From ed65571c2106c43562285c2f1f02e70e6ebe07f2 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Fri, 27 Jan 2023 17:35:24 +0100
Subject: [PATCH] cleanup: SCHWED-5783 drop assignment matrices
Qualified name value is not useful. Plus they are redundant with
the details.
---
modules/mol/alg/pymod/ligand_scoring.py | 42 +++-----------------
modules/mol/alg/tests/test_ligand_scoring.py | 8 ----
2 files changed, 5 insertions(+), 45 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 5e5f4742a..3ff13d926 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -159,10 +159,8 @@ class LigandScorer:
# lazily computed scores
self._rmsd = None
- self._rmsd_assignment = None
self._rmsd_details = None
self._lddt_pli = None
- self._lddt_pli_assignment = None
self._lddt_pli_details = None
# lazily precomputed variables
@@ -563,20 +561,18 @@ class LigandScorer:
self._rmsd_full_matrix,
"rmsd")
self._rmsd = mat_tuple[0]
- self._rmsd_assignment = mat_tuple[1]
- self._rmsd_details = mat_tuple[2]
+ self._rmsd_details = mat_tuple[1]
def _assign_matrices(self, mat1, mat2, data, main_key):
"""
:param mat1: the main ligand assignment criteria (RMSD or lDDT-PLI)
:param mat2: the secondary ligand assignment criteria (lDDT-PLI or RMSD)
:param data: the data (either self._rmsd_full_matrix or self._lddt_pli_matrix
- :return: a tuple with 3 dictionaries of matrices containing the main
- data, assignement, and details, respectively.
+ :return: a tuple with 2 dictionaries of matrices containing the main
+ data, and details, respectively.
"""
assignments = self._find_ligand_assignment(mat1, mat2)
out_main = {}
- out_assignment = {}
out_details = {}
for assignment in assignments:
trg_idx, mdl_idx = assignment
@@ -585,15 +581,12 @@ class LigandScorer:
mdl_restuple = (mdl_lig.number.num, mdl_lig.number.ins_code)
if mdl_cname not in out_main:
out_main[mdl_cname] = {}
- out_assignment[mdl_cname] = {}
out_details[mdl_cname] = {}
out_main[mdl_cname][mdl_restuple] = data[
trg_idx, mdl_idx][main_key]
- out_assignment[mdl_cname][mdl_restuple] = data[
- trg_idx, mdl_idx]["target_ligand"].qualified_name
out_details[mdl_cname][mdl_restuple] = data[
trg_idx, mdl_idx]
- return out_main, out_assignment, out_details
+ return out_main, out_details
def _assign_ligands_lddt_pli(self):
""" Assign ligands based on lDDT-PLI.
@@ -605,8 +598,7 @@ class LigandScorer:
self._lddt_pli_full_matrix,
"lddt_pli")
self._lddt_pli = mat_tuple[0]
- self._lddt_pli_assignment = mat_tuple[1]
- self._lddt_pli_details = mat_tuple[2]
+ self._lddt_pli_details = mat_tuple[1]
@property
def rmsd_matrix(self):
@@ -665,18 +657,6 @@ class LigandScorer:
self._assign_ligands_rmsd()
return self._rmsd
- @property
- def rmsd_assignment(self):
- """Get a dictionary of RMSD-based ligand assignment, keyed by model
- ligand qualified names. Values are the qualified names of the
- corresponding target ligand.
-
- :rtype: :class:`dict`
- """
- if self._rmsd_assignment is None:
- self._assign_ligands_rmsd()
- return self._rmsd_assignment
-
@property
def rmsd_details(self):
"""Get a dictionary of RMSD score details (dictionaries), keyed by
@@ -713,18 +693,6 @@ class LigandScorer:
self._assign_ligands_lddt_pli()
return self._lddt_pli
- @property
- def lddt_pli_assignment(self):
- """Get a dictionary of lDDT-PLI-based ligand assignment, keyed by model
- ligand qualified names. Values are the qualified names of the
- corresponding target ligand.
-
- :rtype: :class:`dict`
- """
- if self._lddt_pli_assignment is None:
- self._assign_ligands_lddt_pli()
- return self._lddt_pli_assignment
-
@property
def lddt_pli_details(self):
"""Get a dictionary of lDDT-PLI score details (dictionaries), keyed by
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 0116a948d..335242008 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -291,18 +291,13 @@ class TestLigandScoring(unittest.TestCase):
expected_keys = {"J", "F"}
self.assertFalse(expected_keys.symmetric_difference(sc.rmsd.keys()))
- self.assertFalse(expected_keys.symmetric_difference(sc.rmsd_assignment.keys()))
self.assertFalse(expected_keys.symmetric_difference(sc.rmsd_details.keys()))
self.assertFalse(expected_keys.symmetric_difference(sc.lddt_pli.keys()))
- self.assertFalse(expected_keys.symmetric_difference(sc.lddt_pli_assignment.keys()))
self.assertFalse(expected_keys.symmetric_difference(sc.lddt_pli_details.keys()))
# rmsd
self.assertAlmostEqual(sc.rmsd["J"][(1, "\x00")], 3.8498, 3)
self.assertAlmostEqual(sc.rmsd["F"][(1, "\x00")], 57.6295, 3)
- # rmsd_assignment
- self.assertEqual(sc.rmsd_assignment, {'J': {(1, "\x00"): 'L.G3D1'},
- 'F': {(1, "\x00"): 'I.G3D1'}})
# rmsd_details
self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["chain_mapping"], {'A': 'B', 'H': 'C'})
self.assertEqual(sc.rmsd_details["J"][(1, "\x00")]["bs_num_res"], 16)
@@ -318,9 +313,6 @@ class TestLigandScoring(unittest.TestCase):
# lddt_pli
self.assertAlmostEqual(sc.lddt_pli["J"][(1, "\x00")], 0.91194, 5)
self.assertAlmostEqual(sc.lddt_pli["F"][(1, "\x00")], 0.0014598, 6)
- # lddt_pli_assignment
- self.assertEqual(sc.lddt_pli_assignment, {'J': {(1, "\x00"): 'I.G3D1'},
- 'F': {(1, "\x00"): 'J.G3D1'}})
# lddt_pli_details
self.assertAlmostEqual(sc.lddt_pli_details["J"][(1, "\x00")]["rmsd"], 4.1008, 4)
self.assertEqual(sc.lddt_pli_details["J"][(1, "\x00")]["lddt_pli_n_contacts"], 5224)
--
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