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import unittest
import msgpack
import numpy
from mmtf import fetch,parse,parse_gzip, converters
from mmtf.api.default_api import ungzip_data,write_mmtf,MMTFDecoder,_internet_on
from mmtf.codecs import encoders
from mmtf.utils.codec_utils import parse_header
from mmtf.utils.constants import BASE_URL
from mmtf.codecs.default_codec import codec_dict
from mmtf.codecs.decoders import numpy_decoders as decoders
def run_all(unit_test, encoded_data, decoded_data, param, codec_id):
"""Test that a given codec can work in the forward backward and round trip both ways."""
try:
unit_test.assertEqual(codec_dict[codec_id].decode(encoded_data, param).tolist(), decoded_data.tolist())
except:
unit_test.assertEqual(codec_dict[codec_id].decode(encoded_data, param), decoded_data.tolist())
try:
unit_test.assertEqual(
codec_dict[codec_id].decode(codec_dict[codec_id].encode(decoded_data, param),
param).tolist(), decoded_data.tolist())
except:
unit_test.assertEqual(codec_dict[codec_id].decode(codec_dict[codec_id].encode(decoded_data, param),
param), decoded_data.tolist())
unit_test.assertEqual(codec_dict[codec_id].encode(decoded_data, param), encoded_data)
unit_test.assertEqual(codec_dict[codec_id].encode(codec_dict[codec_id].decode(encoded_data, param),
param), encoded_data)
class CodecTest(unittest.TestCase):
def test_delt_rec_float(self):
test_data = b'\x7f\xffD\xab\x01\x8f\xff\xca'
output_data = numpy.array([50.346, 50.745, 50.691])
run_all(self, test_data, output_data, 1000, 10)
def test_run_len_float(self):
test_data = b'\x00\x00\x00d\x00\x00\x00\x03'
output_data = numpy.array([1.00,1.00,1.00])
run_all(self, test_data, output_data, 100, 9)
def test_run_len_delta_int(self):
test_data = b'\x00\x00\x00\x01\x00\x00\x00\x07'
output_data = numpy.array([1,2,3,4,5,6,7])
run_all(self, test_data, output_data, 0, 8)
def test_run_len_char(self):
test_data = b'\x00\x00\x00\x41\x00\x00\x00\x04'
output_data = numpy.array(["A","A","A","A"])
run_all(self, test_data, output_data, 0, 6)
def test_enc_str(self):
test_data = b'B\x00\x00\x00A\x00\x00\x00C\x00\x00\x00A\x00\x00\x00A\x00\x00\x00A\x00\x00\x00'
output_data = numpy.array(["B","A","C","A","A","A"])
run_all(self, test_data, output_data, 0, 5)
def test_byte_to_int(self):
test_data = b'\x07\x06\x06\x07\x07'
output_data = numpy.array([7,6,6,7,7])
run_all(self, test_data, output_data, 0, 2)
def test_four_byte_int(self):
test_data = b'\x00\x00\x00\x01\x00\x02\x00\x01\x00\x00\x00\x00\x00\x00\x00\x02'
output_data = numpy.array([1, 131073, 0, 2])
run_all(self, test_data, output_data, 0, 4)
class DecoderTests(unittest.TestCase):
def test_run_length_decode(self):
input_data = numpy.array([15,3,100,2,111,4,10000,6])
output_data_test = [15,15,15,100,100,111,111,111,111,10000,10000,10000,10000,10000,10000]
output_data = decoders.run_length_decode(input_data).tolist()
self.assertEqual(output_data, output_data_test)
def test_empty_run_length_decode(self):
input_data = numpy.array([])
output_data_test = []
output_data = decoders.run_length_decode(input_data).tolist()
self.assertEqual(output_data, output_data_test)
def test_delta_decode(self):
input_data = numpy.asarray([15,3,100,-1,11,4],dtype=numpy.int32)
output_data_test = [15,18,118,117,128,132]
output_data = decoders.delta_decode(input_data).tolist()
self.assertEqual(output_data, output_data_test)
def test_empty_delta_decode(self):
input_data = numpy.asarray([],dtype=numpy.int32)
output_data_test = []
output_data = decoders.delta_decode(input_data).tolist()
self.assertEqual(output_data, output_data_test)
class EncoderTests(unittest.TestCase):
