From c5a0089e655866fb5b90817489cc0ab0a9ce85e9 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 12 May 2023 00:10:16 +0200
Subject: [PATCH] add TM-score to compare-structures action
---
actions/ost-compare-structures | 24 +++++++++++++++++++++++-
modules/doc/actions.rst | 6 ++++++
2 files changed, 29 insertions(+), 1 deletion(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index f94d79bc1..dce074bfa 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -277,6 +277,13 @@ def _ParseArgs():
"https://github.com/kliment-olechnovic/voronota). Searches PATH "
"if not set."))
+ parser.add_argument(
+ "--usalign-exec",
+ dest="usalign_exec",
+ default=None,
+ help=("Path to USalign executable to compute TM-score. If not given, "
+ "an OpenStructure internal copy of USalign code is used."))
+
parser.add_argument(
"--qs-score",
dest="qs_score",
@@ -346,6 +353,16 @@ def _ParseArgs():
"as string in form <num><inscode>. The respective scores are "
"available as keys \"patch_qs\" and \"patch_dockq\""))
+ parser.add_argument(
+ "--tm-score",
+ dest="tm_score",
+ default=False,
+ action="store_true",
+ help=("Computes TM-score with the USalign tool. Also computes a "
+ "chain mapping in case of complexes that is stored in the "
+ "same format as the default mapping. TM-score and the mapping "
+ "are available as keys \"tm_score\" and \"usalign_mapping\""))
+
return parser.parse_args()
def _Rename(ent):
@@ -483,7 +500,8 @@ def _Process(model, reference, args):
scorer = scoring.Scorer(model, reference,
resnum_alignments = args.residue_number_alignment,
cad_score_exec = args.cad_exec,
- custom_mapping = mapping)
+ custom_mapping = mapping,
+ usalign_exec = args.usalign_exec)
ir = _GetInconsistentResidues(scorer.aln)
if len(ir) > 0 and args.enforce_consistency:
@@ -559,6 +577,10 @@ def _Process(model, reference, args):
out["patch_qs"] = scorer.patch_qs
out["patch_dockq"] = scorer.patch_dockq
+ if args.tm_score:
+ out["tm_score"] = scorer.tm_score
+ out["usalign_mapping"] = scorer.usalign_mapping
+
if args.dump_structures:
try:
io.SavePDB(scorer.model, model.GetName() + args.dump_suffix)
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index c8ddb6da5..3b6fdc277 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -250,6 +250,12 @@ Details on the usage (output of ``ost compare-structures --help``):
Residues are represented as string in form
<num><inscode>. The respective scores are available as
keys "patch_qs" and "patch_dockq"
+ --tm-score Computes TM-score with the USalign tool. Also computes
+ a chain mapping in case of complexes that is stored
+ in the same format as the default mapping. TM-score
+ and the mapping are available as keys "tm_score" and
+ "usalign_mapping"
+
.. _ost compare ligand structures:
--
GitLab