How to enumerate stereoisomers for undefined stereocenters? Indigo Isomer Enumeration node seems not working for such a purpose

Hi guys,

I want to enumerate all the possible stereo-isomers that a molecules can have when it contain one or more undefined stereocenters (or the groups orientation around one or more double bonds is undefined). This is very useful when 2D structures must be converted into 3D ones.

In a first moment I thought Indigo Isomer Enumeration node was designed just for this, as in its description it state: “the node enumerates all the isomers of the input molecules.” Nevertheless after a first trial (see attached workflow) I realize that it works just in the opposite way, meaning that it enumerate the stereoisomers only for the defined stereocenters (and defined regio-chemistry around the double bond).

Please, can anybody tell if the current behavior of the Indigo Isomer Enumeration node is the desired one? And, more importantly, can anybody suggest me how can I enumerate stereoisomers only for undefined stereocenters? Does exist any workaround in KNIME?

Any help is much appreciated. 


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