def test_count_spins(self):
"""Test that the number of spins can be properly counted.
The function tested is pipe_control.mol_res_spin.count_spins().
"""
# Test the number of spins counted.
self.assertEqual(mol_res_spin.count_spins(), 4)
self.assertEqual(mol_res_spin.count_spins(skip_desel=False), 8)
self.assertEqual(mol_res_spin.count_spins(selection='@N5'), 1)
self.assertEqual(mol_res_spin.count_spins(selection='@N5', skip_desel=False), 2)
def test_count_spins(self):
"""Test that the number of spins can be properly counted.
The function tested is pipe_control.mol_res_spin.count_spins().
"""
# Test the number of spins counted.
self.assertEqual(mol_res_spin.count_spins(), 4)
self.assertEqual(mol_res_spin.count_spins(skip_desel=False), 8)
self.assertEqual(mol_res_spin.count_spins(selection='@N5'), 1)
self.assertEqual(
mol_res_spin.count_spins(selection='@N5', skip_desel=False), 2)
def compare_sequence(pipe1=None, pipe2=None, fail=True):
"""Compare the sequence in two data pipes.
@keyword pipe1: The name of the first data pipe.
@type pipe1: str
@keyword pipe2: The name of the second data pipe.
@type pipe2: str
@keyword fail: A flag which if True causes a RelaxError to be raised.
@type fail: bool
@return: 1 if the sequence is the same, 0 if different.
@rtype: int
@raises RelaxError: If the sequence is different and the fail flag is True.
"""
# Failure status.
status = 1
# Molecule number.
if count_molecules(pipe=pipe1) != count_molecules(pipe=pipe2):
status = 0
if fail:
raise RelaxDiffMolNumError(pipe1, pipe2)
# Residue number.
if count_residues(pipe=pipe1) != count_residues(pipe=pipe2):
status = 0
if fail:
raise RelaxDiffResNumError(pipe1, pipe2)
# Spin number.
if count_spins(pipe=pipe1) != count_spins(pipe=pipe2):
status = 0
if fail:
raise RelaxDiffSpinNumError(pipe1, pipe2)
# Create a string representation of the 2 sequences.
seq1 = ''
seq2 = ''
for spin, spin_id in spin_loop(return_id=True, pipe=pipe1):
seq1 = seq1 + spin_id + '\n'
for spin, spin_id in spin_loop(return_id=True, pipe=pipe2):
seq2 = seq2 + spin_id + '\n'
# Sequence check.
if seq1 != seq2:
status = 0
if fail:
raise RelaxDiffSeqError(pipe1, pipe2)
# Return the status.
return status
def compare_sequence(pipe1=None, pipe2=None, fail=True):
"""Compare the sequence in two data pipes.
@keyword pipe1: The name of the first data pipe.
@type pipe1: str
@keyword pipe2: The name of the second data pipe.
@type pipe2: str
@keyword fail: A flag which if True causes a RelaxError to be raised.
@type fail: bool
@return: 1 if the sequence is the same, 0 if different.
@rtype: int
@raises RelaxError: If the sequence is different and the fail flag is True.
"""
# Failure status.
status = 1
# Molecule number.
if count_molecules(pipe=pipe1) != count_molecules(pipe=pipe2):
status = 0
if fail:
raise RelaxDiffMolNumError(pipe1, pipe2)
# Residue number.
if count_residues(pipe=pipe1) != count_residues(pipe=pipe2):
status = 0
if fail:
raise RelaxDiffResNumError(pipe1, pipe2)
# Spin number.
if count_spins(pipe=pipe1) != count_spins(pipe=pipe2):
status = 0
if fail:
raise RelaxDiffSpinNumError(pipe1, pipe2)
# Create a string representation of the 2 sequences.
seq1 = ''
seq2 = ''
for spin, spin_id in spin_loop(return_id=True, pipe=pipe1):
seq1 = seq1 + spin_id + '\n'
for spin, spin_id in spin_loop(return_id=True, pipe=pipe2):
seq2 = seq2 + spin_id + '\n'
# Sequence check.
if seq1 != seq2:
status = 0
if fail:
raise RelaxDiffSeqError(pipe1, pipe2)
# Return the status.
return status
def determine_seq_type(spin_id=None):
"""Determine the spin sequence data type.
The purpose is to identify systems whereby only spins or only residues exist.
@keyword spin_id: The spin identification string.
@type spin_id: str
@return: The spin sequence data type. This can be one of 'spin', 'res,' or 'mixed'.
