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test_parser.py
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import unittest
from tempfile import NamedTemporaryFile
from pathlib import Path
from rna3db.parser import parse_file, Residue, Chain
class TestmmCIFWriter(unittest.TestCase):
test_trna_path = Path(__file__).parent / "test_data" / "1ehz.cif"
test_old_path = Path(__file__).parent / "test_data" / "old_1ehz_A.cif"
test_two_chain_path = Path(__file__).parent / "test_data" / "3cgs.cif"
def test_simple_mmcif_read(self):
sf = parse_file(self.test_trna_path)
self.assertEqual(list(sf.chains.keys()), ["A"])
seq = "GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA"
example_chain = Chain("A")
for i, s in enumerate(seq):
example_chain.add_residue(Residue(s, s, i))
self.assertEqual(sf["A"], example_chain)
def test_simple_mmcif_read_two_chain(self):
sf = parse_file(self.test_two_chain_path)
self.assertEqual(list(sf.chains.keys()), ["A", "B"])
chain_A = Chain("A")
for i, s in enumerate("GCGCGUAGUAGC"):
chain_A.add_residue(Residue(s, s, i))
chain_B = Chain("B")
for i, s in enumerate("CGCUACUGACGCG"):
chain_B.add_residue(Residue(s, s, i))
self.assertEqual(sf["A"], chain_A)
self.assertEqual(sf["B"], chain_B)
def test_residue_eq(self):
# exact same
self.assertEqual(
Residue(three_letter_code="C", one_letter_code="C", index=0, atoms={}),
Residue(three_letter_code="C", one_letter_code="C", index=0, atoms={}),
)
# different index
self.assertNotEqual(
Residue(three_letter_code="C", one_letter_code="C", index=0, atoms={}),
Residue(three_letter_code="C", one_letter_code="C", index=1, atoms={}),
)
# totally different
self.assertNotEqual(
Residue(three_letter_code="C", one_letter_code="C", index=0, atoms={}),
Residue(
three_letter_code="G",
one_letter_code="G",
index=1,
atoms={"P": (0, 0, 0)},
),
)
# different atoms
self.assertNotEqual(
Residue(three_letter_code="C", one_letter_code="C", index=0, atoms={}),
Residue(
three_letter_code="C",
one_letter_code="C",
index=0,
atoms={"P": (0, 0, 0)},
),
)
# exactly same with atoms
self.assertEqual(
Residue(
three_letter_code="C",
one_letter_code="C",
index=0,
atoms={"B": (0, 0, 1), "A": (0, 0, 0)},
),
Residue(
three_letter_code="C",
one_letter_code="C",
index=0,
atoms={"A": (0, 0, 0), "B": (0, 0, 1)},
),
)
# different atom coords
self.assertNotEqual(
Residue(
three_letter_code="C",
one_letter_code="C",
index=0,
atoms={"A": (1, 0, 1), "B": (0, 0, 0)},
),
Residue(
three_letter_code="C",
one_letter_code="C",
index=0,
atoms={"A": (0, 0, 0), "B": (0, 0, 0)},
),
)
def test_chain_eq(self):
a = Chain("A")
b = Chain("A")
a.residues = [
Residue("A", "A", 0, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 1, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 2, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 3, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
]
b.residues = [
Residue("A", "A", 0, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 1, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 2, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 3, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
]
# exactly the same
self.assertEqual(a, b)
b.residues = [
Residue("A", "A", 0, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 1, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 2, atoms={}),
Residue("A", "A", 3, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
]
# missing atoms
self.assertNotEqual(a, b)
b.residues = [
Residue("A", "A", 0, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("C", "C", 1, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("G", "G", 2, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("U", "U", 3, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
]
# different sequences
self.assertNotEqual(a, b)
b = Chain("B")
b.residues = [
Residue("A", "A", 0, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 1, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 2, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
Residue("A", "A", 3, atoms={"A": (0, 0, 0), "B": (0, 0, 0)}),
]
# different author_id, otherwise same
self.assertEqual(a, b)
def test_full_io(self):
sf_read = parse_file(self.test_trna_path, include_atoms=True)
with NamedTemporaryFile() as f:
sf_read.write_mmcif_chain(f.name + ".cif", "A")
sf_write = parse_file(f.name + ".cif", include_atoms=True)
for auth_id in sf_write.chains.keys():
self.assertEqual(sf_read[auth_id], sf_write[auth_id])
def test_full_io_two_chains(self):
sf_read = parse_file(self.test_two_chain_path, include_atoms=True)
with NamedTemporaryFile() as f:
for chain in sf_read:
sf_read.write_mmcif_chain(
f.name + f"_{chain.author_id}.cif", chain.author_id
)
sf_write = parse_file(
f.name + f"_{chain.author_id}.cif", include_atoms=True
)
for auth_id in sf_write.chains.keys():
self.assertEqual(sf_read[auth_id], sf_write[auth_id])
def test_backwards_compatibility(self):
sf_old = parse_file(self.test_old_path, include_atoms=True)
sf_new = parse_file(self.test_trna_path, include_atoms=True)
self.assertEqual(sf_old.chains.keys(), sf_new.chains.keys())
for k in sf_new.chains.keys():
self.assertEqual(sf_old[k], sf_new[k])
def test_atom_read(self):
sf = parse_file(self.test_trna_path, include_atoms=True)
self.assertDictEqual(
sf["A"][0].atoms,
{
"OP3": (50.193, 51.19, 50.534),
"P": (50.626, 49.73, 50.573),
"OP1": (49.854, 48.893, 49.562),
"OP2": (52.137, 49.542, 50.511),
"O5'": (50.161, 49.136, 52.023),
"C5'": (50.216, 49.948, 53.21),
"C4'": (50.968, 49.231, 54.309),
"O4'": (50.45, 47.888, 54.472),
"C3'": (52.454, 49.03, 54.074),
"O3'": (53.203, 50.177, 54.425),
"C2'": (52.781, 47.831, 54.957),
"O2'": (53.018, 48.156, 56.313),
"C1'": (51.502, 47.007, 54.836),
"N9": (51.628, 45.992, 53.798),
"C8": (51.064, 46.007, 52.547),
"N7": (51.379, 44.966, 51.831),
"C5": (52.197, 44.218, 52.658),
"C6": (52.848, 42.992, 52.425),
"O6": (52.826, 42.291, 51.404),
"N1": (53.588, 42.588, 53.534),
"C2": (53.685, 43.282, 54.716),
"N2": (54.452, 42.733, 55.671),
"N3": (53.077, 44.429, 54.946),
"C4": (52.356, 44.836, 53.879),
},
)
if __name__ == "__main__":
unittest.main()