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from ost import io,mol,geom
import unittest
import os
import random
class TestConvenientSuperpose(unittest.TestCase):
def setUp(self):
pass
def assertEqualAtomOrder(self, view1, view2):
self.assertEqual(len(view1.atoms),len(view2.atoms))
for a1, a2 in zip(view1.atoms, view2.atoms):
self.assertEqual(a1.element, a2.element)
self.assertTrue(geom.Equal(a1.pos, a2.pos))
def testAssertion(self):
ent1_ent = io.LoadEntity(os.path.join("testfiles","1aho.pdb"))
ent1_view = ent1_ent.Select("")
self.assertEqualAtomOrder(ent1_ent, ent1_ent)
self.assertEqualAtomOrder(ent1_ent, ent1_view)
self.assertEqualAtomOrder(ent1_view, ent1_ent)
self.assertEqualAtomOrder(ent1_view, ent1_view)
self.assertRaises(AssertionError, self.assertEqualAtomOrder, ent1_view.Select("ele!=H"), ent1_view)
def testCorrectlyOrdered(self):
ent1_ent = io.LoadEntity(os.path.join("testfiles","1aho.pdb"))
ent1_view = ent1_ent.Select("")
## test MatchResidueByNum
view1, view2 = mol.alg.MatchResidueByNum(ent1_ent, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent1_view, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent1_ent, ent1_view)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent1_view, ent1_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByIdx
view1, view2 = mol.alg.MatchResidueByIdx(ent1_ent, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent1_view, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent1_ent, ent1_view)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent1_view, ent1_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByGlobalAln
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_ent, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_view, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_ent, ent1_view)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_view, ent1_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByLocalAln
view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_ent, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_view, ent1_ent)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_ent, ent1_view)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_view, ent1_view)
self.assertEqualAtomOrder(view1, view2)
def testMissingFirstAtom(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_missing = ent_view.Select("not (cname=A and rnum=1 and aname=N)")
## test MatchResidueByNum
view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByIdx
view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByGlobalAln
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByLocalAln
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
def testMissingManyAtoms(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_missing = ent_view.Select("not (cname=A and rnum=3,19,32 and aname=CB,CA,CD)")
## test MatchResidueByNum
view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByIdx
view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByGlobalAln
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByLocalAln
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
def testMissingFirstResidue(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_missing = ent_view.Select("not (cname=A and rnum=1)")
## test MatchResidueByNum
view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByGlobalAln
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByLocalAln
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
def testMissingHydrogens(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_missing = ent_view.Select("ele!=H")
## test MatchResidueByNum
view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByIdx
view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
self.assertEqualAtomOrder(view1, view2)
def testWrongAtomOrder(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_wrong = ent_view.CreateEmptyView()
for c in ent_view.chains:
ent_view_wrong.AddChain(c)
for r in c.residues:
ent_view_wrong.AddResidue(r)
atoms = list(r.atoms)
random.shuffle(atoms)
for a in atoms:
ent_view_wrong.AddAtom(a)
## test MatchResidueByNum
view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_wrong)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByIdx
view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_wrong)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByIdx(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByGlobalAln
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_wrong)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
## test MatchResidueByLocalAln
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_wrong)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
def testWrongResidueOrder(self):
ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
ent_view_wrong = ent_view.CreateEmptyView()
for c in ent_view.chains:
ent_view_wrong.AddChain(c)
residues = list(c.residues)
random.shuffle(residues)
for r in residues:
ent_view_wrong.AddResidue(r)
for a in r.atoms:
av=ent_view_wrong.AddAtom(a)
## test MatchResidueByNum
view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_wrong)
self.assertEqualAtomOrder(view1, view2)
view1, view2 = mol.alg.MatchResidueByNum(ent_view_wrong, ent_view)
self.assertEqualAtomOrder(view1, view2)
def testPeptideFilter(self):
# check that CA only chains are ok and ligand chains are skipped
ent_1_full = io.LoadPDB(os.path.join("testfiles", "5tglA.pdb"))
ent_2_full = io.LoadPDB(os.path.join("testfiles", "5tglA_modified.pdb"))
exp_atom_count = 253
# check CA-only chain
ent_1 = ent_1_full.Select("cname=A")
ent_2 = ent_2_full.Select("cname=A")
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_1, ent_2)
self.assertEqual(view1.atom_count, exp_atom_count)
self.assertEqual(view2.atom_count, exp_atom_count)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_1, ent_2)
self.assertEqual(view1.atom_count, exp_atom_count)
self.assertEqual(view2.atom_count, exp_atom_count)
# check ligand chain
ent_1_ligand = ent_1_full.Select("cname='_'")
ent_2_ligand = ent_2_full.Select("cname='_'")
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_1_ligand, ent_2_ligand)
self.assertEqual(view1.atom_count, 0)
self.assertEqual(view2.atom_count, 0)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_1_ligand, ent_2_ligand)
self.assertEqual(view1.atom_count, 0)
self.assertEqual(view2.atom_count, 0)
# check both together
view1, view2 = mol.alg.MatchResidueByLocalAln(ent_1_full, ent_2_full)
self.assertEqual(view1.atom_count, exp_atom_count)
self.assertEqual(view2.atom_count, exp_atom_count)
view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_1_full, ent_2_full)
self.assertEqual(view1.atom_count, exp_atom_count)
self.assertEqual(view2.atom_count, exp_atom_count)
# try case where local alignment fails
ev1 = ent_1.Select('rindex<2') # seq = GI
ev2 = ent_2.Select('rindex=2:3') # seq = RA
view1, view2 = mol.alg.MatchResidueByLocalAln(ev1, ev2)
self.assertEqual(view1.atom_count, 0)
self.assertEqual(view2.atom_count, 0)
if __name__ == "__main__":
from ost import testutils
testutils.RunTests()
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