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Tool for mining structure-property relationships from chemical datasets

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Automatic tool for mining structure-property relationships from chemical data sets


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.


pip install spci


  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 (
  3. Online tool for visualization, plot customization and figure downloading ( Demo version is here (
  4. Per atom contributions can be visualized with RDKit similarity maps.


The short manual is included.


  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 - - 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 - - integrated structural and physicochemical interpretation.

Home page



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 to limit maximum size of output fragments
  • skip fragments with H as a context from output of
  • update README and installation notes


Tool for mining structure-property relationships from chemical datasets






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