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import unittest, os, sys
import ost
from ost import conop
import subprocess
import tempfile
import warnings
def CreateComplib(compound_dict_path, chemlib_out_path, extra_args=None):
prefix_path = ost.GetPrefixPath()
chemdict_tool_path = os.path.join(prefix_path, "bin", "chemdict_tool")
if not os.path.exists(chemdict_tool_path):
raise RuntimeError("Expect chemdict_tool:", chemdict_tool_path)
cmd = [chemdict_tool_path, "create", compound_dict_path, chemlib_out_path, "-q"]
if extra_args:
cmd += extra_args
subprocess.run(cmd, stdout=subprocess.PIPE, check=True)
class TestCompLib(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.tmp_dir = tempfile.TemporaryDirectory()
compound_dict_path = os.path.join("testfiles", "test_compounds.cif")
complib_path = os.path.join(cls.tmp_dir.name, "test_complib.dat")
CreateComplib(compound_dict_path, complib_path)
cls.complib = conop.CompoundLib.Load(complib_path)
@classmethod
def tearDownClass(cls):
cls.tmp_dir.cleanup()
def test_three_vs_five_letter_code(self):
complib = self.complib
comp_001 = complib.FindCompound("001")
comp_A1LU6 = complib.FindCompound("A1LU6")
comp_yolo = complib.FindCompound("yolo")
self.assertFalse(comp_001 is None)
self.assertFalse(comp_A1LU6 is None)
self.assertTrue(comp_yolo is None)
def test_smiles(self):
complib = self.complib
comp_001 = complib.FindCompound("001")
self.assertTrue(comp_001.smiles == "COc1cc(cc(c1OC)OC)C(C(=O)N2CCCC[C@H]2C(=O)O[C@@H](CCCc3ccccc3)CCCc4cccnc4)(F)F")
def test_charges(self):
complib = self.complib
comp_nh4 = complib.FindCompound("NH4")
self.assertTrue(comp_nh4.atom_specs[0].charge == 1)
self.assertTrue(comp_nh4.atom_specs[1].charge == 0)
def test_obsolete(self):
complib = self.complib
comp_ox = complib.FindCompound("OX")
# First test that we do get data
self.assertTrue(comp_ox.smiles == "O")
# Now the obsolete part
self.assertTrue(comp_ox.obsolete)
self.assertTrue(comp_ox.replaced_by == "O")
# Ensure not everything is obsolete
comp_001 = complib.FindCompound("001")
self.assertFalse(comp_001.obsolete)
def test_default_lib_version(self):
compound_lib = conop.GetDefaultLib()
if compound_lib is None:
warnings.warn("Compound library not available. Some functionality may not work as expected.")
else:
lib_version = compound_lib.GetOSTVersionUsed()
if lib_version < ost.__version__:
warnings.warn("Using old version of the compound library: %s" % lib_version)
def test_ignore_reserved(self):
compound_dict_path = os.path.join("testfiles", "test_compounds.cif")
complib_no_reserved_path = os.path.join(self.tmp_dir.name, "test_complib_no_reserved.dat")
CreateComplib(compound_dict_path, complib_no_reserved_path, ["-i"])
complib_no_reserved = conop.CompoundLib.Load(complib_no_reserved_path)
# 01-98 are reserved
assert self.complib.FindCompound("98") is not None
assert complib_no_reserved.FindCompound("98") is None
# DRG, INH and LIG are reserved
assert self.complib.FindCompound("DRG") is not None
assert complib_no_reserved.FindCompound("DRG") is None
assert self.complib.FindCompound("INH") is not None
assert complib_no_reserved.FindCompound("INH") is None
assert self.complib.FindCompound("LIG") is not None
assert complib_no_reserved.FindCompound("LIG") is None
# OX is obsolete but not reserved
assert complib_no_reserved.FindCompound("OX") is not None
# 00, 000, 001, 010, 986, 98B are not reserved
assert complib_no_reserved.FindCompound("00") is not None
assert complib_no_reserved.FindCompound("000") is not None
assert complib_no_reserved.FindCompound("001") is not None
assert complib_no_reserved.FindCompound("010") is not None
assert complib_no_reserved.FindCompound("986") is not None
assert complib_no_reserved.FindCompound("98B") is not None
def test_ignore_obsolete(self):
compound_dict_path = os.path.join("testfiles", "test_compounds.cif")
complib_no_obsolete_path = os.path.join(self.tmp_dir.name, "test_complib_no_obsolete.dat")
CreateComplib(compound_dict_path, complib_no_obsolete_path, ["-o"])
complib_no_obsolete = conop.CompoundLib.Load(complib_no_obsolete_path)
# 01-98, DRG, INH and LIG are reserved but not obsolete
assert complib_no_obsolete.FindCompound("98") is not None
assert complib_no_obsolete.FindCompound("DRG") is not None
assert complib_no_obsolete.FindCompound("INH") is not None
assert complib_no_obsolete.FindCompound("LIG") is not None
# OX is obsolete
assert complib_no_obsolete.FindCompound("OX") is None
def test_bird(self):
""" the test file in test_compounds.cif contains two entries from
BIRD:
- PRD_900116 is not in a compound format and should not be added
to the compound lib.
- PRDCC_900116 is in a valid format and should be read in
"""
complib = self.complib
# PRD_900116 not added
comp = complib.FindCompound("PRD_900116")
self.assertIsNone(comp)
# PRD_900116 is added
comp = complib.FindCompound("PRDCC_900116")
self.assertIsNotNone(comp)
self.assertEqual(
comp.smiles,
"C1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2CO[C@H]([C@@H]([C@H]2O)O)O)O)O)O")
# The release flag is REF_ONLY and compound should not be marked as
# obsolete
self.assertFalse(comp.obsolete)
# Contains atoms and bonds
self.assertEqual(len(comp.atom_specs), 37)
self.assertEqual(len(comp.bond_specs), 38)
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
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