diff --git a/doc/tests/scripts/modelling_close_small_deletions.py b/doc/tests/scripts/modelling_close_small_deletions.py
index 54809c2fdb1591cce6257fcca98ceb1e47baaf5c..80e8c3e590b9bd3d4d80449ee34bb7eac4c68263 100644
--- a/doc/tests/scripts/modelling_close_small_deletions.py
+++ b/doc/tests/scripts/modelling_close_small_deletions.py
@@ -9,6 +9,5 @@ aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
# close small deletion
print 'Number of gaps before: %d' % len(mhandle.gaps)
-modelling.SetupDefaultBackboneScorer(mhandle)
modelling.CloseSmallDeletions(mhandle)
print 'Number of gaps after: %d' % len(mhandle.gaps)
diff --git a/doc/tests/scripts/modelling_fill_loops_by_database.py b/doc/tests/scripts/modelling_fill_loops_by_database.py
index 16f0944bbf7b86130d3e66412d089da6348cada5..6aaec8a41a098be6c6249db20cad543ef3328e2e 100644
--- a/doc/tests/scripts/modelling_fill_loops_by_database.py
+++ b/doc/tests/scripts/modelling_fill_loops_by_database.py
@@ -11,7 +11,6 @@ aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
# merge gaps
print 'Number of gaps before: %d' % len(mhandle.gaps)
-modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, loop.LoadFragDB(),
loop.LoadStructureDB(),
loop.LoadTorsionSamplerCoil())
diff --git a/doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py b/doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py
index e8e02a052f0c533026c85afe3de68e109c24fc84..880c9938721c4c405dde458136883ed3075662a4 100644
--- a/doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py
+++ b/doc/tests/scripts/modelling_fill_loops_by_monte_carlo.py
@@ -11,7 +11,6 @@ aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
# merge gaps
print 'Number of gaps before: %d' % len(mhandle.gaps)
-modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle,
loop.LoadTorsionSamplerCoil())
print 'Number of gaps after: %d' % len(mhandle.gaps)
diff --git a/doc/tests/scripts/modelling_model_termini.py b/doc/tests/scripts/modelling_model_termini.py
index 464857d455f6cdba5a92b8e1ab6b1482322b74cd..1371741d58099a10acbd790f7b24c182a6a1476d 100644
--- a/doc/tests/scripts/modelling_model_termini.py
+++ b/doc/tests/scripts/modelling_model_termini.py
@@ -11,7 +11,6 @@ aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
# merge gaps
print 'Number of gaps before: %d' % len(mhandle.gaps)
-modelling.SetupDefaultBackboneScorer(mhandle)
modelling.ModelTermini(mhandle,
loop.LoadTorsionSamplerCoil())
print 'Number of gaps after: %d' % len(mhandle.gaps)
diff --git a/modelling/doc/pipeline.rst b/modelling/doc/pipeline.rst
index 7ae07b4858f1f77c96592261aee018e11de06b58..3c2930ab87d67c47e9bba28cc998a4a38b542ea3 100644
--- a/modelling/doc/pipeline.rst
+++ b/modelling/doc/pipeline.rst
@@ -199,18 +199,10 @@ Modelling Steps
:attr:`~ModellingHandle.backbone_scorer_env` of `mhandle`.
:type mhandle: :class:`~promod3.modelling.ModellingHandle`
-.. function:: IsBackboneScorerSet(mhandle)
+.. function:: IsBackboneScoringSetUp(mhandle)
- :return: True, if :attr:`~ModellingHandle.backbone_scorer` of `mhandle` is
- set.
- :rtype: :class:`bool`
- :param mhandle: Modelling handle to check.
- :type mhandle: :class:`ModellingHandle`
-
-.. function:: IsBackboneScorerEnvSet(mhandle)
-
- :return: True, if :attr:`~ModellingHandle.backbone_scorer_env` of `mhandle` is
- set.
+ :return: True, if :attr:`~ModellingHandle.backbone_scorer` and
+ :attr:`~ModellingHandle.backbone_scorer_env` of `mhandle` are set.
:rtype: :class:`bool`
:param mhandle: Modelling handle to check.
