def test_copy_molecule_within_pipe(self):
"""Test the copying of the molecule data within a single data pipe.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule a few times.
self.molecule_fns.copy(mol_from='#Old mol', mol_to='#2')
self.molecule_fns.copy(mol_from='#Old mol', pipe_to='orig', mol_to='#3')
# Change the first molecule's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Copy the molecule once more.
self.molecule_fns.copy(mol_from='#Old mol', mol_to='#4')
# Test the original molecule.
self.assertEqual(dp.mol[0].name, 'Old mol')
self.assertEqual(dp.mol[0].res[0].num, 1)
self.assertEqual(dp.mol[0].res[0].name, 'Ala')
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new molecule 2.
self.assertEqual(dp.mol[1].name, '2')
self.assertEqual(dp.mol[1].res[0].num, 1)
self.assertEqual(dp.mol[1].res[0].name, 'Ala')
self.assertEqual(dp.mol[1].res[0].spin[0].num, 111)
self.assertEqual(dp.mol[1].res[0].spin[0].x, 1)
# Test the new molecule 3.
self.assertEqual(dp.mol[2].name, '3')
self.assertEqual(dp.mol[2].res[0].num, 1)
self.assertEqual(dp.mol[2].res[0].name, 'Ala')
self.assertEqual(dp.mol[2].res[0].spin[0].num, 111)
self.assertEqual(dp.mol[2].res[0].spin[0].x, 1)
# Test the new molecule 4.
self.assertEqual(dp.mol[3].name, '4')
self.assertEqual(dp.mol[3].res[0].num, 1)
self.assertEqual(dp.mol[3].res[0].name, 'Ala')
self.assertEqual(dp.mol[3].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[3].res[0].spin[0].x, 2)
def setup_data(self):
"""Function for setting up some data for the unit tests."""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first residue and add some data to its spin container.
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
dp.mol[0].name = 'Old mol'
# Create a second molecule.
dp.mol.add_item('New mol')
# Copy the residue to the new molecule.
copy_residue(res_from=':1', res_to='#New mol')
copy_residue(res_from='#Old mol:1', res_to='#New mol:5')
# Change the first residue's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
def rna_seq(self):
"""Generate the RNA sequence of the noe_rna_hbond.dat restraint file."""
# Info.
mol_names = ["A", "B"]
res_nums = [[1, 2, 3, 4], [4, 3, 2, 1]]
spin_names = [
[["N1", "N6", "H62"], ["H3", "N3", "O4"], ["H1", "N1", "H22", "N2", "O6"], ["N3", "O2", "H42", "N4"]],
[["H3", "N3", "O4"], ["N1", "N6", "H62"], ["N3", "O2", "H42", "N4"], ["H1", "N1", "H22", "N2", "O6"]],
]
# Loop over the molecules.
for i in range(len(mol_names)):
# Create the molecule.
create_molecule(mol_names[i])
# Loop over the residues.
for j in range(len(res_nums[i])):
# Create the residue.
create_residue(res_nums[i][j], mol_name=mol_names[i])
# Loop over the atoms.
for k in range(len(spin_names[i][j])):
# Create the spin.
create_spin(spin_names[i][j][k], res_num=res_nums[i][j], mol_name=mol_names[i])
# Display the sequence for debugging.
self.interpreter.sequence.display()
def setup_data(self):
"""Function for setting up some data for the unit tests."""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first residue and add some data to its spin container.
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
dp.mol[0].name = 'Old mol'
# Create a second molecule.
dp.mol.add_item('New mol')
# Copy the residue to the new molecule.
copy_residue(res_from=':1', res_to='#New mol')
copy_residue(res_from='#Old mol:1', res_to='#New mol:5')
# Change the first residue's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
def test_copy_molecule_between_pipes(self):
"""Test the copying of the molecule data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipes.
dp = pipes.get_pipe('orig')
dp_test = pipes.get_pipe('test')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule to the second data pipe.
self.molecule_fns.copy(mol_from='#Old mol', pipe_to='test')
self.molecule_fns.copy(pipe_from='orig',
mol_from='#Old mol',
pipe_to='test',
mol_to='#New mol')
# Change the first molecule's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Test the original molecule.
self.assertEqual(dp.mol[0].name, 'Old mol')
self.assertEqual(dp.mol[0].res[0].num, 1)
self.assertEqual(dp.mol[0].res[0].name, 'Ala')
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new molecule.
self.assertEqual(dp_test.mol[0].name, 'Old mol')
self.assertEqual(dp_test.mol[0].res[0].num, 1)
self.assertEqual(dp_test.mol[0].res[0].name, 'Ala')
self.assertEqual(dp_test.mol[0].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[0].res[0].spin[0].x, 1)
# Test the second new molecule.
self.assertEqual(dp_test.mol[1].name, 'New mol')
self.assertEqual(dp_test.mol[1].res[0].num, 1)
self.assertEqual(dp_test.mol[1].res[0].name, 'Ala')
self.assertEqual(dp_test.mol[1].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[1].res[0].spin[0].x, 1)
def test_copy_molecule_between_pipes(self):
"""Test the copying of the molecule data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipes.
