CCL - Charge Calculation Language

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. CCL - Charge Calculation Language. In ELIXIR CZ Annual Conference 2018. 2018. ISBN 978-80-86241-60-9.

Basic information

• Original name: CCL - Charge Calculation Language
• Authors: RAČEK, Tomáš (203 Czech Republic, guarantor, belonging to the institution), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, belonging to the institution).
• Edition: ELIXIR CZ Annual Conference 2018, 2018.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10200 1.2 Computer and information sciences
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• RIV identification code: RIV/00216224:14740/18:00108934
• Organization unit: Central European Institute of Technology
• ISBN: 978-80-86241-60-9
• Keywords in English: partial atomic charges; empirical methods; domain specific language
• Tags: rivok

Abstract

Partial atomic charges provide the clues for understanding many biochemical phenomena. Since they are a theoretical concept only, they can‘t be experimentally measured. However, there is a large number of methods for their computation, most of them can be divided into two main groups – quantum mechanical (QM) methods and empirical ones. The QM ones are considered the most accurate, but their computational complexity limits their use to small systems only. Empirical methods on the other hand exhibit high performance with only a reasonable accuracy loss. Underlying concepts common to these methods often include simple atomic properties like electronegativity or hardness. As there is no single method covering each application, different methods and their modifications were published in the past. Unfortunately, most of the methods have no implementation available, and programming is not a viable option for many life scientists. Charge Calculation Language (CCL) was designed as a formal description of the most important empirical methods. Being a domain specific language it hides the implementation details from the user and focuses on the main idea – often a simple equation with annotations of the symbols used as it‘s a common way they are expressed in the literature. Users can, therefore, explore and/or modify the methods in an abstract formalism avoiding low-level details of the implementation. CCL can be translated to Python or C++ which provides the performance almost identical to the hand-written solutions. Connected with a suitable charge framework it facilitates parameterization of these methods, generating library functions or ready-to-use binaries.

Links

• LQ1601, research and development project: Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR