From 7f0022fa5610ff502a3527f6d4faac9c1a66a821 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 12 Jun 2024 17:35:50 +0200
Subject: [PATCH] refactor: drop check_resnames and set it to False
This is in order to be consistent with the behavior of the Scorer
---
modules/mol/alg/pymod/ligand_scoring_lddtpli.py | 10 +++-------
1 file changed, 3 insertions(+), 7 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
index f4ae9c4c6..728af7200 100644
--- a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
+++ b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
@@ -82,9 +82,6 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
:param max_symmetries: Passed to parent constructor - see
:class:`LigandScorer`.
:type max_symmetries: :class:`int`
- :param check_resnames: On by default. Enforces residue name matches
- between mapped model and target residues.
- :type check_resnames: :class:`bool`
:param lddt_pli_radius: lDDT inclusion radius for lDDT-PLI.
:type lddt_pli_radius: :class:`float`
:param add_mdl_contacts: Whether to add mdl contacts.
@@ -105,7 +102,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
def __init__(self, model, target, model_ligands=None, target_ligands=None,
resnum_alignments=False, rename_ligand_chain=False,
substructure_match=False, coverage_delta=0.2,
- max_symmetries=1e5, check_resnames=True, lddt_pli_radius=6.0,
+ max_symmetries=1e5, lddt_pli_radius=6.0,
add_mdl_contacts=False,
lddt_pli_thresholds = [0.5, 1.0, 2.0, 4.0],
lddt_pli_binding_site_radius=None):
@@ -118,7 +115,6 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
coverage_delta = coverage_delta,
max_symmetries = max_symmetries)
- self.check_resnames = check_resnames
self.lddt_pli_radius = lddt_pli_radius
self.add_mdl_contacts = add_mdl_contacts
self.lddt_pli_thresholds = lddt_pli_thresholds
@@ -427,7 +423,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
scorer._ProcessModel(mdl_bs, lddt_chain_mapping,
residue_mapping = lddt_alns,
thresholds = self.lddt_pli_thresholds,
- check_resnames = self.check_resnames)
+ check_resnames = False)
# estimate a penalty for unsatisfied model contacts from chains
# that are not in the local trg binding site, but can be mapped in
@@ -650,7 +646,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
scorer._ProcessModel(mdl_bs, lddt_chain_mapping,
residue_mapping = lddt_alns,
thresholds = self.lddt_pli_thresholds,
- check_resnames = self.check_resnames)
+ check_resnames = False)
for (trg_sym, mdl_sym) in symmetries:
for mdl_i, trg_i in zip(mdl_sym, trg_sym):
--
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