Command line utilities

After installation of pmapper the following utilities can be invoked from the command line.


usage: get_pharm_counts [-h] -i input.smi -o output.txt [-c INTEGER] [-v]

Count the number of pharmacophore features of each type.

optional arguments:
  -h, --help            show this help message and exit
  -i input.smi, --in input.smi
                        input SMILES file. Should contain mol title as a
                        second field. Fields are tab-separated. No header.
  -o output.txt, --out output.txt
                        output text file with calculated number of features.
                        If input molecules cannot be parsed NA values will be
                        inserted in output.
  -c INTEGER, --ncpu INTEGER
                        Number of CPU cores to use. Default: 1.
  -v, --verbose         print progress to STDERR.