From 6334fe2c0fc5efd612d6189e939ec77b07c6e68b Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 7 Jul 2020 21:06:04 +0200
Subject: [PATCH] Move secondary structure assignment in a3m building to
separate function
---
modules/bindings/pymod/hhblits.py | 18 ++++++++++++++++--
1 file changed, 16 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index e8db627ad..d7501ecd8 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -593,10 +593,24 @@ class HHblits:
if not os.path.exists(a3m_file):
raise RuntimeError('Building query profile failed, no output')
- if not assign_ss:
+ if assign_ss:
+ return self.AssignSSToA3M(a3m_file)
+ else:
return a3m_file
- # add secondary structure annotation
+ def AssignSSToA3M(self, a3m_file):
+ """
+ HHblits does not assign predicted secondary structure by default.
+ You can optionally assign it with the addss.pl script provided by the
+ HH-suite. However, your HH-suite installation requires you to specify
+ paths to PSIRED etc. We refer to the HH-suite user guide for further
+ instructions.
+
+ :param a3m_file: Path to file you want to assign secondary structure to
+ :type a3m_file: :class:`str`
+ """
+
+ a3m_file = os.path.abspath(a3m_file)
addss_cmd = "perl %s %s" % (os.path.join(self.hhsuite_root,
'scripts/addss.pl'),
a3m_file)
--
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