3.3 Usage

3.3.1 Command Line Interface

Executing pkatyper with no arguments will result in:

prompt> pkatyper

No argument specified on the command line
Required parameters:
    -in : Input filename
    -out : Output filename
For more help type:
  pkatyper --help'

3.3.1.1 Parameters

For a complete listing of parameters use the ``-help all'' flag as follows.

prompt> pkatyper --help all

-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.
-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. A description of supported file formats can be found in the final chapter of this document.
-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. A description of supported file formats can be found in the final chapter of this document. If the ``-count'' flag is specified true, then molecular format is no longer relevant to the output file.
-param: This can be used to name an input parameter file of pkatyper settings, especially useful for running the program with similar flags as a previous run. Flags coming after -param override parameters set by the parameter file.
-paramfile: The filename for the output parameter file can be set with this flag.
-prefix: Similar to -paramfile, the parameter file will be written to what follows this flag plus the extension `.param'.

3.3.2 Molecular formats

pkaTyper can read and write a variety of molecular formats. For details, please see the chapter on molecular formats below.

3.3.3 Example executions

This section has a series of example pkatyper command-line executions. Each example is followed by a brief description of its behavior.

prompt> pkatyper drugs.sdf enumerated_drugs.smi

Reads the file drugs.sdf in sd format and 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 drugs.sdf enumerated_drugs.sdf

Reads the file drugs.sdf in sd format and enumerates the pKa states of each molecule and writes them into the file enumerated_drugs.sdf in sd format. Molecules with only one identified pKa state are passed through to the output file. Explicit protons will be added where appropriate, and a rule-based method is used to generate coordinates for the proton. However, the heavy-atom coordinates of the molecule are not perturbed, so in cases where the change in protonation-state would lead to a modified heavy-atom geometry, the user must follow-up with a re-generation of the conformation in order to get completely reasonable proton and heavy-atom positions.

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.

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