:type mhandle: :class:`ModellingHandle`
diff --git a/modelling/pymod/_closegaps.py b/modelling/pymod/_closegaps.py
index dde6c8d7adb5f9dd35e948a93373662a50d022a0..191010924689f6ddb46ac38a945044a8b36a4fbc 100644
--- a/modelling/pymod/_closegaps.py
+++ b/modelling/pymod/_closegaps.py
@@ -315,8 +315,6 @@ def _CloseLoopBare(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
actual_chain_idx = actual_extended_gaps[0].GetChainIndex()
# score loops as they are
- scorer = mhandle.backbone_scorer
- weights = _GetWeights()
min_score = float("inf")
optimal_gap = None
optimal_candidate = None
@@ -354,7 +352,6 @@ def _CloseLoopBare(mhandle, gap_orig, actual_candidates, actual_extended_gaps,
mhandle.backbone_scorer_env.SetEnvironment(optimal_candidate,
start_resnum,
actual_chain_idx)
- # TODO: remove debug scoring out
scor_str = "BB"
if actual_db_scores:
scor_str += "_DB"
@@ -494,18 +491,21 @@ def CloseSmallDeletions(mhandle, max_extension=9, clash_thresh=1.0,
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
if len(mhandle.gaps) > 0:
- ost.LogInfo("Trying to close small deletions (no. of gap(s): %d)." % \
- len(mhandle.gaps))
+ ost.LogInfo("Trying to close small deletions (no. of gap(s): %d)." \
+ % len(mhandle.gaps))
else:
return
+ # check/setup scoring
+ if not IsBackboneScoringSetUp(mhandle):
+ SetupDefaultBackboneScorer(mhandle)
clash_scorer = mhandle.backbone_scorer.Get("clash")
- current_gap_index = 0
# iterating mhandle.gaps. The number of gaps may change during the process,
# hence we run by 'while', comparing to the updated list of gaps. If a gap
# gets closed, it is deleted from mhandle.gaps, otherwise, current_gap_index
# as a counter is increased.
+ current_gap_index = 0
while current_gap_index < len(mhandle.gaps):
# in the end this determines if a gap was closed or not
success = False
@@ -761,6 +761,10 @@ def FillLoopsByDatabase(mhandle, fragment_db, structure_db,
else:
return
+ # check/setup scoring
+ if not IsBackboneScoringSetUp(mhandle):
+ SetupDefaultBackboneScorer(mhandle)
+
# some score variants cannot deal with multiple insertions in one "gap"
disallow_ins_merge = (score_variant in [0,3])
add_db_features = (len(mhandle.profiles) > 0)
@@ -1012,10 +1016,15 @@ def FillLoopsByMonteCarlo(mhandle, torsion_sampler, max_loops_to_search=6,
prof = core.StaticRuntimeProfiler.StartScoped(prof_name)
if len(mhandle.gaps) > 0:
- ost.LogInfo("Trying to fill %d gap(s) by Monte Carlo." % len(mhandle.gaps))
+ ost.LogInfo("Trying to fill %d gap(s) by Monte Carlo." \
+ % len(mhandle.gaps))
else:
return
+ # check/setup scoring
+ if not IsBackboneScoringSetUp(mhandle):
+ SetupDefaultBackboneScorer(mhandle)
+
# disable AllAtom scoring here
if score_variant == 3:
score_variant = 0
@@ -1205,8 +1214,6 @@ def CloseGaps(mhandle, merge_distance=4, fragment_db=None, structure_db=None,
'''
# load stuff if needed
- if not IsBackboneScorerSet(mhandle) or not IsBackboneScorerEnvSet(mhandle):
- SetupDefaultBackboneScorer(mhandle)
if fragment_db is None:
fragment_db = loop.LoadFragDB()
if structure_db is None:
