From c9fcbc7c59597d2c96a51d03fef66bd4fef1cace Mon Sep 17 00:00:00 2001
From: Gerardo Tauriello <gerardo.tauriello@unibas.ch>
Date: Tue, 24 Apr 2018 19:43:01 +0200
Subject: [PATCH] CA-only means CA-only for all scores.
---
modules/mol/alg/pymod/qsscoring.py | 30 +++++++++++++++++++-----------
1 file changed, 19 insertions(+), 11 deletions(-)
diff --git a/modules/mol/alg/pymod/qsscoring.py b/modules/mol/alg/pymod/qsscoring.py
index aa37d37da..8686ff05c 100644
--- a/modules/mol/alg/pymod/qsscoring.py
+++ b/modules/mol/alg/pymod/qsscoring.py
@@ -856,7 +856,6 @@ class OligoLDDTScorer(object):
self._lddt_mdl = None
self._oligo_lddt_scorer = None
self._sc_lddt_scorers = None
- self._report = dict()
@property
def lddt_ref(self):
@@ -912,10 +911,17 @@ class OligoLDDTScorer(object):
aln.GetSequence(1).GetString())
modelseq.AttachView(model)
aln.AddSequence(modelseq)
- lddt_scorer = lDDTScorer(
- references=[reference],
- model=model,
- settings=self.settings)
+ # Filter to CA-only if desired (done after AttachView to not mess it up)
+ if self.calpha_only:
+ lddt_scorer = lDDTScorer(
+ references=[reference.Select('aname=CA')],
+ model=model.Select('aname=CA'),
+ settings=self.settings)
+ else:
+ lddt_scorer = lDDTScorer(
+ references=[reference],
+ model=model,
+ settings=self.settings)
lddt_scorer.alignment = aln # a bit of a hack
self._sc_lddt_scorers.append(lddt_scorer)
return self._sc_lddt_scorers
@@ -952,12 +958,14 @@ class OligoLDDTScorer(object):
(ref_res.qualified_name))
else:
assigned_residues.append(ref_res.qualified_name)
- scores.append({
- "residue_number": ref_res.GetNumber().num,
- "residue_name": ref_res.name,
- "lddt": mdl_res_renum.GetFloatProp(self.settings.label),
- "conserved_contacts": mdl_res_renum.GetFloatProp(self.settings.label + "_conserved"),
- "total_contacts": mdl_res_renum.GetFloatProp(self.settings.label + "_total")})
+ # check if property there (may be missing for CA-only)
+ if mdl_res_renum.HasProp(self.settings.label):
+ scores.append({
+ "residue_number": ref_res.GetNumber().num,
+ "residue_name": ref_res.name,
+ "lddt": mdl_res_renum.GetFloatProp(self.settings.label),
+ "conserved_contacts": mdl_res_renum.GetFloatProp(self.settings.label + "_conserved"),
+ "total_contacts": mdl_res_renum.GetFloatProp(self.settings.label + "_total")})
return scores
@property
--
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