From cfd241ca166db324bdf4cbd1647e7e64b748d411 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 5 Feb 2024 15:35:34 +0100
Subject: [PATCH] chain mapping: reduce default for min_pep_length from 10 to 6
That's the minimum length for a peptide chain to be considered in chain
mapping
---
actions/ost-compare-structures | 2 +-
modules/mol/alg/pymod/chain_mapping.py | 2 +-
modules/mol/alg/pymod/scoring.py | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index 6cb962d52..36baa6c04 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -498,7 +498,7 @@ def _ParseArgs():
parser.add_argument(
"--min-pep-length",
dest="min_pep_length",
- default = 10,
+ default = 6,
type=int,
help=("Relevant parameter if short peptides are involved in scoring."
"Minimum peptide length for a chain in the target structure to "
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 417cfa58d..5e90c49dc 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -599,7 +599,7 @@ class ChainMapper:
pep_subst_mat = seq.alg.BLOSUM62, pep_gap_open = -11,
pep_gap_ext = -1, nuc_subst_mat = seq.alg.NUC44,
nuc_gap_open = -4, nuc_gap_ext = -4,
- min_pep_length = 10, min_nuc_length = 4,
+ min_pep_length = 6, min_nuc_length = 4,
n_max_naive = 1e8):
# attributes
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index e568fdf3a..0f8e3ee56 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -167,7 +167,7 @@ class Scorer:
molck_settings = None, cad_score_exec = None,
custom_mapping=None, usalign_exec = None,
lddt_no_stereochecks=False, n_max_naive=40320,
- oum=False, min_pep_length = 10, min_nuc_length = 4):
+ oum=False, min_pep_length = 6, min_nuc_length = 4):
self._target_orig = target
self._model_orig = model
--
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