def test_write_list(self):
"""Test the lib.software.sparky.write_list() function."""
# The data.
res_names = ['LEU', 'GLY', 'SER', 'MET', 'TRP', 'TRP', 'ASN']
res_nums = [3, 4, 5, 6, 40, 40, 55]
atom1_names = ['N', 'N', 'N', 'N', 'N', 'NE1', 'N']
atom2_names = ['HN', 'HN', 'HN', 'HN', 'HN', 'HE1', 'HN']
w1 = [122.454, 111.978, 115.069, 120.910, 123.335, 130.204, 116.896]
w2 = [8.397, 8.720, 8.177, 8.813, 8.005, 10.294, 7.468]
heights = [2535, 5050, 51643, 53663, -65111, -181131, -105322]
# The result.
file_data = [
' Assignment w1 w2 Data Height\n',
'\n',
' LEU3N-HN 122.454 8.397 2535\n',
' GLY4N-HN 111.978 8.720 5050\n',
' SER5N-HN 115.069 8.177 51643\n',
' MET6N-HN 120.910 8.813 53663\n',
' TRP40N-HN 123.335 8.005 -65111\n',
' TRP40NE1-HE1 130.204 10.294 -181131\n',
' ASN55N-HN 116.896 7.468 -105322\n'
]
# Write the data out.
file = DummyFileObject()
write_list(file_prefix=file, res_names=res_names, res_nums=res_nums, atom1_names=atom1_names, atom2_names=atom2_names, w1=w1, w2=w2, data_height=heights)
# Check the file data.
lines = file.readlines()
self.assertEqual(len(lines), len(file_data))
for i in range(len(lines)):
self.assertEqual(lines[i], file_data[i])
def test_helix(self):
"""Test the lib.structure.pdb_write.helix() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.helix(file,
ser_num=1,
helix_id='H1',
init_res_name='ILE',
init_chain_id='A',
init_seq_num=23,
init_icode=None,
end_res_name='GLU',
end_chain_id='A',
end_seq_num=34,
end_icode=None,
helix_class=1,
comment=None,
length=12)
# Test the record.
records = file.readlines()
actual = 'HELIX 1 H1 ILE A 23 GLU A 34 1 12 \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_atom(self):
"""Test the lib.structure.pdb_write.atom() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.atom(file,
serial=158,
name='CG',
res_name='GLU',
res_seq='11',
x=9.59,
y=-1.041,
z=-11.596,
occupancy=1.0,
temp_factor=0.0,
element='C')
# Test the record.
records = file.readlines()
actual = 'ATOM 158 CG GLU 11 9.590 -1.041 -11.596 1.00 0.00 C \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_sheet(self):
"""Test the lib.structure.pdb_write.sheet() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.sheet(file, strand=1, sheet_id='BET', num_strands=5, init_res_name='GLY', init_chain_id='A', init_seq_num=10, init_icode=None, end_res_name='VAL', end_chain_id='A', end_seq_num=17, end_icode=None, sense=0, cur_atom=None, cur_res_name=None, cur_chain_id=None, cur_res_seq=None, cur_icode=None, prev_atom=None, prev_res_name=None, prev_chain_id=None, prev_res_seq=None, prev_icode=None)
# Test the record.
records = file.readlines()
actual = 'SHEET 1 BET 5 GLY A 10 VAL A 17 0 \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_model(self):
"""Test the lib.structure.pdb_write.model() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.model(file, serial=1)
# Test the record.
records = file.readlines()
actual = 'MODEL 1 \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_het(self):
"""Test the lib.structure.pdb_write.het() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.het(file, het_id='CA', chain_id='A', seq_num=1000, icode=None, num_het_atoms=1, text=None)
# Test the record.
records = file.readlines()
actual = 'HET CA A1000 1 \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_helix(self):
"""Test the lib.structure.pdb_write.helix() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.helix(file, ser_num=1, helix_id='H1', init_res_name='ILE', init_chain_id='A', init_seq_num=23, init_icode=None, end_res_name='GLU', end_chain_id='A', end_seq_num=34, end_icode=None, helix_class=1, comment=None, length=12)
# Test the record.
records = file.readlines()
actual = 'HELIX 1 H1 ILE A 23 GLU A 34 1 12 \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_atom(self):
"""Test the lib.structure.pdb_write.atom() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.atom(file, serial=158, name='CG', res_name='GLU', res_seq='11', x=9.59, y=-1.041, z=-11.596, occupancy=1.0, temp_factor=0.0, element='C')
# Test the record.
records = file.readlines()
actual = 'ATOM 158 CG GLU 11 9.590 -1.041 -11.596 1.00 0.00 C \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_model(self):
"""Test the lib.structure.pdb_write.model() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.model(file, serial=1)
# Test the record.
records = file.readlines()
actual = 'MODEL 1 \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_subsubsection(self):
"""Test of the lib.text.sectioning.subsubsection() function."""