@@ -1294,6 +1301,12 @@ def ModelTermini(mhandle, torsion_sampler, fragger_handles=None,
terminal_gaps = [g.Copy() for g in mhandle.gaps if g.IsTerminal() and g.length > 1]
if len(terminal_gaps) > 0:
ost.LogInfo("Trying to model %d terminal gap(s)." % len(terminal_gaps))
+ else:
+ return
+
+ # check/setup scoring
+ if not IsBackboneScoringSetUp(mhandle):
+ SetupDefaultBackboneScorer(mhandle)
# model them
for actual_gap in terminal_gaps:
@@ -1424,6 +1437,10 @@ def CloseLargeDeletions(mhandle, structure_db, linker_length=8,
else:
return
+ # check/setup scoring
+ if not IsBackboneScoringSetUp(mhandle):
+ SetupDefaultBackboneScorer(mhandle)
+
# point to the current gap
gap_idx = 0
diff --git a/modelling/pymod/_mtm.py b/modelling/pymod/_mtm.py
index 3c4614dac2cb5b49337f13a70f1cee6e8d96a5fc..90cd6fdcce367c43ba2d04f33d7e7ee4bbef44cb 100644
--- a/modelling/pymod/_mtm.py
+++ b/modelling/pymod/_mtm.py
@@ -971,8 +971,7 @@ def ModelExtensions(seed_rawmodel, alternative_rawmodels,
ost.LogInfo(log_string)
# make sure the seed has a scorer
- if not (IsBackboneScorerSet(seed_rawmodel) and\
- IsBackboneScorerEnvSet(seed_rawmodel)):
+ if not IsBackboneScoringSetUp(seed_rawmodel):
SetupDefaultBackboneScorer(seed_rawmodel)
# assign default weights if not given
diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 006ab4abd682c2d607598418570266c932f56db5..acc14cf57955f881310a76d999b4da13968bdbf2 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -210,8 +210,6 @@ def BuildSidechains(mhandle, merge_distance=4, fragment_db=None,
mygap = StructuralGap(res.prev, res.next, res.one_letter_code)
mhandle.gaps.append(mygap)
# load stuff if needed
- if not IsBackboneScorerSet(mhandle) or not IsBackboneScorerEnvSet(mhandle):
- SetupDefaultBackboneScorer(mhandle)
if fragment_db is None:
fragment_db = loop.LoadFragDB()
if structure_db is None:
@@ -417,12 +415,10 @@ def BuildFromRawModel(mhandle, alternative_mhandles=None,
modelling pipeline. For reproducibility, we recommend that you keep copies
of custom pipelines.
- If you wish to adapt the scoring used during loop closing, you can set
- :attr:`~ModellingHandle.backbone_scorer` and
- :attr:`~ModellingHandle.backbone_scorer_env` of `mhandle`, but you must
- ensure that both are set and are consistent. Alternatively, you can call
- :func:`SetupDefaultBackboneScorer` and adapt the default scorer and score
- environment for your purposes.
+ If you wish to adapt the scoring used during loop closing, you can set the
+ scorers manually, but you must ensure consistency yourself! Alternatively,
+ you can call :func:`SetupDefaultBackboneScorer` and adapt the default scorer
+ and score environment for your purposes.
If the function fails to close all gaps, it will produce a warning and
return an incomplete model.
@@ -464,11 +460,6 @@ def BuildFromRawModel(mhandle, alternative_mhandles=None,
torsion_sampler = loop.LoadTorsionSamplerCoil()
merge_distance = 4
- if IsBackboneScorerSet(mhandle) and IsBackboneScorerEnvSet(mhandle):
- ost.LogInfo("Using scorer which is already set in modelling handle.")
