From b443a2341f21f107225bb4b162d148eea3ca5a76 Mon Sep 17 00:00:00 2001
From: Nicolas MAILLET <nicolas.maillet@pasteur.fr>
Date: Mon, 21 Jan 2019 15:55:15 +0100
Subject: [PATCH] Correct typo and add doc for -p option
---
docs/userguide.rst | 2 ++
rpg/RapidPeptidesGenerator.py | 2 +-
rpg/core.py | 2 +-
3 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/docs/userguide.rst b/docs/userguide.rst
index f9afdeb..1abf9b1 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 a602566..7eb612b 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 5d4f2ec..06509f7 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.
--
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