The only program I have found is Plexus Suite from chemaxon. (I asked for trial, but no answer to me yet).
The task is: create variation of compounds, where is scaffold and different substituents:
And I need to create dataset/database of all possible variations.
How to deal with this problem? Or I need to use some scripting to make the database?
UPD1: best option - creation of SMILES (Simplified molecular-input line-entry system), 3d structure is automated and easy step if there is correct SMILES/connectivity of molecule (which is the same, as smiles) Using XYZ - it means, you should make substituent database in correct position for adding. I am asking for software with functionality
Vega ZZ has the module for database enumeration, but it is working as Python script.