From b288d57d7844ddb00dbe49f76f82b71411a5ace5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 27 Nov 2019 09:37:54 +0100
Subject: [PATCH] Implement setters for QSscorer properties
Requirement of Python 3 to fulfill our promise of being able to set
various things. This also removes an ugly hack of setting a variable
intended to be private in the unit test.
---
modules/mol/alg/pymod/qsscoring.py | 28 +++++++++++++++++++++++++
modules/mol/alg/tests/test_qsscoring.py | 3 +--
2 files changed, 29 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index ba9c2af9d..8f9286b49 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -228,6 +228,10 @@ class QSscorer:
self._chem_mapping = _GetChemGroupsMapping(self.qs_ent_1, self.qs_ent_2)
return self._chem_mapping
+ @chem_mapping.setter
+ def chem_mapping(self, chem_mapping):
+ self._chem_mapping = chem_mapping
+
@property
def ent_to_cm_1(self):
"""Subset of :attr:`qs_ent_1` used to compute chain mapping and symmetries.
@@ -255,6 +259,10 @@ class QSscorer:
self._ComputeAlignedEntities()
return self._ent_to_cm_1
+ @ent_to_cm_1.setter
+ def ent_to_cm_1(self, ent_to_cm_1):
+ self._ent_to_cm_1 = ent_to_cm_1
+
@property
def ent_to_cm_2(self):
"""Subset of :attr:`qs_ent_1` used to compute chain mapping and symmetries
@@ -264,6 +272,10 @@ class QSscorer:
self._ComputeAlignedEntities()
return self._ent_to_cm_2
+ @ent_to_cm_2.setter
+ def ent_to_cm_2(self, ent_to_cm_2):
+ self._ent_to_cm_2 = ent_to_cm_2
+
@property
def symm_1(self):
"""Symmetry groups for :attr:`qs_ent_1` used to speed up chain mapping.
@@ -384,6 +396,10 @@ class QSscorer:
LogInfo('Mapping found: %s' % str(self._chain_mapping))
return self._chain_mapping
+ @chain_mapping.setter
+ def chain_mapping(self, chain_mapping):
+ self._chain_mapping = chain_mapping
+
@property
def chain_mapping_scheme(self):
"""Mapping scheme used to get :attr:`chain_mapping`.
@@ -440,6 +456,10 @@ class QSscorer:
self.res_num_alignment)
return self._alignments
+ @alignments.setter
+ def alignments(self, alignments):
+ self._alignments = alignments
+
@property
def mapped_residues(self):
"""Mapping of shared residues in :attr:`alignments`.
@@ -454,6 +474,10 @@ class QSscorer:
self._mapped_residues = _GetMappedResidues(self.alignments)
return self._mapped_residues
+ @mapped_residues.setter
+ def mapped_residues(self, mapped_residues):
+ self._mapped_residues = mapped_residues
+
@property
def global_score(self):
"""QS-score with penalties.
@@ -522,6 +546,10 @@ class QSscorer:
self._clustalw_bin = settings.Locate(('clustalw', 'clustalw2'))
return self._clustalw_bin
+ @clustalw_bin.setter
+ def clustalw_bin(self, clustalw_bin):
+ self._clustalw_bin = clustalw_bin
+
def GetOligoLDDTScorer(self, settings, penalize_extra_chains=True):
"""
:return: :class:`OligoLDDTScorer` object, setup for this QS scoring problem.
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index 29aaa6210..0e57f2a3e 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -167,8 +167,7 @@ class TestQSscore(unittest.TestCase):
# enforce different chain mapping
enforced_cm = {'C': 'C', 'E': 'A', 'D': 'D', 'F': 'B'}
qs_scorer_2 = QSscorer(qs_scorer.qs_ent_1, qs_scorer.qs_ent_2)
- # directly overwrite variable intended to be private. Have mercy with me.
- qs_scorer_2._chain_mapping = enforced_cm
+ qs_scorer_2.chain_mapping = enforced_cm
self.assertAlmostEqual(qs_scorer_2.global_score, 0.356, 2)
self.assertAlmostEqual(qs_scorer_2.best_score, 0.419, 2)
self.assertEqual(qs_scorer_2.chain_mapping, enforced_cm)
--
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