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import sys
import unittest
from ost import geom, conop, io
from ost.conop import cleanup
class TestCleanUp(unittest.TestCase):
def setUp(self):
self.comp_lib = conop.GetDefaultLib()
io.profiles['DEFAULT'].processor = conop.RuleBasedProcessor(self.comp_lib)
self.ent = io.LoadPDB("sample_test_cleanup.pdb")
self.ent_no_wat = io.LoadPDB("sample_nowater.pdb")
self.ent_no_lig = io.LoadPDB("sample_noligands.pdb")
def testStripWater(self):
self.new_ent = cleanup.Cleanup(self.ent, strip_water=True, canonicalize=False, remove_ligands=False)
self.assertEqual( self.new_ent.residue_count, self.ent_no_wat.residue_count )
self.assertTrue( self.new_ent.residues[0].IsValid() )
self.assertEqual( self.new_ent.residues[0].qualified_name, self.ent_no_wat.residues[0].qualified_name)
self.assertTrue( self.new_ent.residues[1].IsValid() )
self.assertEqual( self.new_ent.residues[1].qualified_name, self.ent_no_wat.residues[1].qualified_name)
self.assertTrue( self.new_ent.residues[2].IsValid() )
self.assertEqual( self.new_ent.residues[2].qualified_name, self.ent_no_wat.residues[2].qualified_name)
self.assertTrue( self.new_ent.residues[3].IsValid() )
self.assertEqual( self.new_ent.residues[3].qualified_name, self.ent_no_wat.residues[3].qualified_name)
self.assertTrue( self.new_ent.residues[4].IsValid() )
self.assertEqual( self.new_ent.residues[4].qualified_name, self.ent_no_wat.residues[4].qualified_name)
self.assertTrue( self.new_ent.residues[5].IsValid() )
self.assertEqual( self.new_ent.residues[5].qualified_name, self.ent_no_wat.residues[5].qualified_name)
self.assertTrue( self.new_ent.residues[6].IsValid() )
self.assertEqual( self.new_ent.residues[6].qualified_name, self.ent_no_wat.residues[6].qualified_name)
self.assertTrue( self.new_ent.residues[7].IsValid() )
self.assertEqual( self.new_ent.residues[7].qualified_name, self.ent_no_wat.residues[7].qualified_name)
def testCanonicalize(self):
self.new_ent = cleanup.Cleanup(self.ent, strip_water=False, canonicalize=True, remove_ligands=False)
#standard residue must be the same
self.gly = self.ent.residues[1]
self.new_gly = self.new_ent.residues[1]
self.assertTrue(self.new_gly.IsValid())
self.assertTrue(self.new_gly.IsPeptideLinking())
self.assertEqual(self.gly.atom_count, self.new_gly.atom_count)
#TEMP del sidechain of incomplete residue and OXT if present
self.new_cys = self.new_ent.residues[4]
self.new_cys_atoms = set([atm.name for atm in self.new_cys.atoms])
self.assertEqual( len(self.new_cys_atoms), 4, msg = repr(self.new_cys_atoms))
self.assertTrue( "CB" in self.new_cys_atoms)
self.assertTrue( "CA" in self.new_cys_atoms)
self.assertTrue( "C" in self.new_cys_atoms)
self.assertFalse( "OXT" in self.new_cys_atoms)
self.assertTrue( "N" in self.new_cys_atoms)
#test replacement of atoms
self.mse = self.ent.residues[0]
# self.assertTrue( self.mse.IsValid())
# self.assertTrue( self.mse.IsPeptideLinking())
self.sel = self.mse.FindAtom("SE")
# self.assertTrue( self.sel.IsValid())
self.met = self.new_ent.residues[0]
self.assertTrue(self.met.IsValid())
self.assertEqual(self.mse.atom_count, self.met.atom_count)
self.assertEqual(self.met.name, "MET")
self.assertEqual(self.met.one_letter_code, "M")
self.assertTrue(self.met.IsPeptideLinking())
self.sul = self.met.FindAtom("SD")
self.assertTrue(self.sul.IsValid())
self.assertTrue(geom.Equal(self.sul.pos,self.sel.pos), msg = "sul:%s sel:%s"%(str(self.sul.pos), str(self.sel.pos)) )
self.assertEqual(self.sul.element, "S")
# self.AssertTrue( sul.mass == conop.Conopology.Instance().GetDefaultAtomMass("S"))
# self.AssertTrue( sul.radius == conop.Conopology.Instance().GetDefaultAtomRadius("S"))
for atm in self.met.atoms:
self.assertFalse( atm.is_hetatom)
#test addition
self.mly = self.ent.residues[2]
# self.assertTrue( self.mly.IsValid())
# self.assertTrue( self.mly.IsPeptideLinking())
self.new_lys = self.new_ent.residues[2]
self.assertTrue(self.new_lys.IsValid())
self.assertTrue(self.new_lys.IsPeptideLinking())
self.assertEqual(self.new_lys.name, "LYS")
self.assertEqual(self.new_lys.one_letter_code, "K")
self.new_lys_atoms = set([atm.name for atm in self.new_lys.atoms])
self.canon_lys = self.comp_lib.FindCompound("LYS")
self.canon_lys_atoms = set([atom.name for atom in self.canon_lys.atom_specs
