From d7d2ba06adad9e89452ab9d55201cba897d6bb22 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 1 Jul 2024 10:56:56 +0200
Subject: [PATCH] Injection of chain mapping to USalign in scoring.py: take the
rigid one
---
actions/ost-compare-structures | 6 +++---
modules/mol/alg/pymod/scoring.py | 10 +++++-----
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index bdd591344..6b0269a4f 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -316,9 +316,9 @@ def _ParseArgs():
dest="oum",
default=False,
action="store_true",
- help=("Override USalign mapping and inject our own mapping. Only works "
- "if external usalign executable is provided that is reasonably "
- "new and contains that feature."))
+ help=("Override USalign mapping and inject our own rigid mapping. Only "
+ "works if external usalign executable is provided that is "
+ "reasonably new and contains that feature."))
parser.add_argument(
"--qs-score",
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 368a269d4..4444e4637 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -147,9 +147,9 @@ class Scorer:
A structure with stoichiometry A6B2 would be
6!*2! = 1440 etc.
:type n_max_naive: :class:`int`
- :param oum: Override USalign Mapping. Inject mapping of :class:`Scorer`
- object into USalign to compute TM-score. Experimental feature
- with limitations.
+ :param oum: Override USalign Mapping. Inject rigid_mapping of
+ :class:`Scorer` object into USalign to compute TM-score.
+ Experimental feature with limitations.
:type oum: :class:`bool`
:param min_pep_length: Relevant parameter if short peptides are involved in
scoring. Minimum peptide length for a chain in the
@@ -2479,7 +2479,7 @@ class Scorer:
if self.usalign_exec is None:
LogScript("Computing patch TM-score with USalign exectuable")
if self.oum:
- flat_mapping = self.mapping.GetFlatMapping()
+ flat_mapping = self.rigid_mapping.GetFlatMapping()
LogInfo("Overriding TM-score chain mapping")
res = res = bindings.WrappedMMAlign(self.model, self.target,
mapping=flat_mapping)
@@ -2489,7 +2489,7 @@ class Scorer:
LogScript("Computing patch TM-score with built-in USalign")
if self.oum:
LogInfo("Overriding TM-score chain mapping")
- flat_mapping = self.mapping.GetFlatMapping()
+ flat_mapping = self.rigid_mapping.GetFlatMapping()
res = tmtools.USAlign(self.model, self.target,
usalign = self.usalign_exec,
custom_chain_mapping = flat_mapping)
--
GitLab