diff --git a/docs/userguide.rst b/docs/userguide.rst index f9afdeb5d73a7b130e454cd03003f5607a80d4af..1abf9b1af662099f5bc1d453bd3ef1e1c14d5cb4 100644 --- a/docs/userguide.rst +++ b/docs/userguide.rst @@ -170,6 +170,8 @@ Here are all available options in **RPG**: **-o, -\\-outputfile**: Result file to output resulting peptides (default './peptides.xxx' depending of -\\-fmt). +**-p, -\\-pka**: Define pKa values. Either 'ipc' or 'stryer' (default: ipc). IPC values come from `IPC_peptide <http://isoelectric.org/theory.html>`_ and Stryer values from Biochemistry Stryer, 7th edition. + **-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information. **-q, -\\-quiet**: No standard output, only error(s). diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py index a6025668322e36472c39080378987beb6c043ddc..7eb612bcdc21e4427980d074102c2fe214201a42 100644 --- a/rpg/RapidPeptidesGenerator.py +++ b/rpg/RapidPeptidesGenerator.py @@ -277,7 +277,7 @@ def main(): "overwritten.") parser.add_argument("-p", "--pka", metavar="", choices=['ipc', 'stryer'], default="ipc", help="Define pKa values. Either 'ipc' " - "or 'stryer (default: ipc)") + "or 'stryer' (default: ipc)") group_output = parser.add_mutually_exclusive_group() group_output.add_argument("-o", "--outputfile", type=str, metavar="", default="", help="Optional result file " diff --git a/rpg/core.py b/rpg/core.py index 5d4f2ec428fb0834186272eb0fc04c63c860aac4..06509f7333365df7d5fcf4357a85970dfdd74c48 100644 --- a/rpg/core.py +++ b/rpg/core.py @@ -84,7 +84,7 @@ AA_PKA_IPC = {"Nterm" : 9.564, "R" : 12.503, "Y" : 10.071, "Cterm" : 2.383} -"""pKa of important amino acid to compute pI (from IPC).""" +"""pKa of important amino acid to compute pI (from IPC_peptide. See http://isoelectric.org/theory.html for details).""" def handle_errors(message="", err=1, error_type=""): """Custom handling of errors and warnings.