import unittest from ost import io, mol class TestNonStandard(unittest.TestCase): def test_fastModified(self): # phoshoserine: test if we correctly strip off modifications tpl=io.LoadPDB('testfiles/sep.pdb') new_hdl=mol.CreateEntity(); ed=new_hdl.EditXCS() c=ed.InsertChain('A') ed.AppendResidue(c, 'SER') err, has_cbeta=mol.alg.CopyConserved(tpl.residues[0], new_hdl.residues[0], ed) self.assertTrue(err) self.assertTrue(has_cbeta) residues=new_hdl.residues self.assertEqual(len(residues), 1) self.assertEqual(len(residues[0].atoms), 6) self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "N").IsValid()) self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "CA").IsValid()) self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "C").IsValid()) self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "O").IsValid()) self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "CB").IsValid()) self.assertTrue(new_hdl.FindAtom("A", mol.ResNum(1), "OG").IsValid()) def test_CBeta(self): # test if the dst residues contain cbeta, unless they are glycines tpl=io.LoadPDB('testfiles/cbeta.pdb') new_hdl=mol.CreateEntity(); ed=new_hdl.EditXCS() c=ed.InsertChain('A') ed.AppendResidue(c, 'MET') ed.AppendResidue(c, 'GLY') ed.AppendResidue(c, 'GLY') ed.AppendResidue(c, 'HIS') err, has_cbeta=mol.alg.CopyConserved(tpl.residues[0], new_hdl.residues[0], ed) self.assertTrue(has_cbeta) self.assertTrue(err) err, has_cbeta=mol.alg.CopyConserved(tpl.residues[1], new_hdl.residues[1], ed) self.assertFalse(has_cbeta) self.assertTrue(err) err, has_cbeta=mol.alg.CopyConserved(tpl.residues[2], new_hdl.residues[2], ed) self.assertFalse(has_cbeta) self.assertTrue(err) err, has_cbeta=mol.alg.CopyConserved(tpl.residues[3], new_hdl.residues[3], ed) self.assertTrue(has_cbeta) self.assertTrue(err) residues=new_hdl.residues self.assertEqual(len(residues), 4) self.assertTrue(residues[0].FindAtom("CB").IsValid()) self.assertFalse(residues[1].FindAtom("CB").IsValid()) self.assertFalse(residues[2].FindAtom("CB").IsValid()) self.assertTrue(residues[3].FindAtom("CB").IsValid()) def test_CBetaFail(self): # make sure that we can handle cases where CB reconstruction fails # NOTES: # - SNN is (since June 2011) labeled as a modified ASN but has a weird # backbone structure without any overlap in atom names with ASN # -> we hence expect it to a) always fall back to CopyNonConserved # and b) fail to copy any atoms (and hence also fail to) # - SNN also removes N of following residue which is expected to have an # incomplete backbone which would make it impossible to create a CB pos. # source of file: residues A.198 and A.199 from PDB ID 2YHW tpl = io.LoadPDB('testfiles/cbeta_fail.pdb') new_hdl = mol.CreateEntity(); ed = new_hdl.EditXCS() c = ed.InsertChain('A') ed.AppendResidue(c, 'GLY') ed.AppendResidue(c, 'ALA') ed.AppendResidue(c, 'ASN') ed.AppendResidue(c, 'GLY') ed.AppendResidue(c, 'ALA') # SNN to GLY err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed) self.assertFalse(err) self.assertEqual(new_hdl.residues[0].atom_count, 0) # SNN to ALA err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[1], ed) self.assertFalse(err) self.assertEqual(new_hdl.residues[1].atom_count, 0) # SNN to ASN err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[2], ed) self.assertFalse(err) self.assertEqual(new_hdl.residues[2].atom_count, 0) # GLY to GLY err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[3], ed) self.assertTrue(err) self.assertEqual(new_hdl.residues[3].atom_count, 3) self.assertFalse(new_hdl.residues[3].FindAtom("CB").IsValid()) # GLY to ALA err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[4], ed) self.assertFalse(err) self.assertEqual(new_hdl.residues[4].atom_count, 3) self.assertFalse(new_hdl.residues[4].FindAtom("CB").IsValid()) def test_CopyResidue(self): tpl = io.LoadPDB('testfiles/cbeta.pdb') new_hdl = mol.CreateEntity(); ed = new_hdl.EditXCS() c = ed.InsertChain('A') ed.AppendResidue(c, 'MET') ed.AppendResidue(c, 'GLY') ed.AppendResidue(c, 'GLY') ed.AppendResidue(c, 'HIS') ed.AppendResidue(c, 'HIS') ed.AppendResidue(c, 'GLY') ed.AppendResidue(c, 'HIS') ed.AppendResidue(c, 'MET') # MET to MET err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[0], ed) self.assertTrue(err) #GLY to GLY err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[1], ed) self.assertTrue(err) # GLY to GLY err = mol.alg.CopyResidue(tpl.residues[2], new_hdl.residues[2], ed) self.assertTrue(err) #now we copy a HIS to a HIS err = mol.alg.CopyResidue(tpl.residues[3], new_hdl.residues[3], ed) self.assertTrue(err) # copy a GLY to a HIS err, has_cbeta = mol.alg.CopyNonConserved(tpl.residues[1], new_hdl.residues[4], ed) self.assertFalse(has_cbeta) # copy a MET to a GLY err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[5], ed) self.assertFalse(err) # copy a MET to a HIS err = mol.alg.CopyResidue(tpl.residues[0], new_hdl.residues[6], ed) self.assertFalse(err) # copy a GLY to a MET with adding CB err = mol.alg.CopyResidue(tpl.residues[1], new_hdl.residues[7], ed) self.assertFalse(err) residues = new_hdl.residues self.assertEqual(len(residues), 8) # MET to MET self.assertTrue(residues[0].FindAtom("CB").IsValid()) #GLY to GLY self.assertFalse(residues[1].FindAtom("CB").IsValid()) #now we copy a GLY to a GLY self.assertFalse(residues[2].FindAtom("CB").IsValid()) #now we copy a HIS to a HIS self.assertTrue(residues[3].FindAtom("CB").IsValid()) #now we copy a GLY to a HIS without adding CB self.assertFalse(residues[4].FindAtom("CB").IsValid()) #now we copy a MET to a GLY self.assertFalse(residues[5].FindAtom("CB").IsValid()) # copy a MET to a HIS self.assertTrue(residues[6].FindAtom("CB").IsValid()) # copy a GLY to a MET with adding CB self.assertTrue(residues[7].FindAtom("CB").IsValid()) if __name__ == "__main__": from ost import testutils if testutils.DefaultCompoundLibIsSet(): testutils.RunTests() else: print('No compound library available. Ignoring test_nonstandard.py tests.')