Tool for mining structure-property relationships from chemical datasets
Python
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manual
sirms @ 6c06716
utils
.gitignore
.gitmodules
README.txt
calc_atomic_properties_chemaxon.py
calc_frag_contrib.py
default.smarts
extractsdf.py
filter_descriptors.py
find_frags_auto_rdkit.py
find_frags_rdkit.py
find_murcko_rdkit.py
model.py
mol_context.py
plot_contributions.py
plot_property_distribution.py
predict.py
sdf_field2title.py
setup.txt
sirms_file_class.py
spci.py
std_rules.xml

README.txt

SPCI
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Tool for mining structure-property relationships from chemical datasets

Description
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Retrieves structure-property relationship from datasets 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.

Features
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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:
  a) ring systems;
  b) Murcko scaffolds;
  c) common functional groups and rings;
  d) user-defined fragments;
  e) automatically generated fragments (based on SMARTS pattern matched broken bonds).

Visualization of results
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1. Built-in visualization.
2. rspci - R package for custom visualization (https://github.com/DrrDom/rspci)
3. Online tool for visualization, plot customization and figure downloading (link will be published soon)

Manual
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Short manual is included.

Publications
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Structural interpretation was published in the paper http://dx.doi.org/10.1002/minf.201300029
Integrated structural and physicochemical interpretation was published in the paper http://dx.doi.org/10.1021/acs.jcim.6b00371

Citation
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If you use this tool please cite this repository and the publication J. Chem. Inf. Model.  56, 8, 1455-1469 (http://dx.doi.org/10.1021/acs.jcim.6b00371)

Home page
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http://qsar4u.com/pages/sirms_qsar.php

License
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GPLv3

What's new
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**1.0.0**
- 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