diff --git a/modules/mol/alg/tests/test_ligand_scoring.py b/modules/mol/alg/tests/test_ligand_scoring.py
index c2b2a762f4001747d8c977dca9b4d521aa59fea3..e06e64cfbe59ffa1039ad5d3be26d4bc5bed6fbf 100644
--- a/modules/mol/alg/tests/test_ligand_scoring.py
+++ b/modules/mol/alg/tests/test_ligand_scoring.py
@@ -1,8 +1,8 @@
import unittest, os, sys
+from functools import lru_cache
import numpy as np
-import ost
from ost import io, mol, geom
# check if we can import: fails if numpy or scipy not available
try:
@@ -13,22 +13,42 @@ except ImportError:
"networkx is missing. Ignoring test_ligand_scoring.py tests.")
sys.exit(0)
-#ost.PushVerbosityLevel(ost.LogLevel.Debug)
+
+def _GetTestfilePath(filename):
+ """Get the path to the test file given filename"""
+ return os.path.join('testfiles', filename)
+
+
+@lru_cache(maxsize=None)
+def _LoadMMCIF(filename):
+ path = _GetTestfilePath(filename)
+ ent, seqres = io.LoadMMCIF(path, seqres=True)
+ return ent
+
+
+@lru_cache(maxsize=None)
+def _LoadPDB(filename):
+ path = _GetTestfilePath(filename)
+ ent = io.LoadPDB(path)
+ return ent
+
+
+@lru_cache(maxsize=None)
+def _LoadEntity(filename):
+ path = _GetTestfilePath(filename)
+ ent = io.LoadEntity(path)
+ return ent
+
class TestLigandScoring(unittest.TestCase):
def test_extract_ligands_mmCIF(self):
"""Test that we can extract ligands from mmCIF files.
"""
- 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)
+ trg = _LoadMMCIF("1r8q.cif.gz")
+ mdl = _LoadMMCIF("P84080_model_02.cif.gz")
sc = LigandScorer(mdl, trg, None, None)
- # import ipdb; ipdb.set_trace()
- # import ost.mol.alg.scoring
- # scr = ost.mol.alg.scoring.Scorer(sc.model, sc.target)
- # scr.lddt
- # scr.local_lddt
assert len(sc.target_ligands) == 7
assert len(sc.model_ligands) == 1
@@ -39,8 +59,8 @@ class TestLigandScoring(unittest.TestCase):
"""Test that we can instantiate the scorer with ligands contained in
the target and model entity and given in a list.
"""
- 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)
+ trg = _LoadMMCIF("1r8q.cif.gz")
+ mdl = _LoadMMCIF("P84080_model_02.cif.gz")
# Pass entity views
trg_lig = [trg.Select("rname=MG"), trg.Select("rname=G3D")]
@@ -87,10 +107,10 @@ class TestLigandScoring(unittest.TestCase):
io.SaveEntity(lig_ent, "%s_ligand_%d.sdf" % (prefix, lig_num))
lig_num += 1
"""
- mdl = io.LoadPDB(os.path.join('testfiles', "P84080_model_02_nolig.pdb"))
- mdl_ligs = [io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))]
- trg = io.LoadPDB(os.path.join('testfiles', "1r8q_protein.pdb.gz"))
- trg_ligs = [io.LoadEntity(os.path.join('testfiles', "1r8q_ligand_%d.sdf" % i)) for i in range(7)]
+ mdl = _LoadPDB("P84080_model_02_nolig.pdb")
+ mdl_ligs = [_LoadEntity("P84080_model_02_ligand_0.sdf")]
+ trg = _LoadPDB("1r8q_protein.pdb.gz")
+ trg_ligs = [_LoadEntity("1r8q_ligand_%d.sdf" % i) for i in range(7)]
# Pass entities
sc = LigandScorer(mdl, trg, mdl_ligs, trg_ligs)
@@ -114,18 +134,18 @@ class TestLigandScoring(unittest.TestCase):
"""Test that we reject input if multiple ligands with the same chain
name/residue number are given.
"""
- mdl = io.LoadPDB(os.path.join('testfiles', "P84080_model_02_nolig.pdb"))
- mdl_ligs = [io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))]
- trg = io.LoadPDB(os.path.join('testfiles', "1r8q_protein.pdb.gz"))
- trg_ligs = [io.LoadEntity(os.path.join('testfiles', "1r8q_ligand_%d.sdf" % i)) for i in range(7)]
+ mdl = _LoadPDB("P84080_model_02_nolig.pdb")
+ mdl_ligs = [_LoadEntity("P84080_model_02_ligand_0.sdf")]
+ trg = _LoadPDB("1r8q_protein.pdb.gz")
+ trg_ligs = [_LoadEntity("1r8q_ligand_%d.sdf" % i) for i in range(7)]
# Reject identical model ligands
with self.assertRaises(RuntimeError):
sc = LigandScorer(mdl, trg, [mdl_ligs[0], mdl_ligs[0]], trg_ligs)
# Reject identical target ligands
- lig0 = trg_ligs[0]
- lig1 = trg_ligs[1]
+ lig0 = trg_ligs[0].Copy()
+ lig1 = trg_ligs[1].Copy()
ed1 = lig1.EditXCS()
ed1.RenameChain(lig1.chains[0], lig0.chains[0].name)
ed1.SetResidueNumber(lig1.residues[0], lig0.residues[0].number)
@@ -135,7 +155,7 @@ class TestLigandScoring(unittest.TestCase):
def test__ResidueToGraph(self):
"""Test that _ResidueToGraph works as expected
"""
- mdl_lig = io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))
+ mdl_lig = _LoadEntity("P84080_model_02_ligand_0.sdf")
graph = ligand_scoring._ResidueToGraph(mdl_lig.residues[0])
assert len(graph.edges) == 34
@@ -152,8 +172,8 @@ class TestLigandScoring(unittest.TestCase):
def test__ComputeSymmetries(self):
"""Test that _ComputeSymmetries works.
