From ddfa2ab5c2ca56fe82f9e2a26efd7a0070526e16 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 12 Feb 2024 13:23:15 +0100
Subject: [PATCH] chain mapping: replace GlobalAlign with SemiGlobalAlign in
chain alignment
Terminal residues can be weird in GlobalAlign. E.g.
AAABAAB
AAA---B
instead of
AAABAAB
AAAB---
SemiGlobalAlign produces the latter
---
modules/mol/alg/pymod/chain_mapping.py | 12 ++++++------
modules/mol/alg/tests/test_qsscore.py | 16 ++++++++--------
2 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 5e90c49dc..466679ec2 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1687,13 +1687,13 @@ class _Aligner:
:returns: Alignment with s1 as first and s2 as second sequence
"""
if chem_type == mol.ChemType.AMINOACIDS:
- return seq.alg.GlobalAlign(s1, s2, self.pep_subst_mat,
- gap_open=self.pep_gap_open,
- gap_ext=self.pep_gap_ext)[0]
+ return seq.alg.SemiGlobalAlign(s1, s2, self.pep_subst_mat,
+ gap_open=self.pep_gap_open,
+ gap_ext=self.pep_gap_ext)[0]
elif chem_type == mol.ChemType.NUCLEOTIDES:
- return seq.alg.GlobalAlign(s1, s2, self.nuc_subst_mat,
- gap_open=self.nuc_gap_open,
- gap_ext=self.nuc_gap_ext)[0]
+ return seq.alg.SemiGlobalAlign(s1, s2, self.nuc_subst_mat,
+ gap_open=self.nuc_gap_open,
+ gap_ext=self.nuc_gap_ext)[0]
else:
raise RuntimeError("Invalid ChemType")
return aln
diff --git a/modules/mol/alg/tests/test_qsscore.py b/modules/mol/alg/tests/test_qsscore.py
index 5aed15ee8..a9b3c6131 100644
--- a/modules/mol/alg/tests/test_qsscore.py
+++ b/modules/mol/alg/tests/test_qsscore.py
@@ -130,8 +130,8 @@ class TestQSScore(unittest.TestCase):
res = mapper.GetRigidMapping(ent_2, strategy="greedy_iterative_rmsd")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
- self.assertAlmostEqual(score_result.QS_global, 0.3131, 2)
- self.assertAlmostEqual(score_result.QS_best, 0.941, 2)
+ self.assertAlmostEqual(score_result.QS_global, 0.3191, 2)
+ self.assertAlmostEqual(score_result.QS_best, 0.9781, 2)
def test_hetero_case_2_switched_order(self):
# different stoichiometry
@@ -141,8 +141,8 @@ class TestQSScore(unittest.TestCase):
res = mapper.GetRigidMapping(ent_2, strategy="greedy_iterative_rmsd")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
- self.assertAlmostEqual(score_result.QS_global, 0.3131, 2)
- self.assertAlmostEqual(score_result.QS_best, 0.941, 2)
+ self.assertAlmostEqual(score_result.QS_global, 0.3191, 2)
+ self.assertAlmostEqual(score_result.QS_best, 0.9781, 2)
def test_hetero_case_3(self):
# more chains
@@ -196,8 +196,8 @@ class TestQSScore(unittest.TestCase):
res = mapper.GetRigidMapping(model, strategy="greedy_iterative_rmsd")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
- self.assertAlmostEqual(score_result.QS_global, 0.323, 2)
- self.assertAlmostEqual(score_result.QS_best, 0.921, 2)
+ self.assertAlmostEqual(score_result.QS_global, 0.321, 2)
+ self.assertAlmostEqual(score_result.QS_best, 0.932, 2)
def test_hetero_model_switched_order(self):
# same as above but with switched order to test for symmetric behaviour
@@ -208,8 +208,8 @@ class TestQSScore(unittest.TestCase):
res = mapper.GetRigidMapping(model, strategy="greedy_iterative_rmsd")
qs_scorer = QSScorer.FromMappingResult(res)
score_result = qs_scorer.Score(res.mapping)
- self.assertAlmostEqual(score_result.QS_global, 0.323, 2)
- self.assertAlmostEqual(score_result.QS_best, 0.921, 2)
+ self.assertAlmostEqual(score_result.QS_global, 0.321, 2)
+ self.assertAlmostEqual(score_result.QS_best, 0.932, 2)
def test_homo_1(self):
# different stoichiometry SOD
--
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