From 700e07e8c08392eac28d151af6274a4eda71f2f5 Mon Sep 17 00:00:00 2001
From: Nico Maillet <nicolas.maillet@pasteur.fr>
Date: Tue, 25 May 2021 16:49:28 +0200
Subject: [PATCH] Remove 'deprecated' for ipc
---
docs/userguide.rst | 2 +-
rpg/RapidPeptidesGenerator.py | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/docs/userguide.rst b/docs/userguide.rst
index 466f952..c3a57d3 100644
--- a/docs/userguide.rst
+++ b/docs/userguide.rst
@@ -174,7 +174,7 @@ 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 'ipc2', 'stryer' or 'ipc' (default: ipc2, ipc is deprecated). 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>`_.
**-r, -\\-randomname**: Random (not used) output name file. See :ref:`random` for more information.
diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py
index 259def2..decca71 100644
--- a/rpg/RapidPeptidesGenerator.py
+++ b/rpg/RapidPeptidesGenerator.py
@@ -274,7 +274,7 @@ def main():
"overwritten.")
parser.add_argument("-p", "--pka", metavar="", choices=['ipc2', 'stryer', 'ipc'],
default="ipc2", help="Define pKa values. Either 'ipc2' "
- "'stryer' or 'ipc' (deprecated) (default: ipc2)")
+ "'stryer' or 'ipc' (default: ipc2)")
group_output = parser.add_mutually_exclusive_group()
group_output.add_argument("-o", "--outputfile", type=str, metavar="",
default="", help="Optional result file "
--
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