From df7df1592a3e1784178400ef7f06a8dcde9ed698 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Mon, 15 Jul 2019 16:36:40 +0200
Subject: [PATCH] SCHWED-4334: fix gap handling in MM to allow reporting later.
---
modelling/pymod/_pipeline.py | 7 +++++--
modelling/tests/test_pipeline.py | 15 +++++++++++++++
2 files changed, 20 insertions(+), 2 deletions(-)
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index b8aef45f..63117e0f 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -371,8 +371,11 @@ def MinimizeModelEnergy(mhandle, max_iterations=12, max_iter_sd=20,
# update model
simulation_ent = _GetSimEntity(sim)
- mhandle.model = mol.CreateEntityFromView(simulation_ent.Select("ele!=H"),
- True)
+ new_model = mol.CreateEntityFromView(simulation_ent.Select("ele!=H"), True)
+ # transfer gaps before overwriting model
+ for gap in mhandle.gaps:
+ gap.Transfer(new_model.FindChain(gap.GetChainName()))
+ mhandle.model = new_model
# return model with hydrogens
return simulation_ent
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index 61c8f44d..90471ecb 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -390,12 +390,27 @@ class PipelineTests(unittest.TestCase):
# single chain
mhandle = self.getRawModel()
self.checkFinalModel(mhandle, exp_gaps=1, num_chains=1)
+ # repeat after sidechain reconstruction and MM
+ mhandle = self.getRawModel()
+ modelling.BuildSidechains(mhandle)
+ modelling.MinimizeModelEnergy(mhandle)
+ self.checkFinalModel(mhandle, exp_gaps=1, num_chains=1)
# homo-dimer
mhandle = self.getRawModelOligo("data/2aoh-1_cut")
self.checkFinalModel(mhandle, exp_gaps=2, num_chains=2)
+ # repeat after sidechain reconstruction and MM
+ mhandle = self.getRawModelOligo("data/2aoh-1_cut")
+ modelling.BuildSidechains(mhandle)
+ modelling.MinimizeModelEnergy(mhandle)
+ self.checkFinalModel(mhandle, exp_gaps=2, num_chains=2)
# hetero-dimer
mhandle = self.getRawModelOligo("data/5d52-1_cut")
self.checkFinalModel(mhandle, exp_gaps=2, num_chains=2)
+ # repeat after sidechain reconstruction and MM
+ mhandle = self.getRawModelOligo("data/5d52-1_cut")
+ modelling.BuildSidechains(mhandle)
+ modelling.MinimizeModelEnergy(mhandle)
+ self.checkFinalModel(mhandle, exp_gaps=2, num_chains=2)
def testCheckFinalModelRingPunches(self):
'''Check that we report models with ring punches.'''
--
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