CCL - Charge Calculation Language

a 2018

CCL - Charge Calculation Language

RAČEK, Tomáš, Radka SVOBODOVÁ VAŘEKOVÁ a Jaroslav KOČA

Základní údaje

Originální název

CCL - Charge Calculation Language

Autoři

RAČEK, Tomáš (203 Česká republika, garant, domácí), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, domácí) a Jaroslav KOČA (203 Česká republika, domácí)

Vydání

ELIXIR CZ Annual Conference 2018, 2018

Další údaje

Jazyk

angličtina

Typ výsledku

Konferenční abstrakt

Obor

10200 1.2 Computer and information sciences

Stát vydavatele

Česká republika

Utajení

není předmětem státního či obchodního tajemství

Kód RIV

RIV/00216224:14740/18:00108934

Organizační jednotka

Středoevropský technologický institut

ISBN

978-80-86241-60-9

Klíčová slova anglicky

partial atomic charges; empirical methods; domain specific language

Štítky

rivok

Změněno: 26. 3. 2020 16:54, Mgr. Pavla Foltynová, Ph.D.

Anotace

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.

Návaznosti

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

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

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