def test_run_length_encode(self):
output_data_test = [15, 3, 100, 2, 111, 4, 10000, 6]
input_data = [15, 15, 15, 100, 100, 111, 111, 111, 111, 10000, 10000, 10000, 10000, 10000, 10000]
output_data = encoders.run_length_encode(input_data)
self.assertEqual(output_data, output_data_test)
def test_empty_run_length_encode(self):
input_data = []
output_data_test = []
output_data = encoders.run_length_encode(input_data)
self.assertEqual(output_data, output_data_test)
def test_delta_encode(self):
output_data_test = [15, 3, 100, -1, 11, 4]
input_data = [15, 18, 118, 117, 128, 132]
output_data = encoders.delta_encode(input_data)
self.assertEqual(output_data, output_data_test)
def test_empty_delta_encode(self):
input_data = []
output_data_test = []
output_data = encoders.delta_encode(input_data)
self.assertEqual(output_data, output_data_test)
class ConverterTests(unittest.TestCase):
def test_convert_chain_list(self):
in_bytes = b'A\x00\x00\x00A\x00\x00\x00A\x00\x00\x00A\x00\x00\x00A\x00\x00\x00A\x00\x00\x00'
out_strings_test = ["A", "A","A","A","A","A"]
self.assertEqual(out_strings_test, converters.decode_chain_list(in_bytes))
self.assertEqual(in_bytes, converters.encode_chain_list(out_strings_test))
def test_convert_int_to_float(self):
in_array = numpy.asarray([10001,100203,124542])
out_array_test = [10.001,100.203,124.542]
converted = converters.convert_ints_to_floats(in_array, 1000.0).tolist()
for i in range(len(out_array_test)):
self.assertAlmostEqual(out_array_test[i], converted[i],places=3)
self.assertEqual(in_array.tolist(), converters.convert_floats_to_ints(out_array_test, 1000.0))
def test_recursive_enc(self):
in_arr = [1,420,32767,120,-32768,34767]
out_array_test = [1,420,32767,0,120,-32768,0,32767,2000]
self.assertEqual(out_array_test, converters.recursive_index_encode(in_arr))
def test_recursive_dec(self):
in_arr = numpy.asarray([1,420,32767,0,120,-32768,0,32767,2000],dtype=numpy.int32)
out_array_test = [1,420,32767,120,-32768,34767]
self.assertEqual(out_array_test, converters.recursive_index_decode(in_arr).tolist())
def test_convert_one_byte_int(self):
in_bytes = b'\x07\x06\x06\x07\x07'
out_array_test = [7,6,6,7,7]
self.assertEqual(out_array_test, converters.convert_bytes_to_ints(in_bytes,1).tolist())
self.assertEqual(in_bytes, converters.convert_ints_to_bytes(out_array_test,1))
self.assertEqual(in_bytes,converters.convert_ints_to_bytes(converters.convert_bytes_to_ints(in_bytes,1),1))
def test_convert_two_byte_int(self):
in_bytes = b'\x00\x00\x00\x01\x00\x02\x00\x01\x00\x00\x00\x00\x00\x00\x00\x02'
out_array_test = [0,1,2,1,0,0,0,2]
self.assertEqual(out_array_test, converters.convert_bytes_to_ints(in_bytes,2).tolist())
self.assertEqual(in_bytes, converters.convert_ints_to_bytes(out_array_test, 2))
self.assertEqual(in_bytes,converters.convert_ints_to_bytes(converters.convert_bytes_to_ints(in_bytes,2),2))
def test_convert_four_byte_int(self):
in_bytes = b'\x00\x00\x00\x01\x00\x02\x00\x01\x00\x00\x00\x00\x00\x00\x00\x02'
out_array_test = [1, 131073, 0, 2]
self.assertEqual(out_array_test, converters.convert_bytes_to_ints(in_bytes,4).tolist())
self.assertEqual(in_bytes, converters.convert_ints_to_bytes(out_array_test,4))
self.assertEqual(in_bytes,converters.convert_ints_to_bytes(converters.convert_bytes_to_ints(in_bytes,4),4))
def test_parse_header(self):
in_bytes = b'\x00\x00\x00\x01\x00\x02\x00\x01\x00\x00\x00\x00\x00\x00\x00\x02'
codec,length,param, bytearray = parse_header(in_bytes)
self.assertEqual(length,131073)
self.assertEqual(param,0)
self.assertEqual(len(bytearray),4)
def test_convert_int_to_char(self):
int_array = [66,63,67]
out_array_test = ["B", "?","C"]
