def test_properStrandRead():
structure_name = '1ehz'
file_format = 'pdb'
desired_output = list(
'gCGGAUUUAgCUCAGuuGGGAGAGCgCCAGAcUgAAgAucUGGAGgUCcUGUGuuCGaUCCACAGAAUUCGCACCA'
.upper())
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
strand = inputParser.read_models_from_pdb_file(file)[0]
assert desired_output == strand['A']
def test_strandLensToughModel():
structure_name = '1ehz'
file_format = 'pdb'
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
models = inputParser.read_models_from_pdb_file(file)
assert 1 == len(models[0].keys())
assert 'G' == models[0]['A'][0]
assert 'G' == models[0]['A'][9]
for model in models:
assert len(model['A']) == 76
def test_strandTwoChains():
structure_name = '2z74'
file_format = 'pdb'
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
models = inputParser.read_models_from_pdb_file(file)
assert len(models[0].keys()) == 2
assert models[0]['A'][0] == 'A'
assert models[0]['A'][-1] == 'U'
assert models[0]['B'][0] == 'G'
assert models[0]['B'][-1] == 'A'
def test_strandLensMultipleModels():
structure_name = '2lbk'
file_format = 'pdb'
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
models = inputParser.read_models_from_pdb_file(file)
assert len(models) == 8
assert models[0]['A'][0] == 'G'
assert models[0]['A'][-1] == 'C'
for model in models:
assert len(model['A']) == 17
def test_build_dot_notation_canonical_only_one_layer():
structure_name = '2lbk'
file_format = 'pdb'
desired_output = ".(((((.....)))))."
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
models = inputParser.read_models_from_pdb_file(file)
text_strand = inputParser.build_txt_strand_from_chains(models[0])
base_pairs = inputParser.annotate_basepairs(file)
dot_notation = inputParser.make_dot_notation(text_strand, base_pairs[0])
assert desired_output == dot_notation
def test_properLongStrandRead():
structure_name = '3g78'
file_format = 'pdb'
desired_output = list(
"uGUGCCCGGCAUGGGUGCAGUCUAUAGGGUGAGAGUCCCGAACUGUGAAGGCAGAAGUA\
ACAGUUAGCCUAACGCAAGGGUGUCCGUGGCGACAUGGAAUCUGAAGGAAGCGGACGGCA\
AACCUUCGGUCUGAGGAACACGAACUUCAUAUGAGGCUAGGUAUCAAUGGAUGAGUUUGC\
AUAACAAAACAAAGUCCUUUCUGCCAAAGUUGGUACAGAGUAAAUGAAGCAGAUUGAUGA\
AGGGAAAGACUGCAUUCUUACCCGGGGAGGUCUGGAAACAGAAGUCAGCAGAAGUCAUAG\
UACCCUGUUCGCAGGGGAAGGACGGAACAAGUAUGGCGUUCGCGCCUAAGCUUGAACCGC\
CGUAUACCGAACGGUACGUACGGUGGUGUG".upper())
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
models = inputParser.read_models_from_pdb_file(file)
assert desired_output == models[0]['A']