"""
- 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)
+ trg = _LoadMMCIF("1r8q.cif.gz")
+ mdl = _LoadMMCIF("P84080_model_02.cif.gz")
trg_mg1 = trg.FindResidue("E", 1)
trg_g3d1 = trg.FindResidue("F", 1)
@@ -168,7 +188,7 @@ class TestLigandScoring(unittest.TestCase):
assert len(sym) == 72
# Test that we can match ions read from SDF
- sdf_lig = io.LoadEntity(os.path.join('testfiles', "1r8q_ligand_0.sdf"))
+ sdf_lig = _LoadEntity("1r8q_ligand_0.sdf")
sym = ligand_scoring._ComputeSymmetries(trg_mg1, sdf_lig.residues[0], by_atom_index=True)
assert len(sym) == 1
@@ -195,8 +215,8 @@ class TestLigandScoring(unittest.TestCase):
def test_SCRMSD(self):
"""Test that SCRMSD works.
"""
- 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)
+ trg = _LoadMMCIF("1r8q.cif.gz")
+ mdl = _LoadMMCIF("P84080_model_02.cif.gz")
trg_mg1 = trg.FindResidue("E", 1)
trg_g3d1 = trg.FindResidue("F", 1)
@@ -240,8 +260,8 @@ class TestLigandScoring(unittest.TestCase):
def test__compute_scores(self):
"""Test that _compute_scores works.
"""
- 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)
+ trg = _LoadMMCIF("1r8q.cif.gz")
+ mdl = _LoadMMCIF("P84080_model_02.cif.gz")
mdl_lig = io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))
sc = LigandScorer(mdl, trg, [mdl_lig], None)
@@ -273,8 +293,8 @@ class TestLigandScoring(unittest.TestCase):
"""Test check_resname argument works
"""
# 4C0A has mismatching sequence and fails with check_resnames=True
- mdl_1r8q, _ = io.LoadMMCIF(os.path.join('testfiles', "1r8q.cif.gz"), seqres=True)
- trg_4c0a, _ = io.LoadMMCIF(os.path.join('testfiles', "4c0a.cif.gz"), seqres=True)
+ mdl_1r8q = _LoadMMCIF("1r8q.cif.gz")
+ trg_4c0a = _LoadMMCIF("4c0a.cif.gz")
mdl = mdl_1r8q.Select("cname=D or cname=F")
trg = trg_4c0a.Select("cname=C or cname=I")
@@ -290,8 +310,8 @@ class TestLigandScoring(unittest.TestCase):
"""Test that the scores are computed correctly
"""
# 4C0A has more ligands
- trg, trg_seqres = io.LoadMMCIF(os.path.join('testfiles', "1r8q.cif.gz"), seqres=True)
- trg_4c0a, _ = io.LoadMMCIF(os.path.join('testfiles', "4c0a.cif.gz"), seqres=True)
+ trg = _LoadMMCIF("1r8q.cif.gz")
+ trg_4c0a = _LoadMMCIF("4c0a.cif.gz")
sc = LigandScorer(trg, trg_4c0a, None, None, check_resnames=False)
expected_keys = {"J", "F"}
@@ -344,19 +364,18 @@ class TestLigandScoring(unittest.TestCase):
For RMSD, A: A results in a better chain mapping. However, C: A is a
better global chain mapping from an lDDT perspective (and lDDT-PLI).
"""
- 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)
- mdl_lig = io.LoadEntity(os.path.join('testfiles', "P84080_model_02_ligand_0.sdf"))
+ trg = _LoadMMCIF("1r8q.cif.gz")
+ mdl = _LoadMMCIF("P84080_model_02.cif.gz")
# Local by default
- sc = LigandScorer(mdl, trg, [mdl_lig], None)
- assert sc.rmsd_details["00001_L_2"][1]["chain_mapping"] == {'A': 'A'}
- assert sc.lddt_pli_details["00001_L_2"][1]["chain_mapping"] == {'C': 'A'}
+ sc = LigandScorer(mdl, trg, None, None)
+ assert sc.rmsd_details["L_2"][1]["chain_mapping"] == {'A': 'A'}
+ assert sc.lddt_pli_details["L_2"][1]["chain_mapping"] == {'C': 'A'}
# Global
- sc = LigandScorer(mdl, trg, [mdl_lig], None, global_chain_mapping=True)
- assert sc.rmsd_details["00001_L_2"][1]["chain_mapping"] == {'C': 'A'}
- assert sc.lddt_pli_details["00001_L_2"][1]["chain_mapping"] == {'C': 'A'}
+ sc = LigandScorer(mdl, trg, None, None, global_chain_mapping=True)
+ assert sc.rmsd_details["L_2"][1]["chain_mapping"] == {'C': 'A'}
+ assert sc.lddt_pli_details["L_2"][1]["chain_mapping"] == {'C': 'A'}
if __name__ == "__main__":