecules and reactions to (and from) their corresponding OCT formats from (and to) popular external formats. Initial support shall be for popular MDL formats.

STATUS

The toolkit is currently in its initial stages, and is not yet usable.

TECHNOLOGY

The main programming language is Java. It may well become the only language used, as well! Currently, version 1.7 is required to use OCT. In future, we look forward to using 1.8. The toolkit makes extensive use of the elegant Guava library. The molecule catalogue and the various kinds of reaction rules are proposed to be stored in a no-SQL database instance.

CONTRIBUTING

Participation by way of comments, (constructive) criticism or feature requests is most welcome, and shall be gratefully acknowledged. Please read the file LICENSE for the terms of Apache License which govern your contributions.