Example Commands

The following section shows several common command-line executions of pkatyper. Each example is followed by an explanation of what the program will do.

prompt> pkatyper drugs.sdf enumerated_drugs.smi

Reads the file drugs.sdf in SD format, enumerates the pKa states of each molecule and writes them into the file enumerated_drugs.smi. Molecules with only one identified pKa state are passed through to the output file.

prompt> pkatyper -in drugs.sdf -out enumerated_drugs.smi

This command generates the exact same behavior as described above.

prompt> pkatyper -count drugs.sdf drugCounts

This command reads each of the molecules in drugs.sdf and counts the number of pKa states. For each molecule, a single line is added to the drugCounts output file that contains the molecule title and the number of states.