Cuby: An integrative framework for computational chemistry

Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calcu...

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Bibliographic Details
Published in:Journal of computational chemistry Vol. 37; no. 13; pp. 1230 - 1237
Main Author: ezac, Jan
Format: Journal Article
Language:English
Published: United States Blackwell Publishing Ltd 15.05.2016
Wiley Subscription Services, Inc
Subjects:
Chemistry
Computational chemistry
Computer simulation
datasets
Downloading
Mathematical analysis
Molecular dynamics
Molecular structure
Object oriented programming
Programmers
Programming
Programming languages
QM/MM
Ruby
Simulation
Software
software framework
Test procedures
workflow automation
QM/MM
datasets
workflow automation
Ruby
software framework
ISSN:0192-8651, 1096-987X, 1096-987X
Online Access:Get full text
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Description
Summary:Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows. For users, Cuby provides a unified and userfriendly way to automate their work, seamlessly integrating calculations carried out in different computational chemistry programs. For example, the QM/MM module allows combining methods across the interfaced programs and the builtin molecular dynamics engine makes it possible to run a simulation on the resulting potential. For programmers, it provides high‐level, object‐oriented environment that allows rapid development and testing of new methods and computational protocols. The Cuby framework is available for download at http://cuby4.molecular.cz. © 2016 Wiley Periodicals, Inc. Cuby is a software framework that provides unified access to a wide range of computational methods by interfacing external software and implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows.
Bibliography:istex:C78675F09AB332E35125A4F090E2CAB58478B778
ark:/67375/WNG-35QXLQCS-Q
ArticleID:JCC24312
Czech Science Foundation - No. P208/13/01214P
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ISSN:0192-8651
1096-987X
1096-987X
DOI:10.1002/jcc.24312