I notice that the Fingerprint Similarity node has the option to use the Tversky Index which is a modification of the Tanimoto Index with alpha and beta parameters.
I am completely unsure what alpha and beta values the node uses for the Tversky Index. Ideally I would like to be able to specify the values myself, this can be really powerful. If this is selected from the dropdown, can two boxes in the node appear to specify alpha and beta.
If you have a molecule A you are searching against with a set of molecules B, then;
Specifying an alpha value of 0, allows you to search for molecules which are substructures of A. i.e. the highly scored molecules will have substructures represented in A without having other substructures present which are NOT present in A. This is useful for finding molecular fragments of A.
Specifying a beta value of 0, allows you to search for molecules which are superstructures of A. i.e. the highly scored molecules will have the most substructures to that of A regardless of the fact that the molecules may contain additional functionalities which are NOT present in A. This is useful for finding molecules which contain all of A, or close to all of A, and more. For example A maybe a fragment with some low level activity and you want to find molecules which contain A plus more chemical features.
As an aside, what type of fingerprint is the Indigo fingerprint, is it an Extended Connectivity/Functional Class type fingerprint, i.e. Morgan algorithm/Daylight type where it is defining patterns in connectivity or is it assigning functional groups to bits, and identifying TRUE or FALSE for the presence of many functionalities like MACCS fingerprints.
Thanks in advance,