def test_superpose(self):
npdb1 = numpdb.NumPdb(data("1U19.pdb"))
npdb2 = numpdb.NumPdb(data("3DQB.pdb"))
sele = numpdb.numsele("1-326:A")
sp, msg = numpdb.superpose(npdb1, npdb2, sele, sele, align=False)
np.testing.assert_almost_equal(sp.rmsd, 2.8033625498819172)
def test_tmscore(self):
npdb1 = numpdb.NumPdb(data("trajec_1.pdb"))
coords1 = npdb1.get('xyz', atomname='CA')
npdb2 = numpdb.NumPdb(data("trajec_2.pdb"))
coords2 = npdb2.get('xyz', atomname='CA')
result = tmscore(coords1, coords2)
np.testing.assert_almost_equal(result, 0.780818185612)
def test_info(self):
npdb = numpdb.NumPdb(
data("1CRN.pdb"), {
"phi_psi": False,
"sstruc": True,
"backbone_only": False,
"protein_only": False,
"detect_incomplete": False,
"configuration": False,
"info": True
})
self.assertDictEqual(
npdb._info, {
"title":
"WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC "
"RESOLUTION. PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS "
"OF CRAMBIN",
'header': ['PLANT PROTEIN', '30-APR-81', '1CRN'],
"obsolete": [],
"model_type": {},
"experiment":
"X-RAY DIFFRACTION",
"keywords": ["PLANT SEED PROTEIN", "PLANT PROTEIN"],
"splited_entry": [],
"resolution":
1.5
})
def test_secondary_structure(self):
npdb = numpdb.NumPdb(
data("1CRN.pdb"), {
"phi_psi": False,
"sstruc": True,
"backbone_only": False,
"protein_only": False,
"detect_incomplete": False,
"configuration": False
})
self.assertEquals(npdb._sstruc[0].resname1, "THR")
def test_missing(self):
npdb = numpdb.NumPdb(
data("3SN6.pdb"), {
"phi_psi": False,
"sstruc": True,
"backbone_only": False,
"protein_only": False,
"detect_incomplete": False,
"configuration": False,
"detect_missing": True
})
self.assertEqual(
str(npdb._missing[7]),
"MissingRecord(type='Residue', model=' ', " +
"resname='MET', chain=' A', ssseqi=1, identifier=' ', " +
"atoms=None)")