From d11fc3327535f152e185cf349fb7aad7d9c2d2d5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Mar 2024 10:30:29 +0100
Subject: [PATCH] chain mapping: adapt naive RMSD mapping threshold to what we
describe in paper
---
modules/mol/alg/pymod/chain_mapping.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 69d0150fd..832f01ec0 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1078,7 +1078,7 @@ class ChainMapper:
mapping, alns, opt_score = opt_qsscore)
def GetRMSDMapping(self, model, strategy = "heuristic", subsampling=50,
- chem_mapping_result = None, heuristic_n_max_naive = 24):
+ chem_mapping_result = None, heuristic_n_max_naive = 120):
"""Identify chain mapping based on minimal RMSD superposition
Superposition and scoring is based on CA/C3' positions which are present
@@ -1100,9 +1100,9 @@ class ChainMapper:
transformation gets updated with each added chain pair.
* **heuristic**: Uses *naive* strategy if number of possible mappings
- is within *heuristic_n_max_naive*. The default of 24 corresponds
- to a tetramer (4!=24). If the number of possible mappings is larger,
- *greedy_iterative* is used.
+ is within *heuristic_n_max_naive*. The default of 120 corresponds
+ to a homo-pentamer (5!=120). If the number of possible mappings is
+ larger, *greedy_iterative* is used.
:param model: Model to map
:type model: :class:`ost.mol.EntityView`/:class:`ost.mol.EntityHandle`
--
GitLab