From ffd0fbbd88921ce1b636b4d50e0141bf2ef1e2a3 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 10 Jul 2023 09:45:32 +0200
Subject: [PATCH] chain mapping: Change default of GetMapping convencience
function
use greedy full strategy with contact map pruning enabled
---
modules/mol/alg/pymod/chain_mapping.py | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index aa8295fde..c4a017f3d 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1243,8 +1243,8 @@ class ChainMapper:
If number of chains in model and target are <= *n_max_naive*, a naive
QS-score mapping is performed. For anything else, a QS-score mapping
- with the greedy_full strategy is performed (steep_opt_rate = None,
- block_seed_size = 5, block_blocks_per_chem_group = 6).
+ with the greedy_full strategy is performed
+ (greedy_prune_contact_map = True).
"""
n_trg_chains = len(self.target.chains)
res = self.GetChemMapping(model)
@@ -1253,9 +1253,8 @@ class ChainMapper:
return self.GetQSScoreMapping(model, strategy="naive",
chem_mapping_result=res)
else:
- return self.GetQSScoreMapping(model, strategy="greedy_block",
- steep_opt_rate=3, block_seed_size=5,
- block_blocks_per_chem_group=6,
+ return self.GetQSScoreMapping(model, strategy="greedy_full",
+ greedy_prune_contact_map=True,
chem_mapping_result=res)
def GetRepr(self, substructure, model, topn=1, inclusion_radius=15.0,
--
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