if atom.element != "H" and atom.element != "D" and not atom.is_leaving ])
self.assertEqual(self.canon_lys_atoms, self.new_lys_atoms)
self.assertFalse(self.canon_lys_atoms - self.new_lys_atoms)
self.assertFalse(self.new_lys_atoms - self.canon_lys_atoms) #test the reverse
for atm in self.new_lys.atoms:
self.assertFalse( atm.is_hetatom)
#deletions
self.dha = self.ent.residues[3]
# self.assertTrue( self.dha.IsValid())
# self.assertTrue( self.dha.IsPeptideLinking())
self.new_ser = self.new_ent.residues[3]
self.assertTrue(self.new_ser.IsValid())
self.assertTrue(self.new_ser.IsPeptideLinking())
self.assertEqual(self.new_ser.name, "SER")
self.assertEqual(self.new_ser.one_letter_code, "S")
self.new_ser_atoms = set([atm.name for atm in self.new_ser.atoms])
self.canon_ser = self.comp_lib.FindCompound("SER")
self.canon_ser_atoms = set([atom.name for atom in self.canon_ser.atom_specs
if atom.element != "H" and atom.element != "D" and not atom.is_leaving ])
#TEMP
self.assertEqual( len(self.new_ser_atoms), 5)
self.assertTrue( "CB" in self.new_ser_atoms)
self.assertTrue( "CA" in self.new_ser_atoms)
self.assertTrue( "C" in self.new_ser_atoms)
self.assertTrue( "O" in self.new_ser_atoms)
self.assertTrue( "N" in self.new_ser_atoms)
#AFTER TEMP
#self.assertEqual( self.canon_ser_atoms, self.new_ser_atoms)
#self.assertFalse(self.canon_ser_atoms - self.new_ser_atoms)
#self.assertFalse(self.new_ser_atoms - self.canon_ser_atoms) #test the reverse
for atm in self.new_ser.atoms:
self.assertFalse( atm.is_hetatom)
#test deletion of whole residue
self.assertEqual(self.ent.residues[5].chem_class, "D_PEPTIDE_LINKING")
self.assertNotEqual(self.new_ent.residues[5].name, "DAL")
self.assertNotEqual(self.ent.residue_count, self.new_ent.residue_count)
def testRemoveLigands(self):
self.new_ent = cleanup.Cleanup(self.ent, strip_water=False, canonicalize=False, remove_ligands=True)
self.assertEqual(self.new_ent.residue_count, self.ent_no_lig.residue_count )
#MSE
self.assertTrue(self.new_ent.residues[0].IsValid() )
self.assertEqual(self.new_ent.residues[0].qualified_name, self.ent_no_lig.residues[0].qualified_name)
self.assertTrue(self.new_ent.residues[0].IsPeptideLinking())
self.assertTrue(self.new_ent.residues[0].atoms[0].is_hetatom)
#GLY
self.assertTrue(self.new_ent.residues[1].IsValid() )
self.assertEqual(self.new_ent.residues[1].qualified_name, self.ent_no_lig.residues[1].qualified_name)
self.assertTrue(self.new_ent.residues[1].IsPeptideLinking())
self.assertFalse(self.new_ent.residues[1].atoms[0].is_hetatom)
#MLY
self.assertTrue(self.new_ent.residues[2].IsValid() )
self.assertEqual(self.new_ent.residues[2].qualified_name, self.ent_no_lig.residues[2].qualified_name)
self.assertTrue(self.new_ent.residues[2].IsPeptideLinking())
self.assertTrue(self.new_ent.residues[2].atoms[0].is_hetatom)
#DHA
self.assertTrue(self.new_ent.residues[3].IsValid() )
self.assertEqual(self.new_ent.residues[3].qualified_name, self.ent_no_lig.residues[3].qualified_name)
self.assertTrue(self.new_ent.residues[3].IsPeptideLinking())
self.assertTrue(self.new_ent.residues[3].atoms[0].is_hetatom)
#CYS
self.assertTrue(self.new_ent.residues[4].IsValid() )
self.assertEqual(self.new_ent.residues[4].qualified_name, self.ent_no_lig.residues[4].qualified_name)
self.assertTrue(self.new_ent.residues[4].IsPeptideLinking())
self.assertFalse(self.new_ent.residues[4].atoms[0].is_hetatom)
#DAL
self.assertTrue(self.new_ent.residues[5].IsValid() )
self.assertEqual(self.new_ent.residues[5].qualified_name, self.ent_no_lig.residues[5].qualified_name)
self.assertTrue(self.new_ent.residues[5].IsPeptideLinking())
self.assertTrue(self.new_ent.residues[5].atoms[0].is_hetatom)
#HOH
self.assertTrue(self.new_ent.residues[6].IsValid() )
self.assertEqual(self.new_ent.residues[6].qualified_name, self.ent_no_lig.residues[6].qualified_name)
self.assertFalse(self.new_ent.residues[6].IsPeptideLinking()) # here assertFalse instead of assertTrue
self.assertTrue(self.new_ent.residues[6].atoms[0].is_hetatom)
if __name__ == "__main__":
from ost import testutils
if testutils.DefaultCompoundLibIsSet():
testutils.RunTests()
else:
print('No compound library available. Ignoring test_cleanup.py tests.')
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