File: codec_tests.py

package info (click to toggle)
mmtf-python 1.1.3-1
  • links: PTS, VCS
  • area: main
  • in suites: bookworm, forky, sid, trixie
  • size: 300 kB
  • sloc: python: 1,150; makefile: 8
file content (369 lines) | stat: -rw-r--r-- 17,535 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
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()