From f83eb6f934b580c4ce109acacfb2f8a87f90f2ad Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 21 Jul 2023 13:59:56 +0200
Subject: [PATCH] feat: SCHWED-5954 speed up
---
modules/mol/alg/pymod/ligand_scoring.py | 22 +++++++++++++++++-----
1 file changed, 17 insertions(+), 5 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 1bfca88ee..acad9d141 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -305,8 +305,8 @@ class LigandScorer:
self._unassigned_target_ligands = {}
self._unassigned_model_ligands = {}
# Keep track of symmetries/isomorphisms
- # 0: no isomorphism
- # 1: isomorphic
+ # 0.0: no isomorphism
+ # 1.0: isomorphic
# np.nan: not assessed yet
self._assignment_isomorphisms = None
@@ -1249,7 +1249,8 @@ class LigandScorer:
self.model_ligands[ligand_idx],
self.target_ligands[trg_lig_idx],
substructure_match=self.substructure_match,
- by_atom_index=True)
+ by_atom_index=True,
+ return_symmetries=False)
except NoSymmetryError:
assigned = 0.
else:
@@ -1301,7 +1302,8 @@ class LigandScorer:
self.model_ligands[model_lig_idx],
self.target_ligands[ligand_idx],
substructure_match=self.substructure_match,
- by_atom_index=True)
+ by_atom_index=True,
+ return_symmetries=False)
except NoSymmetryError:
assigned = 0.
else:
@@ -1412,7 +1414,7 @@ def SCRMSD(model_ligand, target_ligand, transformation=geom.Mat4(),
def _ComputeSymmetries(model_ligand, target_ligand, substructure_match=False,
- by_atom_index=False):
+ by_atom_index=False, return_symmetries=True):
"""Return a list of symmetries (isomorphisms) of the model onto the target
residues.
@@ -1430,6 +1432,12 @@ def _ComputeSymmetries(model_ligand, target_ligand, substructure_match=False,
Otherwise, if False, the symmetries refer to atom
names.
:type by_atom_index: :class:`bool`
+ :type return_symmetries: If Truthy, return the mappings, otherwise simply
+ return True if a mapping is found (and raise if
+ no mapping is found). This is useful to quickly
+ find out if a mapping exist without the expensive
+ step to find all the mappings.
+ :type return_symmetries: :class:`bool`
:raises: :class:`NoSymmetryError` when no symmetry can be found.
"""
@@ -1451,12 +1459,16 @@ def _ComputeSymmetries(model_ligand, target_ligand, substructure_match=False,
model_graph, target_graph, node_match=lambda x, y:
x["element"] == y["element"])
if gm.is_isomorphic():
+ if not return_symmetries:
+ return True
symmetries = [
(list(isomorphism.values()), list(isomorphism.keys()))
for isomorphism in gm.isomorphisms_iter()]
assert len(symmetries) > 0
LogDebug("Found %s isomorphic mappings (symmetries)" % len(symmetries))
elif gm.subgraph_is_isomorphic() and substructure_match:
+ if not return_symmetries:
+ return True
symmetries = [(list(isomorphism.values()), list(isomorphism.keys())) for isomorphism in
gm.subgraph_isomorphisms_iter()]
assert len(symmetries) > 0
--
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