From 39e528b0e44256ab600ccc8a83b668a25184b1d3 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Mon, 16 Jan 2023 15:35:00 +0100
Subject: [PATCH] feat: SCHWED-5783 add networkx dependency
---
docker/Dockerfile | 1 +
modules/mol/alg/pymod/ligand_scoring.py | 82 +++++++++++++++++++-
modules/mol/alg/tests/test_ligand_scoring.py | 12 ++-
3 files changed, 91 insertions(+), 4 deletions(-)
diff --git a/docker/Dockerfile b/docker/Dockerfile
index 4a1a9bd26..1dce8f696 100644
--- a/docker/Dockerfile
+++ b/docker/Dockerfile
@@ -28,6 +28,7 @@ RUN apt-get update -y && apt-get install -y cmake \
python3-numpy \
python3-scipy \
python3-pandas \
+ python3-networkx \
doxygen \
swig \
clustalw \
diff --git a/modules/mol/alg/pymod/ligand_scoring.py b/modules/mol/alg/pymod/ligand_scoring.py
index 879a75e4c..d38873290 100644
--- a/modules/mol/alg/pymod/ligand_scoring.py
+++ b/modules/mol/alg/pymod/ligand_scoring.py
@@ -1,13 +1,22 @@
import os
+
+import numpy as np
+import networkx
+
from ost import mol
from ost.mol.alg import chain_mapping
-import numpy as np
class LigandScorer:
""" Helper class to access the various small molecule ligand (non polymer)
scores available from ost.mol.alg.
+ .. note ::
+ Extra requirements:
+
+ - Python modules `numpy` and `networkx` must be available
+ (e.g. use ``pip install numpy networkx``)
+
Mostly expects cleaned up structures (you can use the
:class:`~ost.mol.alg.scoring.Scorer` outputs for that).
@@ -215,5 +224,74 @@ class LigandScorer:
new_editor.UpdateICS()
return extracted_ligands
+ def _get_binding_sites(self, ligand, topn=100000):
+ """Find representations of the binding site of *ligand* in the model.
-__all__ = ["LigandScorer"]
+ Ignore other ligands and waters that may be in proximity.
+
+ :param ligand: Defines the binding site to identify.
+ :type ligand: :class:`~ost.mol.ResidueHandle`
+ """
+ if ligand.hash_code not in self._binding_sites:
+
+ # create view of reference binding site
+ ref_residues_hashes = set() # helper to keep track of added residues
+ for ligand_at in ligand.atoms:
+ close_atoms = self.target.FindWithin(ligand_at.GetPos(), self.radius)
+ for close_at in close_atoms:
+ # Skip other ligands and waters.
+ # This assumes that .IsLigand() is properly set on the entity's
+ # residues.
+ ref_res = close_at.GetResidue()
+ if not (ref_res.is_ligand or
+ ref_res.chem_type == mol.ChemType.WATERS):
+ h = ref_res.handle.GetHashCode()
+ if h not in ref_residues_hashes:
+ ref_residues_hashes.add(h)
+
+ # reason for doing that separately is to guarantee same ordering of
+ # residues as in underlying entity. (Reorder by ResNum seems only
+ # available on ChainHandles)
+ ref_bs = self.target.CreateEmptyView()
+ for ch in self.target.chains:
+ for r in ch.residues:
+ if r.handle.GetHashCode() in ref_residues_hashes:
+ ref_bs.AddResidue(r, mol.ViewAddFlag.INCLUDE_ALL)
+
+ # Find the representations
+ self._binding_sites[ligand.hash_code] = self.chain_mapper.GetRepr(
+ ref_bs, self.model, inclusion_radius=self.lddt_bs_radius,
+ topn=topn)
+ return self._binding_sites[ligand.hash_code]
+
+ def _compute_rmsd(self):
+ """"""
+ # Create the matrix
+ self._rmsd_matrix = np.empty((len(self.target_ligands),
+ len(self.model_ligands)), dtype=float)
+ for trg_ligand in self.target_ligands:
+ LogDebug("Compute RMSD for target ligand %s" % trg_ligand)
+
+ for binding_site in self._get_binding_sites(trg_ligand):
+ import ipdb; ipdb.set_trace()
+
+ for mdl_ligand in self.model_ligands:
+ LogDebug("Compute RMSD for model ligand %s" % mdl_ligand)
+
+ # Get symmetry graphs
+ model_graph = model_ligand.spyrmsd_mol.to_graph()
+ target_graph = target_ligand.struct_spyrmsd_mol.to_graph()
+ pass
+
+
+def ResidueToGraph(residue):
+ """Return a NetworkX graph representation of the residue."""
+ nxg = networkx.Graph()
+ nxg.add_nodes_from([a.name for a in residue.atoms], element=[a.element for a in residue.atoms])
+ # 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.
+ nxg.add_edges_from([(b.first.name, b.second.name) for a in residue.atoms for b in a.GetBondList()])
+ return nxg
+
+
+__all__ = ["LigandScorer", "ResidueToGraph"]
diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index ed8cbf98b..baf8b2bf6 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -5,8 +5,8 @@ from ost import io, mol
try:
from ost.mol.alg.ligand_scoring import *
except ImportError:
- print("Failed to import ligand_scoring.py. Happens when numpy or scipy " \
- "missing. Ignoring test_ligand_scoring.py tests.")
+ print("Failed to import ligand_scoring.py. Happens when numpy, scipy or "
+ "networkx is missing. Ignoring test_ligand_scoring.py tests.")
sys.exit(0)
@@ -114,6 +114,14 @@ class TestLigandScoring(unittest.TestCase):
with self.assertRaises(RuntimeError):
sc = LigandScorer(mdl, trg, mdl_ligs, [lig0, lig1])
+ def test_ResidueToGraph(self):
+ """Test that ResidueToGraph works as expected
+ """
+ mdl_lig = io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))
+
+ graph = ResidueToGraph(mdl_lig.residues[0])
+ assert len(graph.edges) == 34
+ assert len(graph.nodes) == 32
if __name__ == "__main__":
--
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