From 651421b64ffdb9dcaa8f8d890684cc3172657641 Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 24 Apr 2018 18:26:08 +0200
Subject: [PATCH] Refactoring: introduce helper functions to remove code
duplication.
---
actions/ost-compare-structures | 7 +-----
modules/mol/alg/pymod/qsscoring.py | 32 ++++++++++++++++++-------
modules/mol/alg/tests/test_qsscoring.py | 15 +++---------
3 files changed, 27 insertions(+), 27 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index fc0e08fbf..3562b2c6c 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -738,12 +738,7 @@ def _Main():
ost.LogInfo("lDDT settings: ")
ost.LogInfo(str(lddt_settings).rstrip())
ost.LogInfo("===")
- oligo_lddt_scorer = qsscoring.OligoLDDTScorer(
- qs_scorer.qs_ent_1.ent,
- qs_scorer.qs_ent_2.ent,
- qs_scorer.alignments,
- qs_scorer.calpha_only,
- lddt_settings)
+ oligo_lddt_scorer = qs_scorer.GetOligoLDDTScorer(lddt_settings)
for scorer_index, lddt_scorer in enumerate(
oligo_lddt_scorer.sc_lddt_scorers):
# Get chains and renumber according to alignment (for lDDT)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index f33b21707..aa37d37da 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -448,6 +448,13 @@ class QSscorer:
self._clustalw_bin = settings.Locate(('clustalw', 'clustalw2'))
return self._clustalw_bin
+ def GetOligoLDDTScorer(self, settings):
+ """
+ :return: :class:`OligoLDDTScorer` object, setup for this QS scoring problem.
+ """
+ return OligoLDDTScorer(self.qs_ent_1.ent, self.qs_ent_2.ent,
+ self.alignments, self.calpha_only, settings)
+
##############################################################################
# Class internal helpers (anything that doesnt easily work without this class)
##############################################################################
@@ -829,11 +836,13 @@ def GetContacts(entity, calpha_only, dist_thr=12.0):
class OligoLDDTScorer(object):
"""A simple class to calculate oligomeric lDDT score."""
+ # TODO: DOCUMENT
+
def __init__(self, ref, mdl, alignments, calpha_only, settings):
if mdl.chain_count > ref.chain_count:
LogWarning('MODEL contains more chains than REFERENCE, '
'lDDT is not considering them')
- # get single chain reference and model
+ # prepare fields
self.ref = ref
self.mdl = mdl
self.alignments = alignments
@@ -852,19 +861,13 @@ class OligoLDDTScorer(object):
@property
def lddt_ref(self):
if self._lddt_ref is None:
- self._lddt_ref, self._lddt_mdl = _MergeAlignedChains(self.alignments,
- self.ref,
- self.mdl,
- self.calpha_only)
+ self._PrepareOligoEntities()
return self._lddt_ref
@property
def lddt_mdl(self):
if self._lddt_mdl is None:
- self._lddt_ref, self._lddt_mdl = _MergeAlignedChains(self.alignments,
- self.ref,
- self.mdl,
- self.calpha_only)
+ self._PrepareOligoEntities()
return self._lddt_mdl
@property
@@ -982,6 +985,17 @@ class OligoLDDTScorer(object):
self._weighted_lddt = 0.0
return self._weighted_lddt
+ ##############################################################################
+ # Class internal helpers (anything that doesnt easily work without this class)
+ ##############################################################################
+
+ def _PrepareOligoEntities(self):
+ # simple wrapper to avoid code duplication
+ self._lddt_ref, self._lddt_mdl = _MergeAlignedChains(self.alignments,
+ self.ref,
+ self.mdl,
+ self.calpha_only)
+
###############################################################################
# HELPERS
diff --git a/modules/mol/alg/tests/test_qsscoring.py b/modules/mol/alg/tests/test_qsscoring.py
index 161d00402..7e63de558 100644
--- a/modules/mol/alg/tests/test_qsscoring.py
+++ b/modules/mol/alg/tests/test_qsscoring.py
@@ -380,13 +380,9 @@ class TestQSscore(unittest.TestCase):
# lDDT is not symmetrical and does not account for overprediction!
ref = _LoadFile('4br6.1.pdb').Select('cname=A,B')
mdl = _LoadFile('4br6.1.pdb')
+ lddt_settings = lDDTSettings(structural_checks=False)
qs_scorer = QSscorer(ref, mdl)
- lddt_oligo_scorer = OligoLDDTScorer(
- qs_scorer.qs_ent_1.ent,
- qs_scorer.qs_ent_2.ent,
- qs_scorer.alignments,
- qs_scorer.calpha_only,
- settings=lDDTSettings(structural_checks=False))
+ lddt_oligo_scorer = qs_scorer.GetOligoLDDTScorer(lddt_settings)
self.assertAlmostEqual(qs_scorer.global_score, 0.171, 2)
self.assertAlmostEqual(qs_scorer.best_score, 1.00, 2)
self.assertAlmostEqual(lddt_oligo_scorer.oligo_lddt, 1.00, 2)
@@ -394,12 +390,7 @@ class TestQSscore(unittest.TestCase):
qs_scorer2 = QSscorer(qs_scorer.qs_ent_2,
qs_scorer.qs_ent_1,
res_num_alignment=True)
- lddt_oligo_scorer2 = OligoLDDTScorer(
- qs_scorer2.qs_ent_1.ent,
- qs_scorer2.qs_ent_2.ent,
- qs_scorer2.alignments,
- qs_scorer2.calpha_only,
- settings=lDDTSettings(structural_checks=False))
+ lddt_oligo_scorer2 = qs_scorer2.GetOligoLDDTScorer(lddt_settings)
self.assertAlmostEqual(qs_scorer2.global_score, 0.171, 2)
self.assertAlmostEqual(qs_scorer2.best_score, 1.00, 2)
self.assertAlmostEqual(lddt_oligo_scorer2.oligo_lddt, 0.4496, 2)
--
GitLab