| Name | sirms JSON |
| Version |
1.2.4
JSON |
| download |
| home_page | https://github.com/DrrDom/sirms |
| Summary | SiRMS: simplex representation of molecular structure |
| upload_time | 2023-04-13 09:20:13 |
| maintainer | |
| docs_url | None |
| author | Pavel Polishchuk |
| requires_python | >=3.6 |
| license | |
| keywords |
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| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# SiRMS
Simplex representation of molecular structure - a chemoinformatic tool for calculation of simplex (fragment) descriptors
#### Background
Simplex - tetraatomic fragment with fixed topology and stereo configuration.
Simplex descriptor - number of identical simplexes in a molecule.
From the version 1.0.0 fragments of any size are supported (not only simplexes).
#### Features
1. Calculate descriptors for single compounds, mixtures, quasi-mixtures and reactions (all-in-one tool).
2. Support incorporation of user-defined atomic properties (e.g. partial charges, H-bond donor/acceptor, etc) in generated descriptors.
3. Work well in QSAR/QSPR modeling tasks.
#### Limitations
This version calculates only 2D descriptors.
#### Installation
`pip install sirms`
#### Usage
Returns 2D simplex descriptors with vertexes labeled by element for single compounds
`sirms -in input.sdf -o output.txt`
Returns 2D simplex descriptors with vertexes labeled by element for reactions
`sirms -in input.rdf -o output.txt`
#### Help
`sirms -h`
#### Wiki
See wiki pages for more information and examples - https://github.com/DrrDom/sirms/wiki.
#### Notes
Standardize structures before descriptors calculation.
#### License
BSD 3-clause
#### Reference
1. Kuz’min, V. E.; Artemenko, A. G.; Polischuk, P. G.; Muratov, E. N.; Khromov, A. I.; Liahovskiy, A. V.; Andronati, S. A.; Makan, S. Y. Hierarchic System of QSAR Models (1D-4D) on the Base of Simplex Representation of Molecular Structure - Journal of Molecular Modelling, 2005, 11, 457-467. (**one of the first descriptions of single compounds representation**)
2. Kuz’min, V. E.; Artemenko, A. G.; Muratov, E. N. Hierarchical QSAR technology based on the Simplex representation of molecular structure - Journal of Computer-Aided Molecular Design, 2008, Volume 22, Issue 6-7, 403-421. (**single compounds representation**)
3. Oprisiu, I.; Varlamova, E.; Muratov, E.; Artemenko, A.; Marcou, G.; Polishchuk, P.; Kuz'min, V.; Varnek, A. QSPR Approach to Predict Nonadditive Properties of Mixtures. Application to Bubble Point Temperatures of Binary Mixtures of Liquids. Molecular Informatics 2012, 31, 491-502. (**old approach of mixtures representation**)
4. Mokshyna, E.; Nedostup, V. I.; Polischuk, P. G.; Kuzmin, V. E. ‘Quasi-Mixture’ Descriptors for QSPR Analysis of Molecular Macroscopic Properties. The Critical Properties of Organic Compounds. Molecular Informatics 2014, 33, 647-654. (**quasi-mixture representation**)
5. Polishchuk, P.; Madzhidov, T.; Gimadiev, T.; Bodrov, A.; Nugmanov, R.; Varnek, A. Structure–reactivity modeling using mixture-based representation of chemical reactions. J Comput Aided Mol Des 2017, 31 (9), 829-839 (**reaction representation & new mixture representation**).
