From a2492881e8f8c73ce667d7cd70f7ff7b9323bfa1 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 25 May 2023 11:17:28 +0200
Subject: [PATCH] Add convenience function for chain mapping
Calls the currently preferred chain mapping method that should
deal with most chain mapping cases in a reasonable runtime.
---
modules/mol/alg/pymod/chain_mapping.py | 19 ++++++++++++++++
modules/mol/alg/pymod/scoring.py | 30 ++++----------------------
2 files changed, 23 insertions(+), 26 deletions(-)
diff --git a/modules/mol/alg/pymod/chain_mapping.py b/modules/mol/alg/pymod/chain_mapping.py
index 692788bb8..896f77257 100644
--- a/modules/mol/alg/pymod/chain_mapping.py
+++ b/modules/mol/alg/pymod/chain_mapping.py
@@ -1228,6 +1228,25 @@ class ChainMapper:
return MappingResult(self.target, mdl, self.chem_groups, chem_mapping,
final_mapping, alns)
+ def GetMapping(self, model):
+ """ 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,
+ 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:
+ 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,
+ chem_mapping_result=res)
def GetRepr(self, substructure, model, topn=1, inclusion_radius=15.0,
thresholds=[0.5, 1.0, 2.0, 4.0], bb_only=False,
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index f9e7ec864..7b6b802b3 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -111,12 +111,6 @@ class Scorer:
colored to True in
:class:`ost.mol.alg.MolckSettings` constructor.
:type molck_settings: :class:`ost.mol.alg.MolckSettings`
- :param naive_chain_mapping_thresh: Chain mappings for targets/models up to
- that number of chains will be fully
- enumerated to optimize for QS-score.
- Everything above is treated with a
- heuristic.
- :type naive_chain_mapping_thresh: :class:`int`
:param cad_score_exec: Explicit path to voronota-cadscore executable from
voronota installation from
https://github.com/kliment-olechnovic/voronota. If
@@ -136,9 +130,9 @@ class Scorer:
:type lddt_no_stereochecks: :class:`bool`
"""
def __init__(self, model, target, resnum_alignments=False,
- molck_settings = None, naive_chain_mapping_thresh=12,
- cad_score_exec = None, custom_mapping=None,
- usalign_exec = None, lddt_no_stereochecks=False):
+ molck_settings = None, cad_score_exec = None,
+ custom_mapping=None, usalign_exec = None,
+ lddt_no_stereochecks=False):
if isinstance(model, mol.EntityView):
model = mol.CreateEntityFromView(model, False)
@@ -203,7 +197,6 @@ class Scorer:
"resnum_alignments are enabled")
self.resnum_alignments = resnum_alignments
- self.naive_chain_mapping_thresh = naive_chain_mapping_thresh
self.cad_score_exec = cad_score_exec
self.usalign_exec = usalign_exec
self.lddt_no_stereochecks = lddt_no_stereochecks
@@ -426,22 +419,7 @@ class Scorer:
:type: :class:`ost.mol.alg.chain_mapping.MappingResult`
"""
if self._mapping is None:
- n_trg_chains = len(self.chain_mapper.target.chains)
- res = self.chain_mapper.GetChemMapping(self.model)
- n_mdl_chains = len(res[2].chains)
- thresh = self.naive_chain_mapping_thresh
- if n_trg_chains <= thresh and n_mdl_chains <= thresh:
- m = self.chain_mapper.GetQSScoreMapping(self.model,
- strategy="naive",
- chem_mapping_result=res)
- else:
- m = self.chain_mapper.GetQSScoreMapping(self.model,
- strategy="greedy_block",
- steep_opt_rate=3,
- block_seed_size=5,
- block_blocks_per_chem_group=6,
- chem_mapping_result=res)
- self._mapping = m
+ self._mapping = self.chain_mapper.GetMapping(self.model)
return self._mapping
@property
--
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