self.assertEqual(out_array_test, converters.convert_ints_to_chars(int_array))
self.assertEqual(int_array, converters.convert_chars_to_ints(out_array_test))
def test_decoder(self):
decoded = parse("mmtf/tests/testdatastore/4CUP.mmtf")
def test_gz_decoder(self):
decoded = parse_gzip("mmtf/tests/testdatastore/4CUP.mmtf.gz")
def test_round_trip(self):
decoded = parse("mmtf/tests/testdatastore/4CUP.mmtf")
packed = decoded.get_msgpack()
decoded.decode_data(msgpack.unpackb(packed))
def test_gzip_open(self):
with open("mmtf/tests/testdatastore/4CUP.mmtf.gz","rb") as fh:
ungzip_data(fh.read())
@unittest.skip("not executing tests requiring network access")
def test_fetch(self):
if _internet_on(BASE_URL):
decoded = fetch("4CUP")
else:
print("Warning - cannot connect to "+BASE_URL)
def array_eq(self,array_one, array_two):
import numpy as np
if [x for x in np.isclose(array_one,array_two) if x]:
return True
else:
try:
if not array_one and not array_two:
return True
except ValueError:
pass
print(array_one)
print(array_two)
print("Arrays not equal")
return False
def char_arr_eq(self,array_one, array_two):
import numpy as np
return np.array_equal(array_one,array_two)
def dict_list_equal(self,list_one,list_two):
list_one = sorted(list_one, key=lambda x:sorted(x.keys()))
list_two = sorted(list_two, key=lambda x:sorted(x.keys()))
len_one = len(list_one)
if len_one != len(list_two):
self.assertTrue(False,"Lists of different lengths")
for i in range(len_one):
if list_one[i]!=list_two[i]:
print(list_one[i])
print(list_two[i])
self.assertTrue(list_one[i]==list_two[i])
def iterate(self, data_one, data_two):
chain_ind = 0
group_ind = 0
atom_ind_one = 0
atom_ind_two = 0
for model in data_one.chains_per_model:
for chain in range(model):
for group in range(data_one.groups_per_chain[chain_ind]):
self.char_arr_eq(data_one.group_list[data_one.group_type_list[group_ind]]["atomNameList"],
data_two.group_list[data_two.group_type_list[group_ind]]["atomNameList"])
self.char_arr_eq(data_one.group_list[data_one.group_type_list[group_ind]]["elementList"],
data_two.group_list[data_two.group_type_list[group_ind]]["elementList"])
self.array_eq(data_one.group_list[data_one.group_type_list[group_ind]]["bondOrderList"],
data_two.group_list[data_two.group_type_list[group_ind]]["bondOrderList"])
self.array_eq(data_one.group_list[data_one.group_type_list[group_ind]]["bondAtomList"],
data_two.group_list[data_two.group_type_list[group_ind]]["bondAtomList"])
self.array_eq(data_one.group_list[data_one.group_type_list[group_ind]]["formalChargeList"],
data_two.group_list[data_two.group_type_list[group_ind]]["formalChargeList"])
self.assertEqual(data_one.group_list[data_one.group_type_list[group_ind]]["groupName"],
data_two.group_list[data_two.group_type_list[group_ind]]["groupName"])
self.assertEqual(data_one.group_list[data_one.group_type_list[group_ind]]["singleLetterCode"],
data_two.group_list[data_two.group_type_list[group_ind]]["singleLetterCode"])
self.assertEqual(data_one.group_list[data_one.group_type_list[group_ind]]["chemCompType"],
data_two.group_list[data_two.group_type_list[group_ind]]["chemCompType"])
group_ind+=1
chain_ind+=1
return True
def check_equal(self, data_one, data_two):
self.assertTrue(self.array_eq(data_one.x_coord_list,data_two.x_coord_list))
self.assertTrue(self.array_eq(data_one.y_coord_list,data_two.y_coord_list))
self.assertTrue(self.array_eq(data_one.z_coord_list,data_two.z_coord_list))
self.assertTrue(self.array_eq(data_one.b_factor_list,data_two.b_factor_list))
self.assertTrue(self.array_eq(data_one.occupancy_list,data_two.occupancy_list))
self.assertTrue(self.array_eq(data_one.atom_id_list,data_two.atom_id_list))