- else:
- SetupDefaultBackboneScorer(mhandle)
-
# try to extend terminal coverage using alternative rawmodels
if alternative_mhandles != None:
# iterate extensions until nothing happens anymore
diff --git a/modelling/pymod/export_model.cc b/modelling/pymod/export_model.cc
index 5acd1fa11600415055d3a0dee06c35fdae62abe9..8781f1b2c28ae557b3fc13d3c2a875e1f94edbf9 100644
--- a/modelling/pymod/export_model.cc
+++ b/modelling/pymod/export_model.cc
@@ -65,14 +65,6 @@ void WrapSetPsipredPredictions(ModellingHandle& mhandle,
SetPsipredPredictions(mhandle, v_predictions);
}
-// not really needed in C++ as we can do the check below directly
-bool WrapIsBackboneScorerSet(ModellingHandle& mhandle) {
- return bool(mhandle.backbone_scorer);
-}
-bool WrapIsBackboneScorerEnvSet(ModellingHandle& mhandle) {
- return bool(mhandle.backbone_scorer_env);
-}
-
boost::python::list WrapPsipredPredictionAccess(ModellingHandle& mhandle){
boost::python::list return_list;
promod3::core::AppendVectorToList(mhandle.psipred_predictions, return_list);
@@ -110,9 +102,12 @@ void export_model()
def("MergeGaps", MergeGaps, (arg("mhandle"),arg("index")));
def("RemoveTerminalGaps", RemoveTerminalGaps, (arg("mhandle")));
def("ReorderGaps", &ReorderGaps, (arg("mhandle")));
- def("SetupDefaultBackboneScorer", &SetupDefaultBackboneScorer, (arg("mhandle")));
- def("SetSequenceProfiles", &WrapSetSequenceProfiles, (arg("mhandle"),arg("profiles")));
- def("SetPsipredPredictions", &WrapSetPsipredPredictions, (arg("mhandle"),arg("psipred_predictions")));
+ def("SetupDefaultBackboneScorer", &SetupDefaultBackboneScorer,
+ (arg("mhandle")));
+ def("SetSequenceProfiles", &WrapSetSequenceProfiles,
+ (arg("mhandle"), arg("profiles")));
+ def("SetPsipredPredictions", &WrapSetPsipredPredictions,
+ (arg("mhandle"), arg("psipred_predictions")));
def("MergeMHandle", &MergeMHandle, (arg("source_mhandle"),
arg("target_mhandle"),
arg("source_chain_idx"),
@@ -121,8 +116,7 @@ void export_model()
arg("end_resnum"),
arg("transform"),
arg("reset_scoring_env") = true));
- def("IsBackboneScorerSet", &WrapIsBackboneScorerSet, (arg("mhandle")));
- def("IsBackboneScorerEnvSet", &WrapIsBackboneScorerEnvSet, (arg("mhandle")));
+ def("IsBackboneScoringSetUp", &IsBackboneScoringSetUp, (arg("mhandle")));
def("BuildRawModel", BuildRawModelHandle,
(arg("aln"),
arg("include_ligands")=false,
diff --git a/modelling/src/model.cc b/modelling/src/model.cc
index b2a292a9c0c8a9c3afd49261a5e9d9eb1048735d..5cd31c4cd0bf1e220132cb2dec89bf82070c3b8d 100644
--- a/modelling/src/model.cc
+++ b/modelling/src/model.cc
@@ -594,7 +594,7 @@ void MergeMHandle(const ModellingHandle& source_mhandle,
//finally reorder the gaps to ensure consistency
ReorderGaps(target_mhandle);
- if(reset_scoring_env && target_mhandle.backbone_scorer_env){
+ if (reset_scoring_env && target_mhandle.backbone_scorer_env) {
target_mhandle.backbone_scorer_env->SetInitialEnvironment(target_mhandle.model);
}
}
diff --git a/modelling/src/model.hh b/modelling/src/model.hh
index afebc691db3eee1b9487a7b5198f5a0900e6668e..330dc17209050df5e1cb3f2b62e3e5dde986e2ea 100644
--- a/modelling/src/model.hh
+++ b/modelling/src/model.hh
@@ -55,11 +55,15 @@ void MergeGaps(ModellingHandle& mhandle, uint index);
// see Python doc
int RemoveTerminalGaps(ModellingHandle& mhandle);
-//see Python doc
+// see Python doc
void ReorderGaps(ModellingHandle& mhandle);
-//see Python doc
+// see Python doc
void SetupDefaultBackboneScorer(ModellingHandle& mhandle);
+// see Python doc
+inline bool IsBackboneScoringSetUp(ModellingHandle& mhandle) {
+ return bool(mhandle.backbone_scorer) && bool(mhandle.backbone_scorer_env);
+}
// see Python doc
void SetSequenceProfiles(ModellingHandle& mhandle,
diff --git a/modelling/tests/test_close_gaps.py b/modelling/tests/test_close_gaps.py
index f7bc1298acf7861e0f8d90f266dc998a7de3f761..60bec07df9d8ba436cc07b12a1c7a0726ce26ca2 100644
--- a/modelling/tests/test_close_gaps.py
+++ b/modelling/tests/test_close_gaps.py
@@ -162,7 +162,6 @@ class CloseGapsTests(unittest.TestCase):
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 1)
# close it
- modelling.SetupDefaultBackboneScorer(mhandle)
nlogs = len(self.log.messages['INFO'])
modelling.CloseSmallDeletions(mhandle)
self.assertEqual(len(mhandle.gaps), 0)
@@ -190,7 +189,6 @@ class CloseGapsTests(unittest.TestCase):
mhandle = modelling.BuildRawModel(alns)
self.assertEqual(len(mhandle.gaps), 2)
# do it
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.CloseSmallDeletions(mhandle)
# check
self.assertEqual(len(mhandle.gaps), 0)
@@ -287,7 +285,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabase(self):
'''Get rid of 2 gaps by db.'''
