From 1cde4be114e93701597aae1f216a31e603709255 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Tue, 19 Apr 2022 14:36:48 +0200
Subject: [PATCH] lDDT: make matching residue names in model/target optional
(on by default)
---
modules/mol/alg/pymod/lddt.py | 9 ++++++---
modules/mol/alg/tests/test_lddt.py | 17 +++++++++++++++++
2 files changed, 23 insertions(+), 3 deletions(-)
diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index 7fba7a74c..2d7b675dd 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -307,7 +307,7 @@ class lDDTScorer:
local_lddt_prop=None, local_contact_prop=None,
chain_mapping=None, no_interchain=False,
penalize_extra_chains=False, residue_mapping=None,
- return_dist_test=False):
+ return_dist_test=False, check_resnames=True):
"""Computes lDDT of *model* - globally and per-residue
:param model: Model to be scored
@@ -373,7 +373,10 @@ class lDDTScorer:
Fifth: numpy matrix of shape
(len(scored_residues), len(thresholds))
specifying how many for each threshold are
- conserved.
+ conserved.
+ :param check_resnames: On by default. Enforces residue name matches
+ between mapped model and target residues.
+ :type check_resnames: :class:`bool`
:returns: global and per-residue lDDT scores as a tuple -
first element is global lDDT score and second element
a list of per-residue scores with length len(*model*.residues)
@@ -437,7 +440,7 @@ class lDDTScorer:
if res_mapper_key not in self.res_mapper:
continue
r_idx = self.res_mapper[res_mapper_key]
- if r.name != self.compound_names[r_idx]:
+ if check_resnames and r.name != self.compound_names[r_idx]:
raise RuntimeError(
f"Residue name mismatch for {r}, "
f" expect {self.compound_names[r_idx]}"
diff --git a/modules/mol/alg/tests/test_lddt.py b/modules/mol/alg/tests/test_lddt.py
index 0a0e365b1..84c274ac7 100644
--- a/modules/mol/alg/tests/test_lddt.py
+++ b/modules/mol/alg/tests/test_lddt.py
@@ -172,6 +172,23 @@ class TestlDDT(unittest.TestCase):
for a,b in zip(per_res_scores_one, per_res_scores_three):
self.assertAlmostEqual(a, b, places=5)
+ def test_resname_match(self):
+ model = _LoadFile("7SGN_C_model.pdb")
+ target = _LoadFile("7SGN_C_target.pdb")
+
+ # introduce name mismatch
+ ed = model.handle.EditXCS()
+ ed.RenameResidue(model.residues[42], "asdf")
+
+ # do scoring and select aname=CA
+ scorer = lDDTScorer(target.Select("aname=CA"),
+ conop.GetDefaultLib())
+
+ with self.assertRaises(RuntimeError):
+ scorer.lDDT(model)
+
+ scorer.lDDT(model, check_resnames=False)
+
if __name__ == "__main__":
from ost import testutils
if testutils.SetDefaultCompoundLib():
--
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