# Write out the subsubsection.
file = DummyFileObject()
subsubsection(file=file, text='Test subsubsection')
# Read the results.
lines = file.readlines()
print("Formatted subsubsection lines: %s" % lines)
# Check the title.
real_lines = [
'\n',
'Test subsubsection\n',
'~~~~~~~~~~~~~~~~~~\n',
'\n',
]
self.assertEqual(len(lines), len(real_lines))
for i in range(len(lines)):
self.assertEqual(lines[i], real_lines[i])
def test_het(self):
"""Test the lib.structure.pdb_write.het() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.het(file,
het_id='CA',
chain_id='A',
seq_num=1000,
icode=None,
num_het_atoms=1,
text=None)
# Test the record.
records = file.readlines()
actual = 'HET CA A1000 1 \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
def test_write_list(self):
"""Test the lib.software.sparky.write_list() function."""
# The data.
res_names = ['LEU', 'GLY', 'SER', 'MET', 'TRP', 'TRP', 'ASN']
res_nums = [3, 4, 5, 6, 40, 40, 55]
atom1_names = ['N', 'N', 'N', 'N', 'N', 'NE1', 'N']
atom2_names = ['HN', 'HN', 'HN', 'HN', 'HN', 'HE1', 'HN']
w1 = [122.454, 111.978, 115.069, 120.910, 123.335, 130.204, 116.896]
w2 = [8.397, 8.720, 8.177, 8.813, 8.005, 10.294, 7.468]
heights = [2535, 5050, 51643, 53663, -65111, -181131, -105322]
# The result.
file_data = [
' Assignment w1 w2 Data Height\n', '\n',
' LEU3N-HN 122.454 8.397 2535\n',
' GLY4N-HN 111.978 8.720 5050\n',
' SER5N-HN 115.069 8.177 51643\n',
' MET6N-HN 120.910 8.813 53663\n',
' TRP40N-HN 123.335 8.005 -65111\n',
' TRP40NE1-HE1 130.204 10.294 -181131\n',
' ASN55N-HN 116.896 7.468 -105322\n'
]
# Write the data out.
file = DummyFileObject()
write_list(file_prefix=file,
res_names=res_names,
res_nums=res_nums,
atom1_names=atom1_names,
atom2_names=atom2_names,
w1=w1,
w2=w2,
data_height=heights)
# Check the file data.
lines = file.readlines()
self.assertEqual(len(lines), len(file_data))
for i in range(len(lines)):
self.assertEqual(lines[i], file_data[i])
def test_title(self):
"""Test of the lib.text.sectioning.title() function."""
# Write out the title.
file = DummyFileObject()
title(file=file, text='Test title')
# Read the results.
lines = file.readlines()
print("Formatted title lines: %s" % lines)
# Check the title.
real_lines = [
'\n',
'\n',
'==============\n',
'= Test title =\n',
'==============\n',
'\n',
]
self.assertEqual(len(lines), len(real_lines))
for i in range(len(lines)):
self.assertEqual(lines[i], real_lines[i])
def test_sheet(self):
"""Test the lib.structure.pdb_write.sheet() function."""
# A dummy file to write to.
file = DummyFileObject()
# Create the PDB record.
pdb_write.sheet(file,
strand=1,
sheet_id='BET',
num_strands=5,
init_res_name='GLY',
init_chain_id='A',
init_seq_num=10,
init_icode=None,
end_res_name='VAL',
end_chain_id='A',
end_seq_num=17,
end_icode=None,
sense=0,
cur_atom=None,
cur_res_name=None,
cur_chain_id=None,
cur_res_seq=None,
cur_icode=None,
prev_atom=None,
prev_res_name=None,
prev_chain_id=None,
prev_res_seq=None,
prev_icode=None)
# Test the record.
records = file.readlines()
actual = 'SHEET 1 BET 5 GLY A 10 VAL A 17 0 \n'
print(repr(records[0]))
print(repr(actual))
self.assertEqual(records[0], actual)
DATA_TYPES.append(['dict', {}])
DATA_TYPES.append(['dict', {'a': 0, 'b': 1}])
# Integers.
DATA_TYPES.append(['int', 2])
DATA_TYPES.append(['int', 10])
DATA_TYPES.append(['int', -10])
# Numpy ints.
DATA_TYPES.append(['int', zeros(2, int8)[0]])
DATA_TYPES.append(['int', zeros(2, int16)[0]])
DATA_TYPES.append(['int', zeros(2, int32)[0]])
DATA_TYPES.append(['int', zeros(2, int64)[0]])
# File descriptor.
DATA_TYPES.append(['file', DummyFileObject()])
# Floats.
DATA_TYPES.append(['float', 0.0])
DATA_TYPES.append(['float', 1e-7])
DATA_TYPES.append(['float', 1000000.0])
# Numpy floats.
DATA_TYPES.append(['float', zeros(2, float32)[0]])
DATA_TYPES.append(['float', zeros(2, float64)[0]])
# Functions.
DATA_TYPES.append(['function', dummy_fn])
DATA_TYPES.append(['function', dummy_fn2])
# Lists.
