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Rubabel: wrapping open Babel with Ruby.

Smith R, Williamson R, Ventura D, Prince JT - J Cheminform (2013)

Bottom Line: Rubabel requires fewer lines of code than any other actively developed wrapper, providing better object organization and navigation, and more intuitive object behavior than extant solutions.Rubabel is powerful, intuitive, concise, freely available, cross-platform, and easy to install.We expect it to be a platform of choice for new users, Ruby users, and some users of current solutions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Brigham Young University, Provo, Utah, USA. 2robsmith@gmail.com.

ABSTRACT

Background: The number and diversity of wrappers for chemoinformatic toolkits suggests the diverse needs of the chemoinformatic community. While existing chemoinformatics libraries provide a broad range of utilities, many chemoinformaticians find compiled language libraries intimidating, time-consuming, arcane, and verbose. Although high-level language wrappers have been implemented, more can be done to leverage the intuitiveness of object-orientation, the paradigms of high-level languages, and the extensibility of languages such as Ruby. We introduce Rubabel, an intuitive, object-oriented suite of functionality that substantially increases the accessibily of the tools in the Open Babel chemoinformatics library.

Results: Rubabel requires fewer lines of code than any other actively developed wrapper, providing better object organization and navigation, and more intuitive object behavior than extant solutions. Moreover, Rubabel provides a convenient interface to the many extensions currently available in Ruby, greatly streamlining otherwise onerous tasks such as creating web applications that serve up Rubabel functionality.

Conclusions: Rubabel is powerful, intuitive, concise, freely available, cross-platform, and easy to install. We expect it to be a platform of choice for new users, Ruby users, and some users of current solutions.

No MeSH data available.


Novel functionality in Rubabel. Besides providing access to native Open Babel functions, Rubabel provides a host of novel functionality.
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Related In: Results  -  Collection

License
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Figure 2: Novel functionality in Rubabel. Besides providing access to native Open Babel functions, Rubabel provides a host of novel functionality.

Mentions: Rubabel’s objects are designed to be intuitive. Table 1 lists the Rubabel objects which wrap Open Babel functionality. Although the names for these objects correspond to similarly named objects in Open Babel, Rubabel augments Open Babel functionality substantially. Figure 2 lists some of the novel methods offered by Rubabel, some of which are not available in any other chemoinformatics toolkit. Additionally, every Rubabel object has full access to the behavior provided by the underlying Open Babel object.


Rubabel: wrapping open Babel with Ruby.

Smith R, Williamson R, Ventura D, Prince JT - J Cheminform (2013)

Novel functionality in Rubabel. Besides providing access to native Open Babel functions, Rubabel provides a host of novel functionality.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3733738&req=5

Figure 2: Novel functionality in Rubabel. Besides providing access to native Open Babel functions, Rubabel provides a host of novel functionality.
Mentions: Rubabel’s objects are designed to be intuitive. Table 1 lists the Rubabel objects which wrap Open Babel functionality. Although the names for these objects correspond to similarly named objects in Open Babel, Rubabel augments Open Babel functionality substantially. Figure 2 lists some of the novel methods offered by Rubabel, some of which are not available in any other chemoinformatics toolkit. Additionally, every Rubabel object has full access to the behavior provided by the underlying Open Babel object.

Bottom Line: Rubabel requires fewer lines of code than any other actively developed wrapper, providing better object organization and navigation, and more intuitive object behavior than extant solutions.Rubabel is powerful, intuitive, concise, freely available, cross-platform, and easy to install.We expect it to be a platform of choice for new users, Ruby users, and some users of current solutions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Brigham Young University, Provo, Utah, USA. 2robsmith@gmail.com.

ABSTRACT

Background: The number and diversity of wrappers for chemoinformatic toolkits suggests the diverse needs of the chemoinformatic community. While existing chemoinformatics libraries provide a broad range of utilities, many chemoinformaticians find compiled language libraries intimidating, time-consuming, arcane, and verbose. Although high-level language wrappers have been implemented, more can be done to leverage the intuitiveness of object-orientation, the paradigms of high-level languages, and the extensibility of languages such as Ruby. We introduce Rubabel, an intuitive, object-oriented suite of functionality that substantially increases the accessibily of the tools in the Open Babel chemoinformatics library.

Results: Rubabel requires fewer lines of code than any other actively developed wrapper, providing better object organization and navigation, and more intuitive object behavior than extant solutions. Moreover, Rubabel provides a convenient interface to the many extensions currently available in Ruby, greatly streamlining otherwise onerous tasks such as creating web applications that serve up Rubabel functionality.

Conclusions: Rubabel is powerful, intuitive, concise, freely available, cross-platform, and easy to install. We expect it to be a platform of choice for new users, Ruby users, and some users of current solutions.

No MeSH data available.