A terminal interface for property driven atom coloration.

ColorAtom uses a QSAR model based on ISIDA descriptors to produce a chemical structure where each atom bears an atomic contribution of the value calculated by the QSAR model. The idea is to evaluate contributions of each atom into the modelled property and to visualize them using a color code. This results in the colored image of 2D molecular structure in which molecular fragments responsible for increase or decrease of y could be easily recognized.

Screenshots of results

Coloration of well soluble (top) and weakly soluble (middle and bottom) compounds according to the fragment based regression model for aqueous solubility (logS). Red and green regions correspond, respectively, to negative and positive contributions to logS. Dark colour corresponds to large positive or negative atomic contributions. As expected, the polar parts of the molecules are coloured in green (good solubilisation) whereas aromatic and aliphatic moieties are in red (bad solubilisation). The numbers correspond to predicted logS values.

Interpretation of the Random Forest classification model for AChE inhibitors (probabilistic estimate as outcome). The presence of the tacrine-like fragment (in green) increases the probability to belong to the inhibitors class, whereas the fragment (in red) not typical for AChE inhibitors decreases this probability. The fragments in grey are found to be not relevant.


Linux 64bits command line


Documentation is available here




G. Marcou, D. Horvath, V. Solov’ev, A. Arrault, P. Vayer and A. Varnek
Interpretability of SAR/QSAR models of any complexity by atomic contributions
Mol. Inf., 2012, 31(9), 639-642, 2012


This software is freely available on demand. Please please fill the form available here to request a download link.