From 7d956e81ca5248dac52be9cad28a64661550fb2b Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Thu, 19 Jan 2023 18:16:35 +0100
Subject: [PATCH] feat: SCHWED-5783 add check_resname
---
modules/mol/alg/pymod/ligand_scoring.py | 13 +++++++++----
modules/mol/alg/tests/test_ligand_scoring.py | 14 ++++++++++++++
2 files changed, 23 insertions(+), 4 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index c44ec74c0..75738e34f 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -87,6 +87,9 @@ class LigandScorer:
based on residue numbers. This can be assumed in
benchmarking setups such as CAMEO/CASP.
:type resnum_alignments: :class:`bool`
+ :param check_resnames: On by default. Enforces residue name matches
+ between mapped model and target residues.
+ :type check_resnames: :class:`bool`
:param chain_mapper: a chain mapper initialized for the target structure.
If None (default), a chain mapper will be initialized
lazily as required.
@@ -103,9 +106,9 @@ class LigandScorer:
:param lddt_bs_radius: :class:`float`
"""
def __init__(self, model, target, model_ligands=None, target_ligands=None,
- resnum_alignments=False, chain_mapper=None,
- substructure_match=False, radius=4.0, lddt_pli_radius=6.0,
- lddt_bs_radius=10.0):
+ resnum_alignments=False, check_resnames=True,
+ chain_mapper=None, substructure_match=False,
+ radius=4.0, lddt_pli_radius=6.0, lddt_bs_radius=10.0):
if isinstance(model, mol.EntityView):
self.model = mol.CreateEntityFromView(model, False)
@@ -135,6 +138,7 @@ class LigandScorer:
self._chain_mapper = chain_mapper
self.resnum_alignments = resnum_alignments
+ self.check_resnames = check_resnames
self.substructure_match = substructure_match
self.radius = radius
self.lddt_pli_radius = lddt_pli_radius
@@ -453,7 +457,8 @@ class LigandScorer:
n_cont, n_cons = lddt_scorer.lDDT(
mdl_bs_ent, chain_mapping={"A": "A", "_": "_"},
no_intrachain=True,
- return_dist_test=True)
+ return_dist_test=True,
+ check_resnames = self.check_resnames)
# Save results?
best_lddt = self._lddt_pli_matrix[target_i, model_i]["lddt_pli"]
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 8e3eb94a7..a09d350fb 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -263,6 +263,20 @@ class TestLigandScoring(unittest.TestCase):
assert sc._lddt_pli_matrix[1, 0]["bs_num_overlap_res"] == 15
assert sc._lddt_pli_matrix[5, 0]["bs_num_overlap_res"] == 15
+ def test_check_resnames(self):
+ """Test check_resname argument works
+ """
+ # 4C0A has mismatching sequence and fails with check_resnames=True
+ trg, trg_seqres = io.LoadMMCIF(os.path.join('testfiles', "1r8q.cif.gz"), seqres=True)
+ trg_4c0a, _ = io.LoadMMCIF(os.path.join('testfiles', "4c0a.cif.gz"), seqres=True)
+
+ with self.assertRaises(RuntimeError):
+ sc = LigandScorer(trg, trg_4c0a, None, None, check_resnames=True)
+ sc._compute_scores()
+
+ sc = LigandScorer(trg, trg_4c0a, None, None, check_resnames=False)
+ sc._compute_scores()
+
if __name__ == "__main__":
from ost import testutils
--
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