mhandle = self.getGapTest()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler)
@@ -299,7 +296,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseDeletion(self):
'''Get rid of deletion by db.'''
mhandle = self.getGapTestDeletion()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler)
@@ -311,7 +307,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseInsertion(self):
'''Get rid of insertion by db.'''
mhandle = self.getGapTestInsertion()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler)
@@ -323,7 +318,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseInsertionTerminal(self):
'''Get rid of insertion by db close to terminal (needs FullExtender).'''
mhandle = self.getGapTestInsertionTerminal()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler,
@@ -336,7 +330,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseTerminal(self):
'''Terminal loops are not altered.'''
mhandle = self.getGapTestTerminal()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler)
@@ -345,7 +338,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseNoSE(self):
'''Get rid of 2 gaps by db (without scoring extender).'''
mhandle = self.getGapTest()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler,
@@ -358,7 +350,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseDeletionNoSE(self):
'''Get rid of deletion by db (without scoring extender).'''
mhandle = self.getGapTestDeletion()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler,
@@ -371,7 +362,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseInsertionNoSE(self):
'''Get rid of insertion by db (without scoring extender).'''
mhandle = self.getGapTestInsertion()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler,
@@ -384,7 +374,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseTerminalNoSE(self):
'''Terminal loops are not altered (without scoring extender).'''
mhandle = self.getGapTestTerminal()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler,
@@ -394,7 +383,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseHomoOligomer(self):
'''Get rid of 2 gaps by db for homo oligomers.'''
mhandle = self.getRawModelOligo("data/2aoh-1_cut")
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler)
@@ -404,7 +392,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByDatabaseHeteroOligomer(self):
'''Get rid of 2 gaps by db for hetero oligomers.'''
mhandle = self.getRawModelOligo("data/5d52-1_cut")
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler)
@@ -416,7 +403,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarlo(self):
'''Get rid of 2 gaps by MC.'''
mhandle = self.getGapTest()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, self.torsion_sampler,
mc_steps=100)
self.assertEqual(len(mhandle.gaps), 0)
@@ -427,7 +413,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarloDeletion(self):
'''Get rid of deletion by MC.'''
mhandle = self.getGapTestDeletion()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, self.torsion_sampler,
mc_steps=100)
self.assertEqual(len(mhandle.gaps), 0)
@@ -438,7 +423,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarloInsertion(self):
'''Get rid of insertion by MC.'''
mhandle = self.getGapTestInsertion()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, self.torsion_sampler,
mc_steps=100)
self.assertEqual(len(mhandle.gaps), 0)
@@ -449,7 +433,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarloTerminal(self):
'''Terminal loops are not altered.'''
mhandle = self.getGapTestTerminal()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, self.torsion_sampler,
mc_steps=100)
self.assertEqual(len(mhandle.gaps), 2)
@@ -457,7 +440,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarloHomoOligomer(self):
'''Get rid of 2 gaps by db for homo oligomers.'''
mhandle = self.getRawModelOligo("data/2aoh-1_cut")
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, self.torsion_sampler,
mc_steps=100)
self.assertEqual(len(mhandle.gaps), 0)
@@ -466,7 +448,6 @@ class CloseGapsTests(unittest.TestCase):
def testFillGapsByMonteCarloHeteroOligomer(self):
'''Get rid of 2 gaps by db for hetero oligomers.'''
