Input file in SDF format

Mol file to align against

Query molecule index in SD-file if not the first

Score cutoff relative to alignment of query to itself

Number of conformers to generate, if 0 then input structures are assumed to already be)

Prune RMSD threshold for excluding conformers

If confomers fall below the RMSD threshold, number of attempts at regeneration before giving up.

Number of EM iterations using the MMFF force field. Default is 0 (i.e. no EM).

Use Crippen (logP) contributions