Do you have any suggestions how to sort molecules, so that simple substituents appear first and in an organized way in an R-group decomposition, i.e., R= H, CH3, OH, followed by molecules with more complex substituents?
R1 R2 R3
H H OH
H OH H
OH H H
H OH OH
Actually we have an option which sets the opposite ordering: heavy groups come first, then H atom matches, finally empty matches. Use
--hitOrdering:g to set this behavior:
rgdecomp --hitOrdering:g -q query.mrv targets.smiles
Refer to the RGroupDecompostion user guide for more details.