From 1590a8f0a89207695d974c5e2a63b94616ec8a7e Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 4 Mar 2021 08:36:53 +0100
Subject: [PATCH] Remove requirement of terminal gaps having length > 1 in
ModelTermini
---
modelling/pymod/_closegaps.py | 4 +---
modelling/pymod/_pipeline.py | 4 ++--
2 files changed, 3 insertions(+), 5 deletions(-)
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index 5fdf7a44..337c281b 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -1275,8 +1275,6 @@ def ModelTermini(mhandle, torsion_sampler, fragger_handles=None,
*fragger_handles* is given) :class:`~promod3.loop.Fragger` lists. The latter
is only used if the gap length is >= the length of fragments stored.
- Terminal gaps of length 1 are ignored by this function!
-
.. literalinclude:: ../../../tests/doc/scripts/modelling_model_termini.py
:param mhandle: Modelling handle on which to apply change.
@@ -1302,7 +1300,7 @@ def ModelTermini(mhandle, torsion_sampler, fragger_handles=None,
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
# get terminal gaps (copies as we'll clear them as we go)
- terminal_gaps = [g.Copy() for g in mhandle.gaps if g.IsTerminal() and g.length > 1]
+ terminal_gaps = [g.Copy() for g in mhandle.gaps if g.IsTerminal()]
if len(terminal_gaps) > 0:
ost.LogInfo("Trying to model %d terminal gap(s)." % len(terminal_gaps))
else:
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 44b2ef01..a4b5e870 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -531,7 +531,7 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list(),
full target sequence(s). 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.
+ limited.
:type model_termini: :class:`bool`
@@ -571,7 +571,7 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list(),
if model_termini:
ModelTermini(mhandle, torsion_sampler, fragger_handles=fragger_handles)
- RemoveTerminalGaps(mhandle) # length=1 ignored above
+ RemoveTerminalGaps(mhandle)
# build sidechains
BuildSidechains(mhandle, merge_distance, fragment_db,
--
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