On 2015 Jul 12, Egon Willighagen commented:

The paper uses the CDK, which you can read about in these two papers:

Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., Willighagen, E., Mar. 2003. The chemistry development kit (CDK):  an Open-Source java library for chemo- and bioinformatics. J. Chem. Inf. Comput. Sci. 43 (2), 493-500. URL http://dx.doi.org/10.1021/ci025584y

Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., Willighagen, E. L., 2006. Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. Current pharmaceutical design 12 (17), 2111-2120. URL http://dx.doi.org/10.2174/138161206777585274

On 2015 Jul 12, Egon Willighagen commented:

The paper uses the CDK, which you can read about in these two papers:

Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., Willighagen, E., Mar. 2003. The chemistry development kit (CDK):  an Open-Source java library for chemo- and bioinformatics. J. Chem. Inf. Comput. Sci. 43 (2), 493-500. URL http://dx.doi.org/10.1021/ci025584y

Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., Willighagen, E. L., 2006. Recent developments of the chemistry development kit (CDK) - an open-source java library for chemo- and bioinformatics. Current pharmaceutical design 12 (17), 2111-2120. URL http://dx.doi.org/10.2174/138161206777585274