@rtype: str
"""
# Count the molecules, residues, and spins.
num_mol = count_molecules(spin_id)
num_res = count_residues(spin_id)
num_spin = count_spins(spin_id)
# Only residues.
if num_mol == 1 and num_spin == 1:
return 'res'
# Only spins.
if num_mol == 1 and num_res == 1:
return 'spin'
# Mixed.
return 'mixed'
def determine_seq_type(spin_id=None):
"""Determine the spin sequence data type.
The purpose is to identify systems whereby only spins or only residues exist.
@keyword spin_id: The spin identification string.
@type spin_id: str
@return: The spin sequence data type. This can be one of 'spin', 'res,' or 'mixed'.
@rtype: str
"""
# Count the molecules, residues, and spins.
num_mol = count_molecules(spin_id)
num_res = count_residues(spin_id)
num_spin = count_spins(spin_id)
# Only residues.
if num_mol == 1 and num_spin == 1:
return 'res'
# Only spins.
if num_mol == 1 and num_res == 1:
return 'spin'
# Mixed.
return 'mixed'
def test_pcs_load(self):
"""Test for the loading of some PCS data with the spin ID format."""
# Create a data pipe.
self.interpreter.pipe.create('test', 'N-state')
# Data directory.
dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
# Load the spins.
self.interpreter.sequence.read(file='pcs.txt', dir=dir, spin_name_col=1)
self.interpreter.sequence.display()
# Load the PCSs.
self.interpreter.pcs.read(align_id='tb', file='pcs.txt', dir=dir, spin_name_col=1, data_col=2)
self.interpreter.sequence.display()
# The PCSs.
pcs = [0.004, 0.008, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006, 0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054, 0.075, 0.065, None, 0.070, 0.015, 0.098, 0.060, 0.120]
# Checks.
self.assertEqual(count_spins(), 26)
self.assertEqual(len(cdp.interatomic), 0)
i = 0
for spin in spin_loop():
self.assertEqual(pcs[i], spin.pcs['tb'])
i += 1
def display(sep=None, mol_name_flag=False, res_num_flag=False, res_name_flag=False, spin_num_flag=False, spin_name_flag=False):
"""Display the molecule, residue, and/or spin sequence data.
This calls the write() function to do most of the work.
@keyword sep: The column seperator which, if None, defaults to whitespace.
@type sep: str or None
@keyword mol_name_flag: A flag which if True will cause the molecule name column to be
written.
@type mol_name_flag: bool
@keyword res_num_flag: A flag which if True will cause the residue number column to be
written.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the residue name column to be
written.
@type res_name_flag: bool
@keyword spin_name_flag: A flag which if True will cause the spin name column to be written.
@type spin_name_flag: bool
@keyword spin_num_flag: A flag which if True will cause the spin number column to be
written.
@type spin_num_flag: bool
@param mol_name_flag: The column to contain the molecule name information.
"""
# Test if the sequence data is loaded.
if not count_spins():
raise RelaxNoSequenceError
# Write the data.
write(file=sys.stdout, sep=sep, mol_name_flag=mol_name_flag, res_num_flag=res_num_flag, res_name_flag=res_name_flag, spin_num_flag=spin_num_flag, spin_name_flag=spin_name_flag)
def display(sep=None, mol_name_flag=False, res_num_flag=False, res_name_flag=False, spin_num_flag=False, spin_name_flag=False):
"""Display the molecule, residue, and/or spin sequence data.
This calls the write() function to do most of the work.
@keyword sep: The column seperator which, if None, defaults to whitespace.
@type sep: str or None
@keyword mol_name_flag: A flag which if True will cause the molecule name column to be
written.
@type mol_name_flag: bool
@keyword res_num_flag: A flag which if True will cause the residue number column to be
written.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the residue name column to be
written.
@type res_name_flag: bool
@keyword spin_name_flag: A flag which if True will cause the spin name column to be written.
@type spin_name_flag: bool
@keyword spin_num_flag: A flag which if True will cause the spin number column to be
written.
@type spin_num_flag: bool
@param mol_name_flag: The column to contain the molecule name information.
"""
# Test if the sequence data is loaded.
if not count_spins():
raise RelaxNoSequenceError
# Write the data.
write(file=sys.stdout, sep=sep, mol_name_flag=mol_name_flag, res_num_flag=res_num_flag, res_name_flag=res_name_flag, spin_num_flag=spin_num_flag, spin_name_flag=spin_name_flag)
def test_rdc_load(self):
"""Test for the loading of some RDC data with the spin ID format."""
