PIKAChU: a Python-based informatics kit for analysing chemical units
Abstract 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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-06-01
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| Series: | Journal of Cheminformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13321-022-00616-5 |
| _version_ | 1818207847473741824 |
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| author | Barbara R. Terlouw Sophie P. J. M. Vromans Marnix H. Medema |
| author_facet | Barbara R. Terlouw Sophie P. J. M. Vromans Marnix H. Medema |
| author_sort | Barbara R. Terlouw |
| collection | DOAJ |
| description | Abstract 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 |
| first_indexed | 2024-12-12T04:35:26Z |
| format | Article |
| id | doaj.art-dbcaeb216882446096e7079775936517 |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-12-12T04:35:26Z |
| publishDate | 2022-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-dbcaeb216882446096e70797759365172022-12-22T00:37:59ZengBMCJournal of Cheminformatics1758-29462022-06-0114111710.1186/s13321-022-00616-5PIKAChU: a Python-based informatics kit for analysing chemical unitsBarbara R. Terlouw0Sophie P. J. M. Vromans1Marnix H. Medema2Bioinformatics Group, Wageningen UniversityBioinformatics Group, Wageningen UniversityBioinformatics Group, Wageningen UniversityAbstract 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 Abstracthttps://doi.org/10.1186/s13321-022-00616-5Cheminformatics kitPythonStructure visualisationIn silico chemistryMolecular fingerprinting |
| spellingShingle | Barbara R. Terlouw Sophie P. J. M. Vromans Marnix H. Medema PIKAChU: a Python-based informatics kit for analysing chemical units Journal of Cheminformatics Cheminformatics kit Python Structure visualisation In silico chemistry Molecular fingerprinting |
| title | 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_short | PIKAChU: a Python-based informatics kit for analysing chemical units |
| title_sort | pikachu a python based informatics kit for analysing chemical units |
| topic | Cheminformatics kit Python Structure visualisation In silico chemistry Molecular fingerprinting |
| url | https://doi.org/10.1186/s13321-022-00616-5 |
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