From f48e52484878cc7247c3e71696f7c52cb6fbc9ed Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 24 May 2023 11:24:50 +0200
Subject: [PATCH] refactor: SCHWED-5540 rename lDDT-BS to lDDT-LP in ligand
scoring
---
actions/ost-compare-ligand-structures | 8 ++++----
modules/mol/alg/pymod/ligand_scoring.py | 18 +++++++++---------
2 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/actions/ost-compare-ligand-structures b/actions/ost-compare-ligand-structures
index abe20e849..74faddae2 100644
--- a/actions/ost-compare-ligand-structures
+++ b/actions/ost-compare-ligand-structures
@@ -197,10 +197,10 @@ def _ParseArgs():
help=("lDDT inclusion radius for lDDT-PLI."))
parser.add_argument(
- "--lddt-bs-radius",
- dest="lddt_bs_radius",
+ "--lddt-lp-radius",
+ dest="lddt_lp_radius",
default=4.0,
- help=("lDDT inclusion radius for lDDT-BS."))
+ help=("lDDT inclusion radius for lDDT-LP."))
parser.add_argument(
'-v',
@@ -305,7 +305,7 @@ def _Process(model, model_ligands, reference, reference_ligands, args):
substructure_match=args.substructure_match,
radius=args.radius,
lddt_pli_radius=args.lddt_pli_radius,
- lddt_bs_radius=args.lddt_bs_radius
+ lddt_lp_radius=args.lddt_lp_radius
)
out = dict()
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 15ca94afd..991c7d27c 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -170,8 +170,8 @@ class LigandScorer:
:type radius: :class:`float`
:param lddt_pli_radius: lDDT inclusion radius for lDDT-PLI.
:type lddt_pli_radius: :class:`float`
- :param lddt_bs_radius: lDDT inclusion radius for lDDT-BS.
- :type lddt_bs_radius: :class:`float`
+ :param lddt_lp_radius: lDDT inclusion radius for lDDT-LP.
+ :type lddt_lp_radius: :class:`float`
:param binding_sites_topn: maximum number of target binding site
representations to assess, per target ligand.
:type binding_sites_topn: :class:`int`
@@ -180,7 +180,7 @@ class LigandScorer:
resnum_alignments=False, check_resnames=True,
rename_ligand_chain=False,
chain_mapper=None, substructure_match=False,
- radius=4.0, lddt_pli_radius=6.0, lddt_bs_radius=10.0,
+ radius=4.0, lddt_pli_radius=6.0, lddt_lp_radius=10.0,
binding_sites_topn=100000):
if isinstance(model, mol.EntityView):
@@ -224,7 +224,7 @@ class LigandScorer:
self.substructure_match = substructure_match
self.radius = radius
self.lddt_pli_radius = lddt_pli_radius
- self.lddt_bs_radius = lddt_bs_radius
+ self.lddt_lp_radius = lddt_lp_radius
self.binding_sites_topn = binding_sites_topn
# scoring matrices
@@ -416,7 +416,7 @@ class LigandScorer:
# Find the representations
self._binding_sites[ligand.hash_code] = self.chain_mapper.GetRepr(
- ref_bs, self.model, inclusion_radius=self.lddt_bs_radius,
+ ref_bs, self.model, inclusion_radius=self.lddt_lp_radius,
topn=self.binding_sites_topn)
return self._binding_sites[ligand.hash_code]
@@ -530,7 +530,7 @@ class LigandScorer:
rmsd_full_matrix[target_i, model_i]["rmsd"] > rmsd:
rmsd_full_matrix[target_i, model_i] = {
"rmsd": rmsd,
- "lddt_bs": binding_site.lDDT,
+ "lddt_lp": binding_site.lDDT,
"bs_ref_res": binding_site.substructure.residues,
"bs_ref_res_mapped": binding_site.ref_residues,
"bs_mdl_res_mapped": binding_site.mdl_residues,
@@ -590,7 +590,7 @@ class LigandScorer:
lddt_pli_full_matrix[target_i, model_i] = {
"lddt_pli": global_lddt,
"rmsd": rmsd,
- "lddt_bs": binding_site.lDDT,
+ "lddt_lp": binding_site.lDDT,
"lddt_pli_n_contacts": lddt_tot,
"bs_ref_res": binding_site.substructure.residues,
"bs_ref_res_mapped": binding_site.ref_residues,
@@ -799,7 +799,7 @@ class LigandScorer:
Each sub-dictionary contains the following information:
* `rmsd`: the RMSD score value.
- * `lddt_bs`: the lDDT-BS score of the binding site.
+ * `lddt_lp`: the lDDT score of the ligand pocket (lDDT-LP).
* `bs_ref_res`: a list of residues (:class:`~ost.mol.ResidueHandle`)
that define the binding site in the reference.
* `bs_ref_res_mapped`: a list of residues
@@ -856,7 +856,7 @@ class LigandScorer:
chain mapping and assignment. This may differ from the RMSD-based
assignment. Note that a different isomorphism than `lddt_pli` may
be used.
- * `lddt_bs`: the lDDT-BS score of the binding site.
+ * `lddt_lp`: the lDDT score of the ligand pocket (lDDT-LP).
* `lddt_pli_n_contacts`: number of total contacts used in lDDT-PLI,
summed over all thresholds. Can be divided by 8 to obtain the number
of atomic contacts.
--
GitLab