From 9c000e33d96cb2b2b4eb41b2210ff73f6565fe8a Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 31 May 2023 13:36:58 +0200
Subject: [PATCH] Control exhaustive enumeration in chain mapping from compare
actions
---
actions/ost-compare-ligand-structures | 11 +++++++++++
actions/ost-compare-structures | 13 ++++++++++++-
modules/mol/alg/pymod/ligand_scoring.py | 12 ++++++++++--
modules/mol/alg/pymod/scoring.py | 12 ++++++++++--
4 files changed, 43 insertions(+), 5 deletions(-)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 2af7694d8..b51a6c454 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -226,6 +226,16 @@ def _ParseArgs():
default=3,
help="Set verbosity level. Defaults to 3 (INFO).")
+ parser.add_argument(
+ "--n-max-naive",
+ dest="n_max_naive",
+ required=False,
+ default=12,
+ type=int,
+ help=("If number of chains in model and reference are below or equal "
+ "that number, the global chain mapping will naively enumerate "
+ "all possible mappings. A heuristic is used otherwise."))
+
return parser.parse_args()
@@ -334,6 +344,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
radius=args.radius,
lddt_pli_radius=args.lddt_pli_radius,
lddt_lp_radius=args.lddt_lp_radius,
+ n_max_naive=args.n_max_naive
)
out = dict()
diff --git a/actions/ost-compare-structures b/actions/ost-compare-structures
index cc145d048..48d33839e 100644
--- a/actions/ost-compare-structures
+++ b/actions/ost-compare-structures
@@ -384,6 +384,16 @@ def _ParseArgs():
action="store_true",
help=("Disable stereochecks for lDDT computation"))
+ parser.add_argument(
+ "--n-max-naive",
+ dest="n_max_naive",
+ required=False,
+ default=12,
+ type=int,
+ help=("If number of chains in model and reference are below or equal "
+ "that number, the chain mapping will naively enumerate all "
+ "possible mappings. A heuristic is used otherwise."))
+
return parser.parse_args()
def _Rename(ent):
@@ -541,7 +551,8 @@ def _Process(model, reference, args):
cad_score_exec = args.cad_exec,
custom_mapping = mapping,
usalign_exec = args.usalign_exec,
- lddt_no_stereochecks = args.lddt_no_stereochecks)
+ lddt_no_stereochecks = args.lddt_no_stereochecks,
+ n_max_naive = args.n_max_naive)
ir = _GetInconsistentResidues(scorer.aln)
if len(ir) > 0 and args.enforce_consistency:
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 3d9467bf6..ed1e95522 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -209,6 +209,12 @@ class LigandScorer:
(False) is to use a combination of lDDT-PLI and
RMSD for the assignment.
:type rmsd_assignment: :class:`bool`
+ :param n_max_naive: Parameter for global chain mapping. If *model* and
+ *target* have less or equal that number of chains,
+ the full
+ mapping solution space is enumerated to find the
+ the optimum. A heuristic is used otherwise.
+ :type n_max_naive: :class:`int`
"""
def __init__(self, model, target, model_ligands=None, target_ligands=None,
resnum_alignments=False, check_resnames=True,
@@ -216,7 +222,7 @@ class LigandScorer:
chain_mapper=None, substructure_match=False,
radius=4.0, lddt_pli_radius=6.0, lddt_lp_radius=10.0,
binding_sites_topn=100000, global_chain_mapping=False,
- rmsd_assignment=False):
+ rmsd_assignment=False, n_max_naive=12):
if isinstance(model, mol.EntityView):
self.model = mol.CreateEntityFromView(model, False)
@@ -263,6 +269,7 @@ class LigandScorer:
self.binding_sites_topn = binding_sites_topn
self.global_chain_mapping = global_chain_mapping
self.rmsd_assignment = rmsd_assignment
+ self.n_max_naive = n_max_naive
# scoring matrices
self._rmsd_matrix = None
@@ -296,7 +303,8 @@ class LigandScorer:
def _model_mapping(self):
"""Get the global chain mapping for the model."""
if self.__model_mapping is None:
- self.__model_mapping = self.chain_mapper.GetMapping(self.model)
+ self.__model_mapping = self.chain_mapper.GetMapping(self.model,
+ n_max_naive=self.n_max_naive)
return self.__model_mapping
@staticmethod
diff --git a/modules/mol/alg/pymod/scoring.py b/modules/mol/alg/pymod/scoring.py
index 7b6b802b3..26633216a 100644
--- a/modules/mol/alg/pymod/scoring.py
+++ b/modules/mol/alg/pymod/scoring.py
@@ -128,11 +128,16 @@ class Scorer:
:param lddt_no_stereochecks: Whether to compute lDDT without stereochemistry
checks
:type lddt_no_stereochecks: :class:`bool`
+ :param n_max_naive: Parameter for chain mapping. If *model* and *target*
+ have less or equal that number of chains, the full
+ mapping solution space is enumerated to find the
+ the optimum. A heuristic is used otherwise.
+ :type n_max_naive: :class:`int`
"""
def __init__(self, model, target, resnum_alignments=False,
molck_settings = None, cad_score_exec = None,
custom_mapping=None, usalign_exec = None,
- lddt_no_stereochecks=False):
+ lddt_no_stereochecks=False, n_max_naive=12):
if isinstance(model, mol.EntityView):
model = mol.CreateEntityFromView(model, False)
@@ -200,6 +205,7 @@ class Scorer:
self.cad_score_exec = cad_score_exec
self.usalign_exec = usalign_exec
self.lddt_no_stereochecks = lddt_no_stereochecks
+ self.n_max_naive = n_max_naive
# lazily evaluated attributes
self._stereochecked_model = None
@@ -419,7 +425,9 @@ class Scorer:
:type: :class:`ost.mol.alg.chain_mapping.MappingResult`
"""
if self._mapping is None:
- self._mapping = self.chain_mapper.GetMapping(self.model)
+ self._mapping = \
+ self.chain_mapper.GetMapping(self.model,
+ n_max_naive = self.n_max_naive)
return self._mapping
@property
--
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