My new MCS program is named “fmcs.” It uses RDKit for the cheminformatics and is is available under the BSD 2-clause license. Many thanks to Roche for funding the project and making it available under a free license. Their hope and mine is that fmcs will be included someday as part of RDKit. For now, you can download it from the Bitbucket site…
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fmcs – find the MCS of a set of compounds