From 13c8ab8e4c07aed248cfd1fe237756019b8e5b11 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Tue, 24 Jan 2023 17:00:51 +0100
Subject: [PATCH] refactor: SCHWED-5783 defer assignment
---
modules/mol/alg/pymod/ligand_scoring.py | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index ca90b7e00..45066b1a8 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -381,9 +381,9 @@ class LigandScorer:
def _compute_scores(self):
""""""
# Create the matrix
- self._rmsd_full_matrix = np.empty(
+ rmsd_full_matrix = np.empty(
(len(self.target_ligands), len(self.model_ligands)), dtype=dict)
- self._lddt_pli_full_matrix = np.empty(
+ lddt_pli_full_matrix = np.empty(
(len(self.target_ligands), len(self.model_ligands)), dtype=dict)
for target_i, target_ligand in enumerate(self.target_ligands):
LogVerbose("Analyzing target ligand %s" % target_ligand)
@@ -427,7 +427,7 @@ class LigandScorer:
rmsd = SCRMSD(model_ligand, target_ligand,
transformation=binding_site.transform,
substructure_match=self.substructure_match)
- self._rmsd_full_matrix[target_i, model_i] = {
+ rmsd_full_matrix[target_i, model_i] = {
"rmsd": rmsd,
"chain_mapping": binding_site.GetFlatChainMapping(),
"lddt_bs": binding_site.lDDT,
@@ -451,7 +451,7 @@ class LigandScorer:
# LogWarning("Can't calculate backbone RMSD: %s"
# " - setting to Infinity" % str(err))
# bb_rmsd = float("inf")
- self._lddt_pli_full_matrix[target_i, model_i] = {
+ lddt_pli_full_matrix[target_i, model_i] = {
"lddt_pli": 0,
"lddt_pli_n_contacts": None,
"rmsd": rmsd,
@@ -485,13 +485,15 @@ class LigandScorer:
check_resnames=self.check_resnames)
# Save results?
- best_lddt = self._lddt_pli_full_matrix[
+ best_lddt = lddt_pli_full_matrix[
target_i, model_i]["lddt_pli"]
if global_lddt > best_lddt:
- self._lddt_pli_full_matrix[target_i, model_i].update({
+ lddt_pli_full_matrix[target_i, model_i].update({
"lddt_pli": global_lddt,
"lddt_pli_n_contacts": lddt_tot,
})
+ self._rmsd_full_matrix = rmsd_full_matrix
+ self._lddt_pli_full_matrix = lddt_pli_full_matrix
@staticmethod
def _find_ligand_assignment(mat1, mat2):
--
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