@@ -181,15 +181,15 @@ Here are all available options in **RPG**:
...
@@ -181,15 +181,15 @@ Here are all available options in **RPG**:
**-x, -\\-cleave**: Cleavage site(s) when adding enzyme in non-interactive mode (*e.g.* -x "(D or E,)", similar to -x "(D,)" "(E,)". See :ref:`addenzyme` for more information.
**-x, -\\-cleave**: Cleavage site(s) when adding enzyme in non-interactive mode (*e.g.* -x "(D or E,)", similar to -x "(D,)" "(E,)". See :ref:`addenzyme` for more information.
**-z, --exception**: Exception(s) when adding enzyme in non-interactive mode (*e.g.* -z "(D,)(W)" "(D,)(A)". See :ref:`addenzyme` for more information.
**-z, -\\-exception**: Exception(s) when adding enzyme in non-interactive mode (*e.g.* -z "(D,)(W)" "(D,)(A)". See :ref:`addenzyme` for more information.
**-y, --enzname**: Enzyme's name when adding enzyme in non-interactive mode. See :ref:`addenzyme` for more information.
**-y, -\\-enzname**: Enzyme's name when adding enzyme in non-interactive mode. See :ref:`addenzyme` for more information.
**-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt).
**-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt).
**-p, -\\-pka**: Define pKa values. Either 'ipc2', 'stryer' or 'ipc' (default: ipc2). IPC2 values come from `IPC_peptide in Supplementary Table S1 <https://doi.org/10.1093/nar/gkab295>`_, Stryer values from Biochemistry Stryer, 7th edition and IPC values from `IPC_peptide <http://isoelectric.org/theory.html>`_.
**-p, -\\-pka**: Define pKa values. Either 'ipc2', 'stryer' or 'ipc' (default: ipc2). IPC2 values come from `IPC_peptide in Supplementary Table S1 <https://doi.org/10.1093/nar/gkab295>`_, Stryer values from Biochemistry Stryer, 7th edition and IPC values from `IPC_peptide <http://isoelectric.org/theory.html>`_.
**-w, --mass**: Define atomic mass values. Either 'avg' for average mass or 'mono' for monoisotopic mass.
**-w, -\\-mass**: Define atomic mass values. Either 'avg' for average mass or 'mono' for monoisotopic mass.
**-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information.
**-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information.