| Name | spci JSON |
| Version |
1.1.4
JSON |
| download |
| home_page | https://github.com/DrrDom/spci |
| Summary | SPCI: structural and physicochemical interpretation of QSAR models |
| upload_time | 2024-11-04 08:45:28 |
| maintainer | None |
| docs_url | None |
| author | Pavel Polishchuk |
| requires_python | >=3.6 |
| license | None |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
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# 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
1. Easy to use straightforward workflow with GUI.
2. Automatic model building and cross-validation.
3. Build models for imbalanced data set using the multiple oversampling approach.
4. Prediction with built models.
5. 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
1. Built-in visualization.
2. rspci - R package for custom visualization and analysis (https://github.com/DrrDom/rspci)
3. 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/)
4. Per atom contributions can be visualized with RDKit similarity maps.
#### Manual
The short manual is included.
#### Citation
1. 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.
2. 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
Raw data
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