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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Vydáno v:	Journal of computational chemistry Ročník 37; číslo 13; s. 1230 - 1237
Hlavní autor:	ezac, Jan
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	United States Blackwell Publishing Ltd 15.05.2016 Wiley Subscription Services, Inc
Témata:	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
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Abstract	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.
AbstractList	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 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 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 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 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. 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.
Author	Řezáč, Jan
Author_xml	– sequence: 1 givenname: Jan surname: ezac fullname: ezac, Jan
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Snippet	Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by...
SourceID	proquest pubmed crossref wiley istex
SourceType	Aggregation Database Index Database Enrichment Source Publisher
StartPage	1230
SubjectTerms	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
Title	Cuby: An integrative framework for computational chemistry
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Volume	37
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