From ab68e3e16c0b91d72f710d8eba77bb0f357faafa Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 28 Aug 2024 18:39:09 +0200
Subject: [PATCH] compare-structures: add rigid scores specific chain mapping
in json output
---
actions/ost-compare-structures | 6 +++++-
modules/doc/actions.rst | 4 +++-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 0318a826c..9a466ce05 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -454,7 +454,10 @@ def _ParseArgs():
"8.0] given these positions and transformation, \"oligo_gdtha\": "
"same with thresholds [0.5, 1.0, 2.0, 4.0], \"rmsd\": RMSD given "
"these positions and transformation, \"transform\": the used 4x4 "
- "transformation matrix that superposes model onto reference."))
+ "transformation matrix that superposes model onto reference, "
+ "\"rigid_chain_mapping\": equivalent of \"chain_mapping\" which "
+ "is used for rigid scores (optimized for RMSD instead of "
+ "QS-score/lDDT)."))
parser.add_argument(
"--patch-scores",
@@ -895,6 +898,7 @@ def _Process(model, reference, args, model_format, reference_format):
out["rmsd"] = _RoundOrNone(scorer.rmsd)
data = scorer.rigid_transform.data
out["transform"] = [data[i:i + 4] for i in range(0, len(data), 4)]
+ out["rigid_chain_mapping"] = scorer.rigid_mapping.GetFlatMapping()
if args.patch_scores:
out["model_interface_residues"] = \
diff --git a/modules/doc/actions.rst b/modules/doc/actions.rst
index fb5c7b9a0..d1794c49c 100644
--- a/modules/doc/actions.rst
+++ b/modules/doc/actions.rst
@@ -348,7 +348,9 @@ Details on the usage (output of ``ost compare-structures --help``):
thresholds [0.5, 1.0, 2.0, 4.0], "rmsd": RMSD given
these positions and transformation, "transform": the
used 4x4 transformation matrix that superposes model
- onto reference.
+ onto reference, "rigid_chain_mapping": equivalent of
+ "chain_mapping" which is used for rigid scores
+ (optimized for RMSD instead of QS-score/lDDT).
--patch-scores Local interface quality score used in CASP15. Scores
each model residue that is considered in the interface
(CB pos within 8A of any CB pos from another chain (CA
--
GitLab