From c27d449d4ac5de1da8f5b6a5663ad2be3ca19894 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 23 Dec 2024 11:23:58 +0100
Subject: [PATCH] expose keep_sidechains flag in
promod3.modelling.BuildSidechains
---
modelling/pymod/_pipeline.py | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index db7fc2ad..1302bcf5 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -183,7 +183,7 @@ def _GetSimEntity(sim):
def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
structure_db=None, torsion_sampler=None,
- rotamer_library=None):
+ rotamer_library=None, keep_sidechains=True):
'''Build sidechains for model.
This is a wrapper for :func:`promod3.modelling.ReconstructSidechains`,
@@ -213,7 +213,12 @@ def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
:func:`modelling.ReconstructSidechains`, a default
one is loaded if None.
:type rotamer_library: :class:`~promod3.sidechain.RotamerLib` or
- :class:`~promod3.sidechain.BBDepRotamerLib`
+ :class:`~promod3.sidechain.BBDepRotamerLib`
+ :param keep_sidechains: Used as parameter for
+ :func:`~promod3.modelling.ReconstructSidechains`,
+ controls if complete sidechains in *mhandle* should
+ be kept and not re-modelled.
+ :type keep_sidechains: :class:`bool`
'''
prof = core.StaticRuntimeProfiler.StartScoped('pipeline::BuildSidechains')
ost.LogInfo("Rebuilding sidechains.")
@@ -246,7 +251,7 @@ def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
FillLoopsByDatabase(mhandle, fragment_db, structure_db,
torsion_sampler, ring_punch_detection=2)
# re-build sidechains
- ReconstructSidechains(mhandle.model, keep_sidechains=True,
+ ReconstructSidechains(mhandle.model, keep_sidechains=keep_sidechains,
rotamer_library=rotamer_library)
# restore gaps
mhandle.gaps = StructuralGapList()
--
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