dp = pipes.get_pipe('orig')
dp_test = pipes.get_pipe('test')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule to the second data pipe.
self.molecule_fns.copy(mol_from='#Old mol', pipe_to='test')
self.molecule_fns.copy(pipe_from='orig', mol_from='#Old mol', pipe_to='test', mol_to='#New mol')
# Change the first molecule's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Test the original molecule.
self.assertEqual(dp.mol[0].name, 'Old mol')
self.assertEqual(dp.mol[0].res[0].num, 1)
self.assertEqual(dp.mol[0].res[0].name, 'Ala')
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new molecule.
self.assertEqual(dp_test.mol[0].name, 'Old mol')
self.assertEqual(dp_test.mol[0].res[0].num, 1)
self.assertEqual(dp_test.mol[0].res[0].name, 'Ala')
self.assertEqual(dp_test.mol[0].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[0].res[0].spin[0].x, 1)
# Test the second new molecule.
self.assertEqual(dp_test.mol[1].name, 'New mol')
self.assertEqual(dp_test.mol[1].res[0].num, 1)
self.assertEqual(dp_test.mol[1].res[0].name, 'Ala')
self.assertEqual(dp_test.mol[1].res[0].spin[0].num, 111)
self.assertEqual(dp_test.mol[1].res[0].spin[0].x, 1)
def generate(mol_name=None, res_num=None, res_name=None, spin_num=None, spin_name=None, pipe=None, select=True, verbose=True):
"""Generate the sequence item-by-item by adding a single molecule/residue/spin container as necessary.
@keyword mol_name: The molecule name.
@type mol_name: str or None
@keyword res_num: The residue number.
@type res_num: int or None
@keyword res_name: The residue name.
@type res_name: str or None
@keyword spin_num: The spin number.
@type spin_num: int or None
@keyword spin_name: The spin name.
@type spin_name: str or None
@keyword pipe: The data pipe in which to generate the sequence. This defaults to the current data pipe.
@type pipe: str
@keyword select: The spin selection flag.
@type select: bool
@keyword verbose: A flag which if True will cause info about each spin to be printed out as the sequence is generated.
@type verbose: bool
"""
# The current data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# A new molecule.
if not return_molecule(generate_spin_id(mol_name=mol_name), pipe=pipe):
create_molecule(mol_name=mol_name, pipe=pipe)
# A new residue.
curr_res = return_residue(generate_spin_id(mol_name=mol_name, res_num=res_num, res_name=res_name), pipe=pipe)
if not curr_res or ((res_num != None and curr_res.num != res_num) or (res_name != None and curr_res.name != res_name)):
create_residue(mol_name=mol_name, res_num=res_num, res_name=res_name, pipe=pipe)
# A new spin.
curr_spin = return_spin(generate_spin_id(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name), pipe=pipe)
if not curr_spin or ((spin_num != None and curr_spin.num != spin_num) or (spin_name != None and curr_spin.name != spin_name)):
# Add the spin.
curr_spin = create_spin(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name, pipe=pipe)
# Set the selection flag.
curr_spin.select = select
def generate(mol_name=None, res_num=None, res_name=None, spin_num=None, spin_name=None, pipe=None, select=True, verbose=True):
"""Generate the sequence item-by-item by adding a single molecule/residue/spin container as necessary.
@keyword mol_name: The molecule name.
@type mol_name: str or None
@keyword res_num: The residue number.
@type res_num: int or None
@keyword res_name: The residue name.
@type res_name: str or None
@keyword spin_num: The spin number.
@type spin_num: int or None
@keyword spin_name: The spin name.
@type spin_name: str or None
@keyword pipe: The data pipe in which to generate the sequence. This defaults to the current data pipe.
@type pipe: str
@keyword select: The spin selection flag.
@type select: bool
@keyword verbose: A flag which if True will cause info about each spin to be printed out as the sequence is generated.
