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