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# pkatyper Usage¶

## Required Parameters¶

-in

Input file of molecules. An input file is required, but the -in flag is optional. The first parameter listed with no flag will be automatically mapped to the input file. Unflagged parameters must occur last in the parameter list.

### Optional parameters¶

-count

Only count the number of pKa states rather than enumerating each of the states. If the -count flag is specified true, then the output file will contain the name of each compound followed by the number states of that molecule. This options writes to a text file or stdout. [default = false]

-max

This integer parameter is the maximum number of pKa states which will be enumerated for any single molecule. If a value of zero is passed to this parameter, no limit will be set. [default = 100]

-out

Output file of molecules. Both the output file and the -out flag are optional. The second parameter listed with no flag will be automatically mapped to the output file. Unflagged parameters must occur last in the parameter list. If no output is specified at all, output will be written to std::out in SMILES format. Any OpenEye supported molecule format can be used for output. If the -count flag is specified true, then molecular format is no longer relevant to the output file.

-param

The argument for this flag is the name of a file containing control parameters. The control parameter file acts to either replace or augment the command line interface. All parameters necessary for program execution may be provided in the control parameter file, although any command given explicitly on the command line will supersede options found in the parameter file. pkatyper generates a new parameter file containing the full set of execution parameters upon every execution. The name of the parameter file written by pkatyper is created by combining the prefix base name with the .parm extension.

-paramfile

The filename for the output parameter file can be set with this flag and it overrides -prefix flag for the name of parameter file.

-prefix

The argument for this flag defines the prefix to be used for parameter and log files. The parameter and log files will be written to what follows this flag plus the extension .param or .log. [default = pkatyper]

## 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.