#### Changes
version 1.1.0 (26.07.2016)
1) New canonicalization algorithm was implemented that changed descriptors names (break compatibility with older versions)
version 1.1.1 (20.02.2017)
- multiprocessing calculation of descriptors was implemented for single molecules and svm output format only (sparse format)
- per atom fragmentation was added
version 1.2.0 (06.02.2021)
- reorganized as a Python package
version 1.2.1 (08.02.2021)
- fix README formatting
version 1.2.2 (12.04.2023)
- fix examples in README
version 1.2.4 (13.04.2023)
- fix import calc_atomic_properties_chemaxon
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"description": "# SiRMS\n\nSimplex representation of molecular structure - a chemoinformatic tool for calculation of simplex (fragment) descriptors\n\n#### Background\n\nSimplex - tetraatomic fragment with fixed topology and stereo configuration.\nSimplex descriptor - number of identical simplexes in a molecule.\nFrom the version 1.0.0 fragments of any size are supported (not only simplexes).\n\n#### Features\n\n1. Calculate descriptors for single compounds, mixtures, quasi-mixtures and reactions (all-in-one tool).\n2. Support incorporation of user-defined atomic properties (e.g. partial charges, H-bond donor/acceptor, etc) in generated descriptors.\n3. Work well in QSAR/QSPR modeling tasks.\n\n#### Limitations\n\nThis version calculates only 2D descriptors.\n\n#### Installation\n\n`pip install sirms`\n\n#### Usage\nReturns 2D simplex descriptors with vertexes labeled by element for single compounds \n`sirms -in input.sdf -o output.txt` \nReturns 2D simplex descriptors with vertexes labeled by element for reactions \n`sirms -in input.rdf -o output.txt` \n\n#### Help\n\n`sirms -h`\n\n#### Wiki\n\nSee wiki pages for more information and examples - https://github.com/DrrDom/sirms/wiki.\n\n#### Notes\n\nStandardize structures before descriptors calculation.\n\n#### License\n\nBSD 3-clause\n\n#### Reference\n\n1. Kuz\u2019min, V. E.; Artemenko, A. G.; Polischuk, P. G.; Muratov, E. N.; Khromov, A. I.; Liahovskiy, A. V.; Andronati, S. A.; Makan, S. Y. Hierarchic System of QSAR Models (1D-4D) on the Base of Simplex Representation of Molecular Structure - Journal of Molecular Modelling, 2005, 11, 457-467. (**one of the first descriptions of single compounds representation**)\n2. Kuz\u2019min, V. E.; Artemenko, A. G.; Muratov, E. N. Hierarchical QSAR technology based on the Simplex representation of molecular structure - Journal of Computer-Aided Molecular Design, 2008, Volume 22, Issue 6-7, 403-421. (**single compounds representation**)\n3. Oprisiu, I.; Varlamova, E.; Muratov, E.; Artemenko, A.; Marcou, G.; Polishchuk, P.; Kuz'min, V.; Varnek, A. QSPR Approach to Predict Nonadditive Properties of Mixtures. Application to Bubble Point Temperatures of Binary Mixtures of Liquids. Molecular Informatics 2012, 31, 491-502. (**old approach of mixtures representation**)\n4. Mokshyna, E.; Nedostup, V. I.; Polischuk, P. G.; Kuzmin, V. E. \u2018Quasi-Mixture\u2019 Descriptors for QSPR Analysis of Molecular Macroscopic Properties. The Critical Properties of Organic Compounds. Molecular Informatics 2014, 33, 647-654. (**quasi-mixture representation**)\n5. Polishchuk, P.; Madzhidov, T.; Gimadiev, T.; Bodrov, A.; Nugmanov, R.; Varnek, A. Structure\u2013reactivity modeling using mixture-based representation of chemical reactions. J Comput Aided Mol Des 2017, 31 (9), 829-839 (**reaction representation & new mixture representation**).\n\n#### Changes\n\nversion 1.1.0 (26.07.2016)\n1) New canonicalization algorithm was implemented that changed descriptors names (break compatibility with older versions)\n\nversion 1.1.1 (20.02.2017)\n- multiprocessing calculation of descriptors was implemented for single molecules and svm output format only (sparse format)\n- per atom fragmentation was added\n\nversion 1.2.0 (06.02.2021)\n- reorganized as a Python package\n\nversion 1.2.1 (08.02.2021)\n- fix README formatting\n\nversion 1.2.2 (12.04.2023)\n- fix examples in README\n\nversion 1.2.4 (13.04.2023)\n- fix import calc_atomic_properties_chemaxon\n\n\n",
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