From f32362d6aeff6ec95865512eab8858418ef49130 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Thu, 5 Apr 2018 14:21:53 +0200
Subject: [PATCH] refactor: SCHWED-3120 Create and use OligolDDTScorer
---
actions/ost-compare-structures | 4 +-
modules/mol/alg/pymod/qsscoring.py | 67 +++++++++++++++++++++---------
2 files changed, 49 insertions(+), 22 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 97105e399..72fa92324 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -515,7 +515,7 @@ def _Main():
lddt_scorers.append(lddt_scorer)
# perform oligo lddt scoring
try:
- oligo_lddt = qsscoring.ComputeOligoLDDT(
+ oligo_lddt_scorer = qsscoring.OligoLDDTScorer(
qs_scorer.qs_ent_1.ent,
qs_scorer.qs_ent_2.ent,
qs_scorer.alignments,
@@ -523,7 +523,7 @@ def _Main():
lddt_results["oligo_lddt"] = {
"status": "SUCCESS",
"error": "",
- "global_score": oligo_lddt}
+ "global_score": oligo_lddt_scorer.lddt}
except Exception as ex:
ost.LogError('Oligo lDDT failed:', str(ex))
lddt_results["oligo_lddt"] = {
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index 2b914893c..f6783154c 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -475,7 +475,7 @@ class QSscorer:
def _ComputeScores(self):
"""Fills cached global_score and best_score."""
- if self.qs_ent_1.is_monomer or self.qs_ent_2.is_monomer:
+ if len(self.chain_mapping) < 2:
raise QSscoreError("QS-score is not defined for monomers")
# get contacts
if self.calpha_only:
@@ -551,7 +551,6 @@ class QSscoreEntity(object):
def __init__(self, ent):
# copy entity and process/clean it
self.original_name = ent.GetName()
- self.is_monomer = False
ent = mol.CreateEntityFromView(ent.Select('ele!=H and aname!=HN'), True)
if not conop.GetDefaultLib():
raise RuntimeError("QSscore computation requires a compound library!")
@@ -566,7 +565,6 @@ class QSscoreEntity(object):
elif self.ent.chain_count == 1:
LogWarning('Structure ' + ent.GetName() + ' is a monomer.')
self.is_valid = True
- self.is_monomer = True
else:
self.is_valid = True
# init cached stuff
@@ -824,22 +822,51 @@ def GetContacts(entity, calpha_only, dist_thr=12.0):
return contacts
-def ComputeOligoLDDT(ref, mdl, alignments, calpha_only):
- """Fills cached lddt_score, lddt_mdl and lddt_ref."""
- LogInfo('Computing lDDT score')
- LogInfo('Reference %s has: %s chains' % (ref.GetName(), ref.chain_count))
- LogInfo('Model %s has: %s chains' % (mdl.GetName(), mdl.chain_count))
- 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
- lddt_ref, lddt_mdl = _MergeAlignedChains(alignments,
- ref,
- mdl,
- calpha_only)
- # score them (mdl and ref changed) and keep results
- oligo_lddt_score = _ComputeLDDTScore(lddt_ref, lddt_mdl)
- return oligo_lddt_score
+class OligoLDDTScorer(object):
+ """A simple class to calculate oligomeric lDDT score."""
+
+ def __init__(self, ref, mdl, alignments, calpha_only):
+ 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
+ self.ref = ref
+ self.mdl = mdl
+ self.calpha_only = calpha_only
+ self.alignments = alignments
+ self._lddt = None
+ self._lddt_ref = None
+ self._lddt_mdl = None
+
+ @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)
+ 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)
+ return self._lddt_mdl
+
+ @property
+ def lddt(self):
+ """Fills cached lddt_score, lddt_mdl and lddt_ref."""
+ if self._lddt is None:
+ LogInfo('Computing oligomeric lDDT score')
+ LogInfo('Reference %s has: %s chains' % (self.ref.GetName(), self.ref.chain_count))
+ LogInfo('Model %s has: %s chains' % (self.mdl.GetName(), self.mdl.chain_count))
+
+ # score them (mdl and ref changed) and keep results
+ self._lddt = _ComputeLDDTScore(self.lddt_ref, self.lddt_mdl)
+ return self._lddt
###############################################################################
@@ -2344,4 +2371,4 @@ def _ComputeLDDTScore(ref, mdl):
# specify public interface
__all__ = ('QSscoreError', 'QSscorer', 'QSscoreEntity', 'FilterContacts',
- 'GetContacts', 'ComputeOligoLDDT')
+ 'GetContacts', 'OligoLDDTScorer')
--
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