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import unittest
from ost import *
import subprocess
class TestSDF(unittest.TestCase):
def setUp(self):
pass
def test_LoadEntity(self):
ent = io.LoadSDF('testfiles/sdf/compound.sdf')
self.assertEqual(len(ent.chains), 4)
self.assertEqual(len(ent.atoms), 180)
self.assertEqual(len(ent.bonds), 188)
def test_LoadEntity_crlf(self):
ent = io.LoadSDF('testfiles/sdf/6d5w_rank1_crlf.sdf.gz')
self.assertEqual(len(ent.atoms), 21)
self.assertEqual(len(ent.bonds), 24)
def test_Charge(self):
ent = io.LoadSDF('testfiles/sdf/simple.sdf')
self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "6").charge, 0)
# Write and read charges properly
for chg in range(-3, 4):
ent.FindAtom("00001_Simple Ligand", 1, "6").charge = chg
sdf_str = io.EntityToSDFStr(ent)
ent = io.SDFStrToEntity(sdf_str)
self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "6").charge, chg)
# Only -3 to +3 is supported
# If M CHG is implemented the following tests can be removed
with self.assertRaises(Exception):
ent.FindAtom("00001_Simple Ligand", 1, "6").charge = 4
io.EntityToSDFStr(ent)
with self.assertRaises(Exception):
ent.FindAtom("00001_Simple Ligand", 1, "6").charge = -4
io.EntityToSDFStr(ent)
def test_MChg(self):
ent = io.LoadSDF('testfiles/sdf/m_chg.sdf')
n_at = ent.FindAtom("00001_Simple Ligand", 1, "1")
self.assertEqual(n_at.charge, 1)
cl_at = ent.FindAtom("00001_Simple Ligand", 1, "6")
self.assertEqual(cl_at.charge, -1)
# Charge from atom line is ignored
o_at = ent.FindAtom("00001_Simple Ligand", 1, "3")
self.assertEqual(o_at.charge, 0)
def test_fault_tolerant(self):
"""This file has a "dative" bond (type = 9).
This is a non-standard extension from RDKit which should go through only
in fault tolerant mode"""
with self.assertRaises(Exception):
ent = io.LoadSDF('testfiles/sdf/dative_bond.sdf')
# Directly with fault_tolerant
PushVerbosityLevel(-1) # Expect message at Error level
ent = io.LoadSDF('testfiles/sdf/dative_bond.sdf', fault_tolerant=True)
PopVerbosityLevel()
self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "5").bonds[0].bond_order, 9)
# Sloppy profile
PushVerbosityLevel(-1) # Expect message at Error level
ent = io.LoadSDF('testfiles/sdf/dative_bond.sdf', profile="SLOPPY")
PopVerbosityLevel()
self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "5").bonds[0].bond_order, 9)
# Sloppy profile set as default
old_profile = io.profiles['DEFAULT'].Copy()
io.profiles['DEFAULT'] = "SLOPPY"
PushVerbosityLevel(-1) # Expect message at Error level
ent = io.LoadSDF('testfiles/sdf/dative_bond.sdf')
PopVerbosityLevel()
self.assertEqual(ent.FindAtom("00001_Simple Ligand", 1, "5").bonds[0].bond_order, 9)
# Test that a restored default profile has fault_tolerant again
io.profiles['DEFAULT'] = old_profile
with self.assertRaises(Exception):
ent = io.LoadSDF('testfiles/sdf/dative_bond.sdf')
def test_bond_types(self):
"""Test that bond types are properly converted to V2000 format."""
v3000_ent = io.LoadSDF('testfiles/sdf_v3000/bcl.sdf')
# Find the magnesium atom:
mg_at = v3000_ent.FindAtom("00001_BCL", 1, "12")
for bond in mg_at.bonds:
if bond.first == v3000_ent.FindAtom("00001_BCL", 1, "11"):
self.assertEqual(bond.bond_order, 9)
break
else:
raise Exception("Magnesium atom partner (N 11) not found")
# Now we know we have a coordination bond, we can write it out to SDFV2000:
PushVerbosityLevel(0) # Expect message at Warning level
v2000_str = io.EntityToSDFStr(v3000_ent)
PopVerbosityLevel()
# We can read it without fault_tolerant
v2000_ent = io.SDFStrToEntity(v2000_str)
# Mg atom has been converted to a single bond:
v2000_mg_at = v2000_ent.FindAtom("00001_BCL", 1, "12")
for bond in v2000_mg_at.bonds:
if bond.first == v2000_ent.FindAtom("00001_BCL", 1, "11"):
self.assertEqual(bond.bond_order, 1)
break
else:
raise Exception("Magnesium atom partner (N 11) not found")
if __name__== '__main__':
from ost import testutils
testutils.RunTests()
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