From 6fbe9955e8cb037956d4cc20f1283d520aee8bf9 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Mon, 29 Jul 2024 18:01:18 +0200
Subject: [PATCH] Penalize added model contacts by default in lDDT-PLI
---
CHANGELOG.txt | 5 +++++
actions/ost-compare-ligand-structures | 17 ++++++++++++-----
modules/mol/alg/pymod/ligand_scoring_lddtpli.py | 8 +++++---
3 files changed, 22 insertions(+), 8 deletions(-)
diff --git a/CHANGELOG.txt b/CHANGELOG.txt
index ef6d7297c..fd3b597bf 100644
--- a/CHANGELOG.txt
+++ b/CHANGELOG.txt
@@ -1,3 +1,8 @@
+Changes in Release 2.9.0
+--------------------------------------------------------------------------------
+
+ * lDDT-PLI now penalizes added model contacts by default.
+
Changes in Release 2.8.0
--------------------------------------------------------------------------------
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index 05bed460c..112f8deaa 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -299,11 +299,18 @@ def _ParseArgs():
help=("lDDT inclusion radius for lDDT-PLI."))
parser.add_argument(
- "--lddt-pli-amc",
- dest="lddt_pli_amc",
- default=False,
+ "--lddt-pli-add-mdl-contacts",
+ dest="lddt_pli_add_mdl_contacts",
+ default=True,
action="store_true",
- help=("Add model contacts (amc) when computing lDDT-PLI."))
+ help=("Add model contacts when computing lDDT-PLI."))
+
+ parser.add_argument(
+ "--no-lddt-pli-add-mdl-contacts",
+ dest="lddt_pli_add_mdl_contacts",
+ default=True,
+ action="store_false",
+ help=("DO NOT add model contacts when computing lDDT-PLI."))
# arguments relevant for rmsd
@@ -483,7 +490,7 @@ def _SetupLDDTPLIScorer(model, model_ligands, reference, reference_ligands, args
substructure_match = args.substructure_match,
coverage_delta = args.coverage_delta,
lddt_pli_radius = args.lddt_pli_radius,
- add_mdl_contacts = args.lddt_pli_amc)
+ add_mdl_contacts = args.lddt_pli_add_mdl_contacts)
def _SetupSCRMSDScorer(model, model_ligands, reference, reference_ligands, args):
return ligand_scoring_scrmsd.SCRMSDScorer(model, reference,
diff --git a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
index 5ba88920d..be245c63f 100644
--- a/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
+++ b/modules/mol/alg/pymod/ligand_scoring_lddtpli.py
@@ -1,6 +1,6 @@
import numpy as np
-from ost import LogWarning
+from ost import LogWarning, LogInfo
from ost import geom
from ost import mol
from ost import seq
@@ -84,7 +84,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
:type max_symmetries: :class:`int`
: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.
+ :param add_mdl_contacts: Whether to penalize added model contacts.
:type add_mdl_contacts: :class:`bool`
:param lddt_pli_thresholds: Distance difference thresholds for lDDT.
:type lddt_pli_thresholds: :class:`list` of :class:`float`
@@ -103,7 +103,7 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
resnum_alignments=False, rename_ligand_chain=False,
substructure_match=False, coverage_delta=0.2,
max_symmetries=1e5, lddt_pli_radius=6.0,
- add_mdl_contacts=False,
+ add_mdl_contacts=True,
lddt_pli_thresholds = [0.5, 1.0, 2.0, 4.0],
lddt_pli_binding_site_radius=None):
@@ -141,10 +141,12 @@ class LDDTPLIScorer(ligand_scoring_base.LigandScorer):
""" Implements interface from parent
"""
if self.add_mdl_contacts:
+ LogInfo("Computing lDDT-PLI with added model contacts")
result = self._compute_lddt_pli_add_mdl_contacts(symmetries,
target_ligand,
model_ligand)
else:
+ LogInfo("Computing lDDT-PLI without added model contacts")
result = self._compute_lddt_pli_classic(symmetries,
target_ligand,
model_ligand)
--
GitLab