From command line¶
Transform molecules into fingerprints¶
This function can also be used from the command line, just by running the following command along with the arguments explained below.
Specify the fingerprints and the file format to which the user wants the sdf file to be converted.
usage: drug_learning.two_dimensions.main_fingerprints [-h] [-n N_WORKERS]
[-mo] [-ma] [-rd] [-md]
[-urd] [-voc VOC] [-c]
[-pq] [-f] [-hdf] [-pk]
infile {split} ...
Positional Arguments¶
- infile
Input sdf file(s)
- split
Possible choices: split
Named Arguments¶
- -n, --nworkers
Number of workers to parallelize the sdf transform into fingerprints
Default: 1
- -mo, --morgan
Convert molecules to Morgan fingerprint
- -ma, --maccs
Convert molecules to MACCS fingerprint
- -rd, --rdkit
Convert molecules to RDkit fingerprint
- -md, --mordred
Convert molecules to Mordred fingerprint
- -urd, --unfolded_rdkit
Convert molecules to Unfolded RDkit fingerprint
- -voc, --vocabulary
Vocabulary for unfolded rdkit fingerprint
- -c, --csv
Save output to csv
Default: False
- -pq, --parquet
Save output to parquet
Default: False
- -f, --feather
Save output to feather
Default: False
- -hdf, --hdf
Save output to hdf
Default: False
- -pk, --pickle
Save output to pickle
Default: False