PIKAChU: a Python-based informatics kit for analysing chemical units

As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical research. While such programs exist, they are often dependency-heavy, difficult to navigate, or not written in Python, the programming language of choice for bioinformaticians. Here, we introduce PIKAChU (Python-based Informatics Kit for Analysing CHemical Units): a cheminformatics toolbox with few dependencies implemented in Python. PIKAChU builds comprehensive molecular graphs from SMILES strings, which allow for easy downstream analysis and visualisation of molecules. While the molecular graphs PIKAChU generates are extensive, storing and inferring information on aromaticity, chirality, charge, hybridisation and electron orbitals, PIKAChU limits itself to applications that will be sufficient for most casual users and downstream Python-based tools and databases, such as Morgan fingerprinting, similarity scoring, substructure matching and customisable visualisation. In addition, it comes with a set of functions that assists in the easy implementation of reaction mechanisms. Its minimalistic design makes PIKAChU straightforward to use and install, in stark contrast to many existing toolkits, which are more difficult to navigate and come with a plethora of dependencies that may cause compatibility issues with downstream tools. As such, PIKAChU provides an alternative for researchers for whom basic cheminformatic processing suffices, and can be easily integrated into downstream bioinformatics and cheminformatics tools. PIKAChU is available at https://github.com/BTheDragonMaster/pikachu. Graphical Abstract: [Figure not available: see fulltext.]

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Main Authors: Terlouw, Barbara R., Vromans, Sophie P.J.M., Medema, Marnix H.
Format: Article/Letter to editor biblioteca
Language:English
Subjects:Cheminformatics kit, In silico chemistry, Molecular fingerprinting, Python, Structure visualisation,
Online Access:https://research.wur.nl/en/publications/pikachu-a-python-based-informatics-kit-for-analysing-chemical-uni
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spelling dig-wur-nl-wurpubs-5995612025-01-14 Terlouw, Barbara R. Vromans, Sophie P.J.M. Medema, Marnix H. Article/Letter to editor Journal of Cheminformatics 14 (2022) 1 ISSN: 1758-2946 PIKAChU: a Python-based informatics kit for analysing chemical units 2022 As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical research. While such programs exist, they are often dependency-heavy, difficult to navigate, or not written in Python, the programming language of choice for bioinformaticians. Here, we introduce PIKAChU (Python-based Informatics Kit for Analysing CHemical Units): a cheminformatics toolbox with few dependencies implemented in Python. PIKAChU builds comprehensive molecular graphs from SMILES strings, which allow for easy downstream analysis and visualisation of molecules. While the molecular graphs PIKAChU generates are extensive, storing and inferring information on aromaticity, chirality, charge, hybridisation and electron orbitals, PIKAChU limits itself to applications that will be sufficient for most casual users and downstream Python-based tools and databases, such as Morgan fingerprinting, similarity scoring, substructure matching and customisable visualisation. In addition, it comes with a set of functions that assists in the easy implementation of reaction mechanisms. Its minimalistic design makes PIKAChU straightforward to use and install, in stark contrast to many existing toolkits, which are more difficult to navigate and come with a plethora of dependencies that may cause compatibility issues with downstream tools. As such, PIKAChU provides an alternative for researchers for whom basic cheminformatic processing suffices, and can be easily integrated into downstream bioinformatics and cheminformatics tools. PIKAChU is available at https://github.com/BTheDragonMaster/pikachu. Graphical Abstract: [Figure not available: see fulltext.] en application/pdf https://research.wur.nl/en/publications/pikachu-a-python-based-informatics-kit-for-analysing-chemical-uni 10.1186/s13321-022-00616-5 https://edepot.wur.nl/573770 Cheminformatics kit In silico chemistry Molecular fingerprinting Python Structure visualisation https://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by/4.0/ Wageningen University & Research
institution WUR NL
collection DSpace
country Países bajos
countrycode NL
component Bibliográfico
access En linea
databasecode dig-wur-nl
tag biblioteca
region Europa del Oeste
libraryname WUR Library Netherlands
language English
topic Cheminformatics kit
In silico chemistry
Molecular fingerprinting
Python
Structure visualisation
Cheminformatics kit
In silico chemistry
Molecular fingerprinting
Python
Structure visualisation
spellingShingle Cheminformatics kit
In silico chemistry
Molecular fingerprinting
Python
Structure visualisation
Cheminformatics kit
In silico chemistry
Molecular fingerprinting
Python
Structure visualisation
Terlouw, Barbara R.
Vromans, Sophie P.J.M.
Medema, Marnix H.
PIKAChU: a Python-based informatics kit for analysing chemical units
description As efforts to computationally describe and simulate the biochemical world become more commonplace, computer programs that are capable of in silico chemistry play an increasingly important role in biochemical research. While such programs exist, they are often dependency-heavy, difficult to navigate, or not written in Python, the programming language of choice for bioinformaticians. Here, we introduce PIKAChU (Python-based Informatics Kit for Analysing CHemical Units): a cheminformatics toolbox with few dependencies implemented in Python. PIKAChU builds comprehensive molecular graphs from SMILES strings, which allow for easy downstream analysis and visualisation of molecules. While the molecular graphs PIKAChU generates are extensive, storing and inferring information on aromaticity, chirality, charge, hybridisation and electron orbitals, PIKAChU limits itself to applications that will be sufficient for most casual users and downstream Python-based tools and databases, such as Morgan fingerprinting, similarity scoring, substructure matching and customisable visualisation. In addition, it comes with a set of functions that assists in the easy implementation of reaction mechanisms. Its minimalistic design makes PIKAChU straightforward to use and install, in stark contrast to many existing toolkits, which are more difficult to navigate and come with a plethora of dependencies that may cause compatibility issues with downstream tools. As such, PIKAChU provides an alternative for researchers for whom basic cheminformatic processing suffices, and can be easily integrated into downstream bioinformatics and cheminformatics tools. PIKAChU is available at https://github.com/BTheDragonMaster/pikachu. Graphical Abstract: [Figure not available: see fulltext.]
format Article/Letter to editor
topic_facet Cheminformatics kit
In silico chemistry
Molecular fingerprinting
Python
Structure visualisation
author Terlouw, Barbara R.
Vromans, Sophie P.J.M.
Medema, Marnix H.
author_facet Terlouw, Barbara R.
Vromans, Sophie P.J.M.
Medema, Marnix H.
author_sort Terlouw, Barbara R.
title PIKAChU: a Python-based informatics kit for analysing chemical units
title_short PIKAChU: a Python-based informatics kit for analysing chemical units
title_full PIKAChU: a Python-based informatics kit for analysing chemical units
title_fullStr PIKAChU: a Python-based informatics kit for analysing chemical units
title_full_unstemmed PIKAChU: a Python-based informatics kit for analysing chemical units
title_sort pikachu: a python-based informatics kit for analysing chemical units
url https://research.wur.nl/en/publications/pikachu-a-python-based-informatics-kit-for-analysing-chemical-uni
work_keys_str_mv AT terlouwbarbarar pikachuapythonbasedinformaticskitforanalysingchemicalunits
AT vromanssophiepjm pikachuapythonbasedinformaticskitforanalysingchemicalunits
AT medemamarnixh pikachuapythonbasedinformaticskitforanalysingchemicalunits
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