From 9481742cf2e8246d9dab27929812bcdb6fa4bdcf Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 12 Sep 2022 10:42:33 +0200
Subject: [PATCH] Accept 0.0 QS-score mappings in QS-score based optimization
The reason for that is that one might start with an initial seed
somewhere in Nirvana that leads to no possible increase in QS-score.
Stoping there might hinder a non-zero QS-score when continuing with
other seeds. And even if the QS-score is 0.0 in the end, the mapping
should make sense from an lDDT perspective more or less...
---
modules/mol/alg/pymod/chain_mapping.py | 38 +++++++++++++-------------
1 file changed, 19 insertions(+), 19 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 9455000f7..286b440aa 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -2487,7 +2487,7 @@ def _QSScoreGreedyFull(the_greed, n_mdl_chains):
while something_happened:
something_happened = False
# Try all possible starting points and keep the one giving the best QS score
- best_score = 0.0
+ best_score = -1.0
best_mapping = None
mapped_ref_chains = set(mapping.keys())
mapped_mdl_chains = set(mapping.values())
@@ -2516,11 +2516,11 @@ def _QSScoreGreedyFull(the_greed, n_mdl_chains):
best_score = tmp_score
best_mapping = tmp_mapping
- if best_score == 0.0:
- break # no proper mapping found anymore...
-
- something_happened = True
- mapping = best_mapping
+ if best_mapping is not None and len(best_mapping) > len(mapping):
+ # this even accepts extensions that lead to no increase in QS-score
+ # at least they make sense from an lDDT perspective
+ something_happened = True
+ mapping = best_mapping
# translate mapping format and return
final_mapping = list()
@@ -2577,7 +2577,7 @@ def _QSScoreGreedyBlock(the_greed, seed_size, blocks_per_chem_group):
# extend starting seeds to *seed_size* and retain best scoring block
# for further extension
- best_score = 0.0
+ best_score = -1.0
best_mapping = None
for s in seeds:
seed = dict(mapping)
@@ -2594,7 +2594,7 @@ def _QSScoreGreedyBlock(the_greed, seed_size, blocks_per_chem_group):
starting_blocks.append(best_mapping)
# fully expand initial starting blocks
- best_score = 0.0
+ best_score = -1.0
best_mapping = None
for seed in starting_blocks:
seed = the_greed.ExtendMapping(seed)
@@ -2606,17 +2606,17 @@ def _QSScoreGreedyBlock(the_greed, seed_size, blocks_per_chem_group):
best_score = seed_score
best_mapping = seed
- if best_score == 0.0:
- break # no proper mapping found anymore
-
- something_happened = True
- mapping.update(best_mapping)
- for ref_ch, mdl_ch in best_mapping.items():
- for group_idx in range(len(ref_chem_groups)):
- if ref_ch in ref_chem_groups[group_idx]:
- ref_chem_groups[group_idx].remove(ref_ch)
- if mdl_ch in mdl_chem_groups[group_idx]:
- mdl_chem_groups[group_idx].remove(mdl_ch)
+ if best_mapping is not None and len(best_mapping) > len(mapping):
+ # this even accepts extensions that lead to no increase in QS-score
+ # at least they make sense from an lDDT perspective
+ something_happened = True
+ mapping.update(best_mapping)
+ for ref_ch, mdl_ch in best_mapping.items():
+ for group_idx in range(len(ref_chem_groups)):
+ if ref_ch in ref_chem_groups[group_idx]:
+ ref_chem_groups[group_idx].remove(ref_ch)
+ if mdl_ch in mdl_chem_groups[group_idx]:
+ mdl_chem_groups[group_idx].remove(mdl_ch)
# translate mapping format and return
final_mapping = list()
--
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