From 1d0ebac000201be421696b8bde31618d0a71d80f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 3 Mar 2023 12:41:31 +0100
Subject: [PATCH] enable custom chain mappings in compare-structures action
---
actions/ost-compare-structures-new | 21 +++++++++++++++++++--
1 file changed, 19 insertions(+), 2 deletions(-)
diff --git a/actions/ost-compare-structures-new b/actions/ost-compare-structures-new
index f4e562d5d..a36c3b7c1 100644
--- a/actions/ost-compare-structures-new
+++ b/actions/ost-compare-structures-new
@@ -43,6 +43,10 @@ Example to compute local and per-residue lDDT values as well as QS-score:
ost compare-structures-new -m model.pdb -r reference.cif --lddt --local-lddt \
--qs-score
+
+Example to inject custom chain mapping
+
+ost compare-structures-new -m model.pdb -r reference.cif -c A:B B:A
"""
import argparse
@@ -149,6 +153,16 @@ def _ParseArgs():
action="store_true",
help=("Fault tolerant parsing."))
+ parser.add_argument(
+ "-c",
+ "--chain-mapping",
+ nargs="+",
+ dest="chain_mapping",
+ help=("Custom mapping of chains between the reference and the model. "
+ "Each separate mapping consist of key:value pairs where key "
+ "is the chain name in reference and value is the chain name in "
+ "model."))
+
parser.add_argument(
"--lddt",
dest="lddt",
@@ -354,10 +368,14 @@ def _InterfaceResiduesToJSONDict(interface_dict):
def _Process(model, reference, args):
+ mapping = None
+ if args.chain_mapping is not None:
+ mapping = {x.split(':')[0]: x.split(':')[1] for x in args.chain_mapping}
scorer = scoring.Scorer(model, reference,
resnum_alignments = args.residue_number_alignment,
- cad_score_exec = args.cad_exec)
+ cad_score_exec = args.cad_exec,
+ custom_mapping = mapping)
ir = _GetInconsistentResidues(scorer.aln)
if len(ir) > 0 and args.enforce_consistency:
@@ -427,7 +445,6 @@ def _Process(model, reference, args):
io.SavePDB(scorer.model, model.GetName() + args.dump_suffix)
io.SavePDB(scorer.target, reference.GetName() + args.dump_suffix)
-
return out
def _Main():
--
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