def test_chain_too_long(self):
with self.assertRaises(Exception) as context:
numpdb.numsele(":AX")
self.assertEqual(context.exception.message,
"chain identifier must be one character")
with self.assertRaises(Exception) as context:
numpdb.numsele(":AX.CA")
self.assertEqual(context.exception.message,
"chain identifier must be one character")
def test_chain(self):
self.assertDictEqual(numpdb.numsele(":A"), {
"chain": "A",
"resno": None,
"atomname": None
})
self.assertDictEqual(numpdb.numsele(": "), {
"chain": " ",
"resno": None,
"atomname": None
})
def test_combination(self):
self.assertDictEqual(numpdb.numsele("1:B.CA"), {
"chain": "B",
"resno": 1,
"atomname": "CA"
})
self.assertDictEqual(numpdb.numsele("1: .CA"), {
"chain": " ",
"resno": 1,
"atomname": "CA"
})
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_resno_range(self):
self.assertDictEqual(numpdb.numsele("110-311"), {
"chain": None,
"resno": [110, 311],
"atomname": None
})
self.assertDictEqual(numpdb.numsele("110-312:C"), {
"chain": "C",
"resno": [110, 312],
"atomname": None
})
self.assertDictEqual(numpdb.numsele("110-313.N"), {
"chain": None,
"resno": [110, 313],
"atomname": "N"
})
def __prep_arg(self, value, params):
if not value:
return value
if params.get("type") in ["file", "dir"]:
if "nargs" in params:
return map(self.abspath, value)
return self.abspath(value)
elif params.get("type") == "sele":
return numpdb.numsele(value)
return value
def test_atomname_too_long(self):
with self.assertRaises(Exception) as context:
numpdb.numsele(":A.foobar")
self.assertEqual(context.exception.message,
"atomname must be one to four characters")
def test_atomname(self):
self.assertDictEqual(numpdb.numsele(".CA"), {
"chain": None,
"resno": None,
"atomname": "CA"
})
def test_resno(self):
self.assertDictEqual(numpdb.numsele("312"), {
"chain": None,
"resno": 312,
"atomname": None
})