def test_annotateCanonicalOnly():
fileName = ROOT_DIR + '/downloadedStructures/pdb1ehz.ent'
models = inputParser.annotate_basepairs(fileName)
assert 1 == len(models)
assert 18 == len(models[0])
def test_annotateDownloadedfile():
structure_name = '2lbk'
file_format = 'pdb'
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
models = inputParser.annotate_basepairs(file)
assert len(models) == 8
def mcannotate_part(file_path):
"""
:rtype: void
:param file_path: path to pdb file
"""
base_pairs = inputParser.annotate_basepairs(file_path)
models = inputParser.read_complete_models(file_path)
for i, (model, base_pair) in enumerate(zip(models, base_pairs)):
fixed_base_pairs = inputParser.fix_base_pairs(model, base_pair)
joined_chain_model = inputParser.build_txt_strand_from_chains(model)
dot_notation = inputParser.make_dot_notation(joined_chain_model,
fixed_base_pairs)
pretty_print_model(i, joined_chain_model, dot_notation)
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_fix_base_pairs_two_strand_model():
structure_name = '3g78'
file_format = 'pdb'
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
models = inputParser.read_complete_models(file)
base_pairs = inputParser.annotate_basepairs(file)[0]
fixed_base_pairs = inputParser.fix_base_pairs(models[0], base_pairs)
pair_with_z_strand = [
pair for pair in fixed_base_pairs if pair[1].strand == 'Z'
]
assert pair_with_z_strand[0][1].position == 418
def test_build_dot_notation_canonical_huge_structure():
structure_name = '3g78'
file_format = 'pdb'
desired_count = '-.{[.(.(((<..(((((((((((...(((.......)))..(((((...{{{.{{{...\
)))))..(((...(((..((((.((((((....))))))))))...]>..)))...))).\
..(((((((((((.(.....)...((((.......(......(...((((((..((((..\
[[[[[.))))...)))).}}}.}}}...))...)......)....)))))))))...)))\
)))...)))))))))))...}))).)(...((((....))))...).......(((.(..\
..((..........))...))))....(.(((..(((......)))...))).).(((.(\
((((((((....)))..)))))).)))...----------------------.]]]]]...'.count('.')
file = inputParser.online_input(structure_name=structure_name,
file_format=file_format)
models = inputParser.read_complete_models(file)
text_strand = inputParser.build_txt_strand_from_chains(models[0])
base_pairs = inputParser.annotate_basepairs(file)
fixed_base_pairs = inputParser.fix_base_pairs(models[0], base_pairs[0])
dot_notation = inputParser.make_dot_notation(text_strand, fixed_base_pairs)
assert desired_count < dot_notation.count('.')
def test_annotate():
fileName = ROOT_DIR + '/downloadedStructures/pdb2lbk.ent'
models = inputParser.annotate_basepairs(fileName)
assert len(models) == 8