From 0143ed159e91fced2168c04d11d6eeb32cfd43e2 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 11 Jun 2019 17:56:15 +0200
Subject: [PATCH] Doc update/fix.
---
actions/doc/index.rst | 6 +++---
core/tests/test_pm3argparse.py | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/actions/doc/index.rst b/actions/doc/index.rst
index c404e772..e13e33b5 100644
--- a/actions/doc/index.rst
+++ b/actions/doc/index.rst
@@ -135,13 +135,13 @@ sampling. You can enforce the usage of structural fragments with ``-r``
but this increases runtime due to searching the required fragments.
Setup of the according :class:`promod3.modelling.FraggerHandle`
objects is performed in the
-:class:`promod3.core.pm3argparse.PM3ArgumentParser`. You can find more
-details on the setup procedure in the documentation there.
+:class:`~promod3.core.pm3argparse.PM3ArgumentParser` class as described in
+detail :meth:`here <promod3.core.pm3argparse.PM3ArgumentParser.AddFragments>`.
The default modelling pipeline in ProMod3 is optimized to generate a gap-free
model of the region in the target sequence(s) that is covered with template
information. Terminal extensions without template coverage are negelected.
-You can enforce a model of the full target sequence(s) by adding ``-r``.
+You can enforce a model of the full target sequence(s) by adding ``-t``.
The terminal parts will be modelled with a crude Monte Carlo approach. Be aware
that the accuracy of those termini is likely to be limited. Termini of length 1
won't be modelled.
diff --git a/core/tests/test_pm3argparse.py b/core/tests/test_pm3argparse.py
index 33df7af8..7094be92 100644
--- a/core/tests/test_pm3argparse.py
+++ b/core/tests/test_pm3argparse.py
@@ -1278,7 +1278,7 @@ class PM3ArgParseTests(unittest.TestCase):
opts.fragger_handles[0].sequence)
self.assertEqual(opts.alignments[1].GetSequence(0).GetGaplessString(),
opts.fragger_handles[1].sequence)
- # most of the stuff in the fragger handles should be None
+ # most of the stuff in the fragger handles should be set
self.assertIsNotNone(opts.fragger_handles[0].profile)
self.assertIsNotNone(opts.fragger_handles[0].psipred_pred)
self.assertIsNotNone(opts.fragger_handles[0].torsion_sampler_coil)
--
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