Two individual conformer libraries were used in the paper. They may each be generated using the following commands:
- rms0.5
python $E3FP_PACKAGE/conformer/generate.py -s ../data/chembl20_proto_smiles.smi.bz2 -o conformers_proto_rms0.5 --pool_multiplier 2 -r 0.5 -C 2 - rms1_e20
python $E3FP_PACKAGE/conformer/generate.py -s ../data/chembl20_proto_smiles.smi.bz2 -o conformers_proto_rms1_e20 --pool_multiplier 2 -r 1.0 -e 20 -C 2
- Note: it is highly recommended that you run conformer generation using
one of the parallelization options. Also, if you only need the subset
of conformers used for the final E3FP parameter set (3), then use the
--firstparameter for early termination.