From 896a60cc827d038983e85fa02764b4fe01bd0774 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Tue, 24 Jan 2023 17:29:05 +0100
Subject: [PATCH] fix: SCHWED-5783 add bonds to copied ligand
---
modules/mol/alg/pymod/ligand_scoring.py | 5 +++++
modules/mol/alg/tests/test_ligand_scoring.py | 5 +++--
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 2149af916..d52fbc60c 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -258,6 +258,11 @@ class LigandScorer:
new_chain = new_editor.InsertChain(handle.chain.name)
# Add the residue with its original residue number
new_res = new_editor.AppendResidue(new_chain, handle, deep=True)
+ for old_atom in handle.atoms:
+ for old_bond in old_atom.bonds:
+ new_first = new_res.FindAtom(old_bond.first.name)
+ new_second = new_res.FindAtom(old_bond.second.name)
+ new_editor.Connect(new_first, new_second)
return new_res
def _process_ligand_residue(res):
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 78f4b1275..4bff9e812 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -232,7 +232,8 @@ class TestLigandScoring(unittest.TestCase):
"""
trg, trg_seqres = io.LoadMMCIF(os.path.join('testfiles', "1r8q.cif.gz"), seqres=True)
mdl, mdl_seqres = io.LoadMMCIF(os.path.join('testfiles', "P84080_model_02.cif.gz"), seqres=True)
- sc = LigandScorer(mdl, trg, None, None)
+ mdl_lig = io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))
+ sc = LigandScorer(mdl, trg, [mdl_lig], None)
# Note: expect warning about Binding site of H.ZN1 not mapped to the model
sc._compute_scores()
@@ -246,7 +247,7 @@ class TestLigandScoring(unittest.TestCase):
[np.inf],
[np.inf],
[0.29399303],
- [np.inf]]))
+ [np.inf]]), decimal=5)
# Check lDDT-PLI
self.assertEqual(sc.lddt_pli_matrix.shape, (7, 1))
--
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