From 489e84b27539c6336c79838e47046d3da040cc73 Mon Sep 17 00:00:00 2001
From: Rafal Gumienny <r.gumienny@unibas.ch>
Date: Wed, 25 Apr 2018 11:19:14 +0200
Subject: [PATCH] fix: SCHWED-3121 Consistency check performed on renumbered
entities
---
actions/ost-compare-structures | 13 ++++++-------
1 file changed, 6 insertions(+), 7 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index c89196433..b244c22c0 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -75,6 +75,7 @@ from ost import PushVerbosityLevel
from ost.mol.alg import (qsscoring, Molck, MolckSettings, lDDTSettings,
CheckStructure, ResidueNamesMatch)
from ost.conop import CompoundLib
+from ost.seq.alg.renumber import Renumber
class _DefaultStereochemicalParamAction(argparse.Action):
@@ -449,11 +450,11 @@ def _RevertChainNames(ent):
ost.LogInfo("Reverted chains: %s" % ", ".join(rev_out))
-def _CheckConsistency(reference, model, chain_mapping, log_error):
+def _CheckConsistency(alignments, log_error):
is_cons = True
- for ref_cname, mdl_cname in chain_mapping.iteritems():
- ref_chain = reference.Select("cname=%s" % ref_cname)
- mdl_chain = model.Select("cname=%s" % mdl_cname)
+ for alignment in alignments:
+ ref_chain = Renumber(alignment.GetSequence(0)).CreateFullView()
+ mdl_chain = Renumber(alignment.GetSequence(1)).CreateFullView()
is_cons = ResidueNamesMatch(ref_chain, mdl_chain, log_error)
return is_cons
@@ -669,9 +670,7 @@ def _Main():
ost.LogInfo("Checking consistency between %s and %s" % (
model_name, reference_name))
is_cons = _CheckConsistency(
- reference,
- model,
- qs_scorer.chain_mapping,
+ qs_scorer.alignments,
opts.consistency_checks)
reference_results["info"]["residue_names_consistent"] = is_cons
reference_results["info"]["mapping"] = {
--
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