From b54d96dedf67297c1c7e03b387e04f3c7c97c283 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 8 Mar 2024 13:07:45 +0100
Subject: [PATCH] chain mapping: enable subsampling as default for
GetRMSDMapping
---
modules/mol/alg/pymod/chain_mapping.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 7867619d8..e13a47128 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1077,7 +1077,7 @@ class ChainMapper:
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
mapping, alns, opt_score = opt_qsscore)
- def GetRMSDMapping(self, model, strategy = "heuristic", subsampling=None,
+ def GetRMSDMapping(self, model, strategy = "heuristic", subsampling=50,
chem_mapping_result = None, heuristic_n_max_naive = 24):
"""Identify chain mapping based on minimal RMSD superposition
@@ -1110,7 +1110,7 @@ class ChainMapper:
"greedy_single", "greedy_iterative"]
:type strategy: :class:`str`
:param subsampling: If given, only an equally distributed subset
- of all CA/C3' positions are used for
+ of CA/C3' positions in each chain are used for
superposition/scoring.
:type subsampling: :class:`int`
:param chem_mapping_result: Pro param. The result of
--
GitLab