diff --git a/actions/doc/index.rst b/actions/doc/index.rst index c404e772d50baac51259dbd06793ee4457a15b0c..e13e33b5f76d397e0a2cd48f313a4932f8c5d23c 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 33df7af8cbbed77b0c25218b6d2d818423cd39d1..7094be920f57acae2822d043eb09a37334ce0433 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)