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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,86 +1,52 @@ | ||
| import json | ||
| from collections import OrderedDict | ||
| from nmrstarlib import nmrstarlib | ||
|
|
||
| import collections | ||
| import pytest | ||
|
|
||
| def test_chem_shifts_by_residue_all(): | ||
| starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str", | ||
| "tests/example_data/NMRSTAR2/bmr18569.str") | ||
| starfile1 = next(starfile_generator) | ||
| starfile2 = next(starfile_generator) | ||
| test_chem_shifts1 = starfile1.chem_shifts_by_residue(nmrstar_version="3") | ||
| test_chem_shifts2 = starfile2.chem_shifts_by_residue(nmrstar_version="2") | ||
| from nmrstarlib import nmrstarlib | ||
|
|
||
| with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_all.json", "r") as infile: | ||
| model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict) | ||
| with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_all.json", "r") as infile: | ||
| model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict) | ||
|
|
||
| assert repr(test_chem_shifts1) == repr(model_chem_shifts1) | ||
| assert repr(test_chem_shifts2) == repr(model_chem_shifts2) | ||
| @pytest.mark.parametrize("test_input,test_output,amino_acids,atoms,amino_acids_and_atoms", [ | ||
| (("tests/example_data/NMRSTAR3/bmr18569.str", "tests/example_data/NMRSTAR2/bmr18569.str"), | ||
| ("tests/example_data/NMRSTAR3/chem_shifts_by_residue_all.json", "tests/example_data/NMRSTAR2/chem_shifts_by_residue_all.json"), | ||
| None, None, None), | ||
| (("tests/example_data/NMRSTAR3/bmr18569.str", "tests/example_data/NMRSTAR2/bmr18569.str"), | ||
| ("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER.json", "tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER.json"), | ||
| ["SER"], None, None), | ||
| def test_chem_shifts_by_residue_amino_acids_list(): | ||
| starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str", | ||
| "tests/example_data/NMRSTAR2/bmr18569.str") | ||
| starfile1 = next(starfile_generator) | ||
| starfile2 = next(starfile_generator) | ||
| test_chem_shifts1 = starfile1.chem_shifts_by_residue(amino_acids=("SER",), nmrstar_version="3") | ||
| test_chem_shifts2 = starfile2.chem_shifts_by_residue(amino_acids=("SER",), nmrstar_version="2") | ||
| (("tests/example_data/NMRSTAR3/bmr18569.str", "tests/example_data/NMRSTAR2/bmr18569.str"), | ||
| ("tests/example_data/NMRSTAR3/chem_shifts_by_residue_CA_CB.json", "tests/example_data/NMRSTAR2/chem_shifts_by_residue_CA_CB.json"), | ||
| None, ["CA", "CB"], None), | ||
| with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER.json", "r") as infile: | ||
| model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict) | ||
| with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER.json", "r") as infile: | ||
| model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict) | ||
| (("tests/example_data/NMRSTAR3/bmr18569.str", "tests/example_data/NMRSTAR2/bmr18569.str"), | ||
| ("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER_CA_CB.json", "tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER_CA_CB.json"), | ||
| ["SER"], ["CA", "CB"], None), | ||
| assert repr(test_chem_shifts1) == repr(model_chem_shifts1) | ||
| assert repr(test_chem_shifts2) == repr(model_chem_shifts2) | ||
| (("tests/example_data/NMRSTAR3/bmr18569.str", "tests/example_data/NMRSTAR2/bmr18569.str"), | ||
| ("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER_HA_CA_MET_CA_CB.json", "tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER_HA_CA_MET_CA_CB.json"), | ||
| None, None, {"SER":["HA", "CA"], "MET":["CA", "CB"]}) | ||
| ]) | ||
| def test_chem_shifts_by_residue_all(test_input, test_output, amino_acids, atoms, amino_acids_and_atoms): | ||
| input_file_path1, input_file_path2 = test_input | ||
