From 0128f5b02a635a20a10d32397c995b138053ce23 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 31 May 2023 11:30:49 +0200
Subject: [PATCH] param to control when heuristic kicks in for
ChainMapper.GetMapping
---
modules/mol/alg/pymod/chain_mapping.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 896f77257..25a19259a 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1228,18 +1228,18 @@ class ChainMapper:
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
final_mapping, alns)
- def GetMapping(self, model):
+ def GetMapping(self, model, n_max_naive = 12):
""" Convenience function to get mapping with currently preferred method
- If number of chains in model and target are <= 12, a naive QS-score
- mapping is performed. For anything else, a QS-score mapping with the
- greedy_block strategy is performed (steep_opt_rate = 3,
+ 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_block strategy is performed (steep_opt_rate = 3,
block_seed_size = 5, block_blocks_per_chem_group = 6).
"""
n_trg_chains = len(self.target.chains)
res = self.GetChemMapping(model)
n_mdl_chains = len(res[2].chains)
- if n_trg_chains <= 12 and n_mdl_chains <= 12:
+ if n_trg_chains <= n_max_naive and n_mdl_chains <= n_max_naive:
return self.GetQSScoreMapping(model, strategy="naive",
chem_mapping_result=res)
else:
--
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