CCL - Charge Calculation Language

a 2018

CCL - Charge Calculation Language

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA

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

Language

English

Type of outcome

Konferenční abstrakt

Field of Study

10200 1.2 Computer and information sciences

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

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

Abstract

V originále

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

Citovat

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.

@proceedings{1471685,
   author = {Raček, Tomáš and Svobodová Vařeková, Radka and Koča, Jaroslav},
   booktitle = {ELIXIR CZ Annual Conference 2018},
   keywords = {partial atomic charges; empirical methods; domain specific language},
   language = {eng},
   isbn = {978-80-86241-60-9},
   title = {CCL - Charge Calculation Language},
   year = {2018}
}

TY  - CONF
ID  - 1471685
AU  - Raček, Tomáš - Svobodová Vařeková, Radka - Koča, Jaroslav
PY  - 2018
TI  - CCL - Charge Calculation Language
SN  - 9788086241609
KW  - partial atomic charges
KW  - empirical methods
KW  - domain specific language
N2  - 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.
ER  -

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

Detailed Information on Publication Record