| output_file_path1, output_file_path2 = test_output | ||
|
|
||
| def test_chem_shifts_by_residue_atoms_list(): | ||
| starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str", | ||
| "tests/example_data/NMRSTAR2/bmr18569.str") | ||
| starfile_generator = nmrstarlib.read_files(input_file_path1, input_file_path2) | ||
| starfile1 = next(starfile_generator) | ||
| starfile2 = next(starfile_generator) | ||
| test_chem_shifts1 = starfile1.chem_shifts_by_residue(atoms=("CA", "CB"), nmrstar_version="3") | ||
| test_chem_shifts2 = starfile2.chem_shifts_by_residue(atoms=("CA", "CB"), nmrstar_version="2") | ||
|
|
||
| with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_CA_CB.json", "r") as infile: | ||
| model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict) | ||
| with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_CA_CB.json", "r") as infile: | ||
| model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict) | ||
| test_chem_shifts1 = starfile1.chem_shifts_by_residue(amino_acids=amino_acids, | ||
| atoms=atoms, | ||
| amino_acids_and_atoms=amino_acids_and_atoms, | ||
| nmrstar_version="3") | ||
|
|
||
| assert repr(test_chem_shifts1) == repr(model_chem_shifts1) | ||
| assert repr(test_chem_shifts2) == repr(model_chem_shifts2) | ||
|
|
||
|
|
||
| def test_chem_shifts_by_residue_amino_acids_list_atoms_list(): | ||
| starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str", | ||
| "tests/example_data/NMRSTAR2/bmr18569.str") | ||
| starfile1 = next(starfile_generator) | ||
| starfile2 = next(starfile_generator) | ||
| test_chem_shifts1 = starfile1.chem_shifts_by_residue(amino_acids=("SER",), atoms=("CA", "CB"), nmrstar_version="3") | ||
| test_chem_shifts2 = starfile2.chem_shifts_by_residue(amino_acids=("SER",), atoms=("CA", "CB"), nmrstar_version="2") | ||
| test_chem_shifts2 = starfile2.chem_shifts_by_residue(amino_acids=amino_acids, | ||
| atoms=atoms, | ||
| amino_acids_and_atoms=amino_acids_and_atoms, | ||
| nmrstar_version="2") | ||
|
|
||
| with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER_CA_CB.json", "r") as infile: | ||
| model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict) | ||
| with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER_CA_CB.json", "r") as infile: | ||
| model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict) | ||
| with open(output_file_path1, "r") as infile: | ||
| model_chem_shifts1 = json.load(infile, object_pairs_hook=collections.OrderedDict) | ||
| with open(output_file_path2, "r") as infile: | ||
| model_chem_shifts2 = json.load(infile, object_pairs_hook=collections.OrderedDict) | ||
|
|
||
| assert repr(test_chem_shifts1) == repr(model_chem_shifts1) | ||
| assert repr(test_chem_shifts2) == repr(model_chem_shifts2) | ||
|
|
||
| def test_chem_shifts_by_residue_amino_acids_and_atoms_dict(): | ||
| starfile_generator = nmrstarlib.read_files("tests/example_data/NMRSTAR3/bmr18569.str", | ||
| "tests/example_data/NMRSTAR2/bmr18569.str") | ||
| starfile1 = next(starfile_generator) | ||
| starfile2 = next(starfile_generator) | ||
| test_chem_shifts1 = starfile1.chem_shifts_by_residue(amino_acids_and_atoms={"SER":("HA", "CA"), "MET":("CA", "CB")}, nmrstar_version="3") | ||
| test_chem_shifts2 = starfile2.chem_shifts_by_residue(amino_acids_and_atoms={"SER":("HA", "CA"), "MET":("CA", "CB")}, nmrstar_version="2") | ||
|
|
||
| with open("tests/example_data/NMRSTAR3/chem_shifts_by_residue_SER_HA_CA_MET_CA_CB.json", "r") as infile: | ||
| model_chem_shifts1 = json.load(infile, object_pairs_hook=OrderedDict) | ||
| with open("tests/example_data/NMRSTAR2/chem_shifts_by_residue_SER_HA_CA_MET_CA_CB.json", "r") as infile: | ||
| model_chem_shifts2 = json.load(infile, object_pairs_hook=OrderedDict) | ||
|
|
||
| assert repr(test_chem_shifts1) == repr(model_chem_shifts1) | ||
| assert repr(test_chem_shifts2) == repr(model_chem_shifts2) |