From 244eee73961a4950675182424c4b654e5aa4958b Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavalias-github@xavier.robin.name>
Date: Mon, 30 Jan 2023 16:01:43 +0100
Subject: [PATCH] refactor: don't expose graphs
Reason is, it's unclear if they are useful anywhere else
---
modules/mol/alg/pymod/ligand_scoring.py | 12 ++++++------
modules/mol/alg/tests/test_ligand_scoring.py | 4 ++--
2 files changed, 8 insertions(+), 8 deletions(-)
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 5fd5aa78d..ff0fbfb78 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -725,7 +725,7 @@ class LigandScorer:
return self._lddt_pli_details
-def ResidueToGraph(residue, by_atom_index=False):
+def _ResidueToGraph(residue, by_atom_index=False):
"""Return a NetworkX graph representation of the residue.
:param residue: the residue from which to derive the graph
@@ -738,12 +738,12 @@ def ResidueToGraph(residue, by_atom_index=False):
:type by_atom_index: :class:`bool`
:rtype: :class:`~networkx.classes.graph.Graph`
- Nodes are labeled with the Atom's :attr:`~ost.mol.AtomHandle.mass`.
+ Nodes are labeled with the Atom's lowercase :attr:`~ost.mol.AtomHandle.element`.
"""
nxg = networkx.Graph()
for atom in residue.atoms:
- nxg.add_node(atom.name, element=atom.mass)
+ nxg.add_node(atom.name, element=atom.element.lower())
# This will list all edges twice - once for every atom of the pair.
# But as of NetworkX 3.0 adding the same edge twice has no effect, so we're good.
@@ -844,8 +844,8 @@ def _ComputeSymmetries(model_ligand, target_ligand, substructure_match=False,
"""
# Get the Graphs of the ligands
- model_graph = ResidueToGraph(model_ligand, by_atom_index=by_atom_index)
- target_graph = ResidueToGraph(target_ligand, by_atom_index=by_atom_index)
+ model_graph = _ResidueToGraph(model_ligand, by_atom_index=by_atom_index)
+ target_graph = _ResidueToGraph(target_ligand, by_atom_index=by_atom_index)
if not networkx.is_connected(model_graph):
raise RuntimeError("Disconnected graph for model ligand %s" % model_ligand)
@@ -891,4 +891,4 @@ class NoSymmetryError(Exception):
pass
-__all__ = ["LigandScorer", "ResidueToGraph", "SCRMSD", "NoSymmetryError"]
+__all__ = ["LigandScorer", "SCRMSD", "NoSymmetryError"]
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index 1b2d1b244..37aa4c514 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -137,13 +137,13 @@ class TestLigandScoring(unittest.TestCase):
"""
mdl_lig = io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))
- graph = _ResidueToGraph(mdl_lig.residues[0])
+ graph = ligand_scoring._ResidueToGraph(mdl_lig.residues[0])
assert len(graph.edges) == 34
assert len(graph.nodes) == 32
# Check an arbitrary node
assert [a for a in graph.adj["14"].keys()] == ["13", "29"]
- graph = _ResidueToGraph(mdl_lig.residues[0], by_atom_index=True)
+ graph = ligand_scoring._ResidueToGraph(mdl_lig.residues[0], by_atom_index=True)
assert len(graph.edges) == 34
assert len(graph.nodes) == 32
# Check an arbitrary node
--
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