self.assertTrue(self.char_arr_eq(data_one.alt_loc_list,data_two.alt_loc_list))
self.assertTrue(self.char_arr_eq(data_one.ins_code_list,data_two.ins_code_list))
self.assertTrue(self.array_eq(data_one.group_id_list,data_two.group_id_list))
self.dict_list_equal(data_one.entity_list,data_two.entity_list)
self.dict_list_equal(data_one.bio_assembly,data_two.bio_assembly)
self.assertTrue(self.array_eq(data_one.sequence_index_list,data_two.sequence_index_list))
self.assertEqual(data_one.chains_per_model, data_two.chains_per_model)
self.assertEqual(data_one.groups_per_chain, data_two.groups_per_chain)
self.assertEqual(data_one.chain_name_list, data_two.chain_name_list)
self.assertEqual(data_one.chain_id_list, data_two.chain_id_list)
self.assertEqual(data_one.space_group,data_two.space_group)
self.assertTrue(self.array_eq(data_one.bond_atom_list,data_two.bond_atom_list))
self.assertTrue(self.array_eq(data_one.bond_order_list,data_two.bond_order_list))
self.assertEqual(data_one.structure_id,data_two.structure_id)
self.assertEqual(data_one.title,data_two.title)
self.assertTrue(self.char_arr_eq(data_one.experimental_methods,data_two.experimental_methods))
self.assertEqual(data_one.deposition_date,data_two.deposition_date)
self.assertEqual(data_one.release_date,data_two.release_date)
self.assertTrue(self.array_eq(data_one.sec_struct_list,data_two.sec_struct_list))
self.assertEqual(data_one.r_free,data_two.r_free)
self.assertEqual(data_one.r_work,data_two.r_work)
self.assertEqual(data_one.resolution,data_two.resolution)
self.assertEqual(data_one.unit_cell,data_two.unit_cell)
self.assertEqual(data_one.num_bonds, data_two.num_bonds)
self.assertEqual(data_one.num_chains, data_two.num_chains)
self.assertEqual(data_one.num_models, data_two.num_models)
self.assertEqual(data_one.num_atoms, data_two.num_atoms)
self.assertEqual(data_one.num_groups, data_two.num_groups)
self.assertTrue(self.iterate(data_one, data_two))
def test_round_trip(self):
data_in = parse_gzip("mmtf/tests/testdatastore/4CUP.mmtf.gz")
write_mmtf("test.mmtf", data_in, MMTFDecoder.pass_data_on)
data_rt = parse("test.mmtf")
self.check_equal(data_in, data_rt)
def round_trip(self,pdb_id):
if _internet_on(BASE_URL):
data_in = fetch(pdb_id)
write_mmtf(pdb_id+".mmtf", data_in, MMTFDecoder.pass_data_on)
data_rt = parse(pdb_id+".mmtf")
self.check_equal(data_in, data_rt)
else:
print("Warning - cannot connect to "+BASE_URL)
@unittest.skip("not executing tests requiring network access")
def test_round_trip_list(self):
id_list = [
#
"1a1q",
# // Just added to check
"9pti",
# // An entity that has no chain
"2ja5",
# // A couple of examples of multiple disulpgide bonds being formed.
"3zxw",
"1nty",
# // A weird residue case
"2eax",
# // A Deuterated Structure
"4pdj",
# // Weird bioassembly
"4a1i",
# // Multi model structure
"1cdr",
# // Another weird structure (jose's suggestion)
"3zyb",
# //Standard structure
"4cup",
# // Weird NMR structure
"1o2f",
# // B-DNA structure
"1bna",
# // DNA structure
"4y60",
# // Sugar structure
"1skm",
# // Calpha atom is missing (not marked as calpha)
"1lpv",
# // NMR structure with multiple models - one of which has chain missing
"1msh",
# // No ATOM records just HETATM records (in PDB). Opposite true for MMCif. It's a D-Peptide.
"1r9v",
# // Biosynthetic protein
"5emg",
# // Micro heterogenity
"4ck4",
# // Ribosome
"4v5a",
# // Negative residue numbers
"5esw",
# // A tiny example case
"3njw",
# // A GFP example with weird seqres records
"1ema"]
for pdb_id in id_list:
self.round_trip(pdb_id)
if __name__ == '__main__':
unittest.main()
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