From e08c77a2d1b4e7d927353298674120d960d51909 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Fri, 3 Mar 2023 09:20:48 +0100
Subject: [PATCH] feat: SCHWED-5481 additional arguments
---
actions/ost-compare-ligand-structures | 42 ++++++++++++++++++++++++++-
1 file changed, 41 insertions(+), 1 deletion(-)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index c21537483..cf87c1c13 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -128,14 +128,31 @@ def _ParseArgs():
help=("Fault tolerant parsing."))
parser.add_argument(
- "--residue-number-alignment",
"-rna",
+ "--residue-number-alignment",
dest="residue_number_alignment",
default=False,
action="store_true",
help=("Make alignment based on residue number instead of using "
"a global BLOSUM62-based alignment (NUC44 for nucleotides)."))
+ parser.add_argument(
+ "-cr",
+ "--check-resnames",
+ dest="check_resnames",
+ default=True,
+ action="store_false",
+ help=("Enforce residue name matches between mapped model and target"
+ "residues."))
+
+ parser.add_argument(
+ "-sm",
+ "--substructure-match",
+ dest="substructure_match",
+ default=False,
+ action="store_true",
+ help=("Allow incomplete target ligands."))
+
parser.add_argument(
"--lddt-pli",
dest="lddt_pli",
@@ -150,6 +167,24 @@ def _ParseArgs():
action="store_true",
help=("Compute RMSD score and store as key \"lddt-pli\"."))
+ parser.add_argument(
+ "--radius",
+ dest="radius",
+ default=4.0,
+ help=("."))
+
+ parser.add_argument(
+ "--lddt-pli-radius",
+ dest="lddt_pli_radius",
+ default=6.0,
+ help=("."))
+
+ parser.add_argument(
+ "--lddt-bs-radius",
+ dest="lddt_bs_radius",
+ default=4.0,
+ help=("."))
+
parser.add_argument(
'-v',
'--verbosity',
@@ -261,6 +296,11 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
model_ligands=model_ligands,
target_ligands=reference_ligands,
resnum_alignments=args.residue_number_alignment,
+ check_resnames=args.check_resnames,
+ substructure_match=args.substructure_match,
+ radius=args.radius,
+ lddt_pli_radius=args.lddt_pli_radius,
+ lddt_bs_radius=args.lddt_bs_radius
)
out = dict()
--
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