From 108c8f0ec55cee80e9fe6912b4e14ff81d45f77d Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 27 Sep 2018 09:52:33 +0200
Subject: [PATCH] Avoid loading the rotamer library several times for one
model. This can happen in case of ring punch fixes.
---
modelling/pymod/_pipeline.py | 17 +++++++++++++----
1 file changed, 13 insertions(+), 4 deletions(-)
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index fdea4850..d68c6ddf 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -164,7 +164,8 @@ def _GetSimEntity(sim):
def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
- structure_db=None, torsion_sampler=None):
+ structure_db=None, torsion_sampler=None,
+ rotamer_library=None):
'''Build sidechains for model.
This is a wrapper for :func:`promod3.modelling.ReconstructSidechains`,
@@ -190,10 +191,16 @@ def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
if ring punches are found. A default one is loaded
if None.
:type torsion_sampler: :class:`~promod3.loop.TorsionSampler`
+ :param rotamer_library: Used as parameter for
+ :func:`modelling.ReconstructSidechains`, a default
+ one is loaded if None.
+ :type rotamer_library: :class:`~promod3.sidechain.RotamerLib` or
+ :class:`~promod3.sidechain.BBDepRotamerLib`
'''
prof = core.StaticRuntimeProfiler.StartScoped('pipeline::BuildSidechains')
ost.LogInfo("Rebuilding sidechains.")
- ReconstructSidechains(mhandle.model, keep_sidechains=True)
+ ReconstructSidechains(mhandle.model, keep_sidechains=True,
+ rotamer_library=rotamer_library)
# check for ring punches
rings = GetRings(mhandle.model)
ring_punches = GetRingPunches(rings, mhandle.model)
@@ -221,7 +228,8 @@ 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=True,
+ rotamer_library=rotamer_library)
# restore gaps
mhandle.gaps = StructuralGapList()
for g in old_gaps:
@@ -459,6 +467,7 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()):
fragment_db = loop.LoadFragDB()
structure_db = loop.LoadStructureDB()
torsion_sampler = loop.LoadTorsionSamplerCoil()
+ rotamer_library = sidechain.LoadDunbrackLib()
merge_distance = 4
# remove terminal gaps
@@ -471,7 +480,7 @@ def BuildFromRawModel(mhandle, use_amber_ff=False, extra_force_fields=list()):
# build sidechains
BuildSidechains(mhandle, merge_distance, fragment_db,
- structure_db, torsion_sampler)
+ structure_db, torsion_sampler, rotamer_library)
# minimize energy of final model using molecular mechanics
MinimizeModelEnergy(mhandle, use_amber_ff=use_amber_ff,
--
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