Metadata-Version: 2.1
Name: sirms
Version: 1.2.1
Summary: SiRMS: simplex representation of molecular structure
Home-page: https://github.com/DrrDom/sirms
Author: Pavel Polishchuk
Author-email: pavel_polishchuk@ukr.net
License: UNKNOWN
Description: # 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.py -in input.sdf -o output.txt`  
        Returns 2D simplex descriptors with vertexes labeled by element for reactions  
        `sirms.py -in input.rdf -o output.txt`  
        
        #### Help
        
        `sirms.py -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
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: rdkit
