SPCI: structural and physicochemical interpretation of QSAR models
Project description
SPCI
Automatic tool for mining structure-property relationships from chemical data sets
Description
Retrieves structure-property relationship from data sets in a chemically meaningful way.
Returns estimated contributions of fragments to the investigated property of compounds from a data set and can estimate contribution of different physicochemical factors as well.
Installation
pip install spci
Features
- Easy to use straightforward workflow with GUI.
- Automatic model building and cross-validation.
- Build models for imbalanced data set using the multiple oversampling approach.
- Prediction with built models.
- Several fragmentation schemes to compute fragment contributions of:
- common functional groups and rings;
- Murcko scaffolds;
- user-defined fragments;
- automatically generated fragments (based on SMARTS pattern matching broken bonds);
- per atom fragmentation.
Visualization and analysis of results
- Built-in visualization.
- rspci - R package for custom visualization and analysis (https://github.com/DrrDom/rspci)
- Online tool for visualization, plot customization and figure downloading (http://158.194.101.252:3838/spci-vis/). Demo version is here (http://158.194.101.252:3838/spci-vis-demo/)
- Per atom contributions can be visualized with RDKit similarity maps.
Manual
The short manual is included.
Citation
- Polishchuk, P. G.; Kuz'min, V. E.; Artemenko, A. G.; Muratov, E. N., Universal Approach for Structural Interpretation of Qsar/Qspr Models. Mol. Inf. 2013, 32, 843-853 - http://dx.doi.org/10.1002/minf.201300029 - structural interpretation.
- Polishchuk, P.; Tinkov, O.; Khristova, T.; Ognichenko, L.; Kosinskaya, A.; Varnek, A.; Kuz’min, V., Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis. J. Chem. Inf. Model. 2016, 56, 1455-1469 - http://dx.doi.org/10.1021/acs.jcim.6b00371 - integrated structural and physicochemical interpretation.
Home page
http://qsar4u.com/pages/sirms_qsar.php
License
LGPLv3
What's new
1.0.0 (03.07.2018)
- RDKit is used as a backend instead of Indigo
- multiple undersampling was implemented
- changed default descriptors, that make this version incompatible with previous models and vice versa.
- updated sirms descriptors
- many small fixes and improvements
1.1.0 (07.02.2021)
- added support of RDKit descriptors
- added per atom fragmentation
- reorganized as a Python package
- console scripts have prefix spci_*
1.1.1 (23.03.2021)
- changed license to LGPLv3
- fixed arguments in scpi_descriptors
1.1.2 (28.06.2023)
- add max_size argument to find_frag_auto_rdkit.py to limit maximum size of output fragments
- skip fragments with H as a context from output of find_frag_auto_rdkit.py
- update README and installation notes
1.1.4 (04.11.2024)
- fix calculation of fragment contributions if initial molecules do not contain hydrogens
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