mhandle = self.getRawModelOligo("data/5d52-1_cut")
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByMonteCarlo(mhandle, self.torsion_sampler,
mc_steps=100)
self.assertEqual(len(mhandle.gaps), 0)
@@ -482,7 +463,6 @@ class CloseGapsTests(unittest.TestCase):
mhandle = modelling.BuildRawModel(aln)
self.assertEqual(len(mhandle.gaps), 3)
# model termini
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.ModelTermini(mhandle, self.torsion_sampler,
mc_steps=100)
self.assertEqual(len(mhandle.gaps), 1)
@@ -512,7 +492,6 @@ class CloseGapsTests(unittest.TestCase):
mhandle = modelling.BuildRawModel(alns)
self.assertEqual(len(mhandle.gaps), 4)
# model termini
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.ModelTermini(mhandle, self.torsion_sampler,
mc_steps=100)
self.assertEqual(len(mhandle.gaps), 0)
@@ -529,7 +508,6 @@ class CloseGapsTests(unittest.TestCase):
seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
- modelling.SetupDefaultBackboneScorer(mhandle)
self.assertEqual(len(mhandle.gaps), 1)
modelling.CloseLargeDeletions(mhandle, self.structure_db,
num_fragments=100)
@@ -545,7 +523,6 @@ class CloseGapsTests(unittest.TestCase):
seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.MergeGapsByDistance(mhandle, 1)
self.assertEqual(len(mhandle.gaps), 1)
modelling.CloseLargeDeletions(mhandle, self.structure_db,
@@ -562,7 +539,6 @@ class CloseGapsTests(unittest.TestCase):
seq.CreateSequence('tpl', 'NGGTLLIPNGTYHFLGIQMKSNVHIRVE'))
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
- modelling.SetupDefaultBackboneScorer(mhandle)
self.assertEqual(len(mhandle.gaps), 1)
modelling.CloseLargeDeletions(mhandle, self.structure_db,
num_fragments=100)
@@ -579,7 +555,6 @@ class CloseGapsTests(unittest.TestCase):
aln.AttachView(1, tpl.CreateFullView())
mhandle = modelling.BuildRawModel(aln)
modelling.RemoveTerminalGaps(mhandle)
- modelling.SetupDefaultBackboneScorer(mhandle)
self.assertEqual(len(mhandle.gaps), 1)
modelling.CloseLargeDeletions(mhandle, self.structure_db,
num_fragments=100)
@@ -602,7 +577,6 @@ class CloseGapsTests(unittest.TestCase):
alns.append(aln_A)
alns.append(aln_B)
mhandle = modelling.BuildRawModel(alns)
- modelling.SetupDefaultBackboneScorer(mhandle)
self.assertEqual(len(mhandle.gaps), 2)
modelling.CloseLargeDeletions(mhandle, self.structure_db,
num_fragments=100)
diff --git a/modelling/tests/test_pipeline.py b/modelling/tests/test_pipeline.py
index acaa032be02e4ae2ac086480aa5b89fcf505e37c..50c3d97b8eae10309a067a235e6eadd33d371b69 100644
--- a/modelling/tests/test_pipeline.py
+++ b/modelling/tests/test_pipeline.py
@@ -44,7 +44,6 @@ from promod3 import loop, modelling, core
# io.SavePDB(final_model, 'data/1crn_build.pdb')
# # step-by-step - loop
# mhandle = modelling.BuildRawModel(aln)
-# modelling.SetupDefaultBackboneScorer(mhandle)
# frag_db = loop.LoadFragDB()
# structure_db = loop.LoadStructureDB()
# torsion_sampler = loop.LoadTorsionSamplerCoil()
@@ -218,7 +217,6 @@ class PipelineTests(unittest.TestCase):
def testLoopReconstruction(self):
'''Check loop reconstruction.'''
mhandle = self.getRawModel()
- modelling.SetupDefaultBackboneScorer(mhandle)
modelling.FillLoopsByDatabase(mhandle, self.frag_db,
self.structure_db,
self.torsion_sampler)