def testSeqMapAdd(self):
r2 = Raf.SeqMap(self.rafLine2)
r3 = Raf.SeqMap(self.rafLine3)
length = len(r2.res) + len(r3.res)
r2 += r3
self.assertEqual(len(r2.res), length)
r2.extend(r2)
self.assertEqual(len(r2.res), length * 2)
r4 = r2 + r2
self.assertEqual(len(r4.res), length * 4)
r4.append(Raf.Res())
self.assertEqual(len(r4.res), (length * 4) + 1)
def test_SeqMap_getAtoms_err(self):
r = Raf.SeqMap(self.rafLine)
# There is no overlap with this PDB file...
with open("PDB/1A8O.pdb") as pdb_handle:
out_handle = StringIO()
self.assertRaises(RuntimeError, r.getAtoms,
*(pdb_handle, out_handle))
def testSeqMapAdd(self):
r2 = Raf.SeqMap(self.rafLine2)
r3 = Raf.SeqMap(self.rafLine3)
l = len(r2.res) + len(r3.res)
r2 += r3
assert len(r2.res) == l
r2.extend(r2)
assert len(r2.res) == l * 2
r4 = r2 + r2
assert len(r4.res) == l * 4
r4.append(Raf.Res())
assert len(r4.res) == (l * 4) + 1
def testParse(self):
"""Parse a RAF record."""
r = Raf.SeqMap(self.rafLine)
self.assertEqual(r.pdbid, "101m")
self.assertEqual(r.pdb_datestamp, "010301")
self.assertEqual(r.flags, "111011")
i = r.index("143")
res = r.res[i]
self.assertEqual(res.chainid, "_")
self.assertEqual(res.resid, "143")
self.assertEqual(res.seqres, "A")
self.assertEqual(res.atom, "A")
r = Raf.SeqMap(self.rafLine2)
res = r.res[r.index("6A", chainid="A")]
self.assertEqual(res.resid, "6A")
self.assertEqual(res.atom, "E")
def testParse(self):
"""Can we parse a RAF record?"""
r = Raf.SeqMap(self.rafLine)
assert r.pdbid == "101m"
assert r.pdb_datestamp == "010301"
assert r.flags == "111011"
i = r.index("143")
res = r.res[i]
assert res.chainid == "_"
assert res.resid == "143"
assert res.seqres == "A"
assert res.atom == "A"
r = Raf.SeqMap(self.rafLine2)
res = r.res[r.index("6A", chainid="A")]
assert res.resid == "6A"
assert res.atom == "E"
def testSeqMapSlice(self):
r = Raf.SeqMap(self.rafLine)
r = r[r.index("124") : r.index("135") + 1]
self.assertEqual(len(r.res), 12)
def testSeqMapSlice(self):
r = Raf.SeqMap(self.rafLine)
r = r[r.index("124"):r.index("135") + 1]
assert len(r.res) == 12