@type verbose: bool
"""
# The current data pipe.
if pipe == None:
pipe = pipes.cdp_name()
# A new molecule.
if not return_molecule(generate_spin_id(mol_name=mol_name), pipe=pipe):
create_molecule(mol_name=mol_name, pipe=pipe)
# A new residue.
curr_res = return_residue(generate_spin_id(mol_name=mol_name, res_num=res_num, res_name=res_name), pipe=pipe)
if not curr_res or ((res_num != None and curr_res.num != res_num) or (res_name != None and curr_res.name != res_name)):
create_residue(mol_name=mol_name, res_num=res_num, res_name=res_name, pipe=pipe)
# A new spin.
curr_spin = return_spin(spin_id=generate_spin_id(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name), pipe=pipe)
if not curr_spin or ((spin_num != None and curr_spin.num != spin_num) or (spin_name != None and curr_spin.name != spin_name)):
# Add the spin.
curr_spin = create_spin(mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin_num, spin_name=spin_name, pipe=pipe)[0]
# Set the selection flag.
curr_spin.select = select
def test_copy_molecule_between_pipes_fail_no_pipe(self):
"""Test the failure of copying of the molecule data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule to the second data pipe.
self.assertRaises(RelaxNoPipeError, self.molecule_fns.copy, mol_from='#Old mol', pipe_to='test2')
def rna_seq(self):
"""Generate the RNA sequence of the noe_rna_hbond.dat restraint file."""
# Info.
mol_names = ['A', 'B']
res_nums = [
[1, 2, 3, 4],
[4, 3, 2, 1]
]
spin_names = [
[['N1', 'N6', 'H62'],
['H3', 'N3', 'O4'],
['H1', 'N1', 'H22', 'N2', 'O6'],
['N3', 'O2', 'H42', 'N4']],
[['H3', 'N3', 'O4'],
['N1', 'N6', 'H62'],
['N3', 'O2', 'H42', 'N4'],
['H1', 'N1', 'H22', 'N2', 'O6']]
]
# Loop over the molecules.
for i in range(len(mol_names)):
# Create the molecule.
create_molecule(mol_names[i])
# Loop over the residues.
for j in range(len(res_nums[i])):
# Create the residue.
create_residue(res_nums[i][j], mol_name=mol_names[i])
# Loop over the atoms.
for k in range(len(spin_names[i][j])):
# Create the spin.
create_spin(spin_names[i][j][k], res_num=res_nums[i][j], mol_name=mol_names[i])
# Display the sequence for debugging.
self.interpreter.sequence.display()
def test_copy_molecule_between_pipes_fail_no_pipe(self):
"""Test the failure of copying of the molecule data between different data pipes.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule to the second data pipe.
self.assertRaises(RelaxNoPipeError,
self.molecule_fns.copy,
mol_from='#Old mol',
pipe_to='test2')
def test_copy_molecule_within_pipe(self):
"""Test the copying of the molecule data within a single data pipe.
The function tested is both pipe_control.mol_res_spin.copy_molecule() and
prompt.molecule.copy().
"""
# Get the data pipe.
dp = pipes.get_pipe('orig')
# Create the first molecule and residue and add some data to its spin container.
self.molecule_fns.create('Old mol')
create_residue(1, 'Ala')
dp.mol[0].res[0].spin[0].num = 111
dp.mol[0].res[0].spin[0].x = 1
# Update the metadata.
metadata_update()
# Copy the molecule a few times.
self.molecule_fns.copy(mol_from='#Old mol', mol_to='#2')
self.molecule_fns.copy(mol_from='#Old mol',
pipe_to='orig',
mol_to='#3')
# Change the first molecule's data.
dp.mol[0].res[0].spin[0].num = 222
dp.mol[0].res[0].spin[0].x = 2
# Update the metadata.
metadata_update()
# Copy the molecule once more.
self.molecule_fns.copy(mol_from='#Old mol', mol_to='#4')
# Test the original molecule.
self.assertEqual(dp.mol[0].name, 'Old mol')
self.assertEqual(dp.mol[0].res[0].num, 1)
self.assertEqual(dp.mol[0].res[0].name, 'Ala')
self.assertEqual(dp.mol[0].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[0].res[0].spin[0].x, 2)
# Test the new molecule 2.
self.assertEqual(dp.mol[1].name, '2')
self.assertEqual(dp.mol[1].res[0].num, 1)
self.assertEqual(dp.mol[1].res[0].name, 'Ala')
self.assertEqual(dp.mol[1].res[0].spin[0].num, 111)
self.assertEqual(dp.mol[1].res[0].spin[0].x, 1)
# Test the new molecule 3.
self.assertEqual(dp.mol[2].name, '3')
self.assertEqual(dp.mol[2].res[0].num, 1)
self.assertEqual(dp.mol[2].res[0].name, 'Ala')
self.assertEqual(dp.mol[2].res[0].spin[0].num, 111)
self.assertEqual(dp.mol[2].res[0].spin[0].x, 1)
# Test the new molecule 4.
self.assertEqual(dp.mol[3].name, '4')
self.assertEqual(dp.mol[3].res[0].num, 1)
self.assertEqual(dp.mol[3].res[0].name, 'Ala')
self.assertEqual(dp.mol[3].res[0].spin[0].num, 222)
self.assertEqual(dp.mol[3].res[0].spin[0].x, 2)
