def test_load_rna_pdb_with_secondary_structure(self):
with self.assertRaises(ValueError):
# Need chain for pdb_dotbracket
fuc.load_rna("test/forgi/threedee/data/1FUF.pdb",
"pdb",
False,
dissolve_length_one_stems=False,
pdb_dotbracket="(((((.(.(((((&)))))))))))..")
cg1 = fuc.load_rna("test/forgi/threedee/data/1FUF.pdb",
"pdb",
False,
dissolve_length_one_stems=False,
pdb_chain=["A", "B"],
pdb_dotbracket="(((((.(.(((((&)))))))))))..")
cg2 = fuc.load_rna("test/forgi/threedee/data/1FUF.pdb",
"pdb",
False,
dissolve_length_one_stems=True,
pdb_chain=["A", "B"],
pdb_dotbracket="(((((.(.(((((&)))))))))))..")
self.assertEqual(len(cg1.defines), 6)
self.assertEqual(
cg1.defines, {
"s0": [1, 5, 20, 24],
"s1": [7, 7, 19, 19],
"s2": [9, 13, 14, 18],
"i0": [6, 6],
"i1": [8, 8],
"t0": [25, 26]
})
self.assertEqual(len(cg2.defines), 4)
def test_load_fasta_cleaning_sec_stru(self):
bg = fuc.load_rna("test/forgi/data/pk.fa",
"bg",
False,
dissolve_length_one_stems=False)
bg2 = fuc.load_rna("test/forgi/data/pk.fa",
"bg",
False,
dissolve_length_one_stems=True)
self.assertLess(len(bg2.defines), len(bg.defines))
def test_load_rna_pdb_dissolve_length_one_stems(self):
cg1 = fuc.load_rna("test/forgi/threedee/data/1FUF.pdb",
"pdb",
False,
dissolve_length_one_stems=False)
cg2 = fuc.load_rna("test/forgi/threedee/data/1FUF.pdb",
"pdb",
False,
dissolve_length_one_stems=True)
self.assertGreater(len(list(cg1.stem_iterator())),
len(list(cg2.stem_iterator())))
def test_load_rna_pdb_simple(self):
cg = fuc.load_rna("test/forgi/threedee/data/1y26.pdb",
"pdb",
allow_many=False)
self.assertIsInstance(cg, ftmc.CoarseGrainRNA)
# With allow_many we get a list of length 1
cgs = fuc.load_rna("test/forgi/threedee/data/1y26.pdb",
"pdb",
allow_many=True)
self.assertEqual(len(cgs), 1)
self.assertEqual(cg.defines, cgs[0].defines)
def test_load_rna_pdb_allow_many_and_chain_option(self):
# More than 1 chain in file
with self.assertRaises(ValueError):
fuc.load_rna("test/forgi/threedee/data/1DUQ.pdb", "pdb", False)
cg = fuc.load_rna("test/forgi/threedee/data/1DUQ.pdb",
"pdb",
False,
pdb_chain="A")
self.assertIsInstance(cg, ftmc.CoarseGrainRNA)
# Two chains, forming one stem:
cg = fuc.load_rna("test/forgi/threedee/data/1DUQ.pdb",
"pdb",
False,
pdb_chain=["A", "B"])
self.assertIsInstance(cg, ftmc.CoarseGrainRNA)
cgs = fuc.load_rna("test/forgi/threedee/data/1DUQ.pdb", "pdb", True)
self.assertIsInstance(cgs, list)
# 4 molecules with 2 chains each
self.assertEqual(len(cgs), 4)
self.assertIsInstance(cgs[0], ftmc.CoarseGrainRNA)
def test_load_fasta_types(self):
with self.assertRaises(fuc.WrongFileFormat):
fuc.load_rna("test/forgi/data/pk.fa", "3d", False)
cg = fuc.load_rna("test/forgi/data/pk.fa", "cg", False)
self.assertIsInstance(cg, ftmc.CoarseGrainRNA)
def test_load_fasta_types(self):
with self.assertRaises(fuc.WrongFileFormat):
fuc.load_rna("test/forgi/data/pk.fa", "3d", False)
bg = fuc.load_rna("test/forgi/data/pk.fa", "bg", False)
self.assertEqual(type(bg), fgb.BulgeGraph)