# Create a data pipe.
self.interpreter.pipe.create('test', 'N-state')
# Data directory.
dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
# Load the spins.
self.interpreter.sequence.read(file='tb.txt', dir=dir, spin_id_col=1)
self.interpreter.sequence.attach_protons()
self.interpreter.sequence.display()
# Load the RDCs.
self.interpreter.rdc.read(align_id='tb', file='tb.txt', dir=dir, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
self.interpreter.sequence.display()
# The RDCs.
rdcs = [ -26.2501958629, 9.93081766942, 7.26317614156, -1.24840526981, 5.31803314334, 14.0362909456, 1.33652530397, -1.6021670281]
# Checks.
self.assertEqual(count_spins(), 16)
self.assertEqual(len(cdp.interatomic), 8)
i = 0
for interatom in interatomic_loop():
self.assertAlmostEqual(rdcs[i], interatom.rdc['tb'])
i += 1
def test_rdc_load(self):
"""Test for the loading of some RDC data with the spin ID format."""
# Create a data pipe.
self.interpreter.pipe.create('test', 'N-state')
# Data directory.
dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
# Load the spins.
self.interpreter.sequence.read(file='tb.txt', dir=dir, spin_id_col=1)
self.interpreter.sequence.attach_protons()
self.interpreter.sequence.display()
# Load the RDCs.
self.interpreter.rdc.read(align_id='tb', file='tb.txt', dir=dir, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
self.interpreter.sequence.display()
# The RDCs.
rdcs = [ -26.2501958629, 9.93081766942, 7.26317614156, -1.24840526981, 5.31803314334, 14.0362909456, 1.33652530397, -1.6021670281]
# Checks.
self.assertEqual(count_spins(), 16)
self.assertEqual(len(cdp.interatomic), 8)
i = 0
for interatom in interatomic_loop():
self.assertAlmostEqual(rdcs[i], interatom.rdc['tb'])
i += 1
def write(file, dir=None, sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True, force=False):
"""Write the molecule, residue, and/or sequence data.
This calls the lib.io.write_spin_data() function to do most of the work.
@param file: The name of the file to write the data to.
@type file: str
@keyword dir: The directory to contain the file (defaults to the current directory if None).
@type dir: str or None
@keyword sep: The column seperator which, if None, defaults to whitespace.
@type sep: str or None
@keyword mol_name_flag: A flag which if True will cause the molecule name column to be written.
@type mol_name_flag: bool
@keyword res_num_flag: A flag which if True will cause the residue number column to be written.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the residue name column to be written.
@type res_name_flag: bool
@keyword spin_name_flag: A flag which if True will cause the spin name column to be written.
@type spin_name_flag: bool
@keyword spin_num_flag: A flag which if True will cause the spin number column to be written.
@keyword force: A flag which if True will cause an existing file to be overwritten.
@type force: bin
"""
# Test if the sequence data is loaded.
if not count_spins():
raise RelaxNoSequenceError
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
# Spin loop.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
mol_names.append(mol_name)
res_nums.append(res_num)
res_names.append(res_name)
spin_nums.append(spin.num)
spin_names.append(spin.name)
# Remove unwanted data.
if not mol_name_flag:
mol_names = None
if not res_num_flag:
res_nums = None
if not res_name_flag:
res_names = None
if not spin_num_flag:
spin_nums = None
if not spin_name_flag:
spin_names = None
# Write the data.
write_spin_data(file=file, dir=dir, sep=sep, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, force=force)
def write(file, dir=None, sep=None, mol_name_flag=True, res_num_flag=True, res_name_flag=True, spin_num_flag=True, spin_name_flag=True, force=False):
"""Write the molecule, residue, and/or sequence data.
This calls the lib.io.write_spin_data() function to do most of the work.
@param file: The name of the file to write the data to.
@type file: str
@keyword dir: The directory to contain the file (defaults to the current directory if None).
@type dir: str or None
@keyword sep: The column seperator which, if None, defaults to whitespace.
@type sep: str or None
@keyword mol_name_flag: A flag which if True will cause the molecule name column to be written.
@type mol_name_flag: bool
@keyword res_num_flag: A flag which if True will cause the residue number column to be written.
@type res_num_flag: bool
@keyword res_name_flag: A flag which if True will cause the residue name column to be written.
@type res_name_flag: bool
@keyword spin_name_flag: A flag which if True will cause the spin name column to be written.
@type spin_name_flag: bool
@keyword spin_num_flag: A flag which if True will cause the spin number column to be written.
@keyword force: A flag which if True will cause an existing file to be overwritten.
@type force: bin
"""
# Test if the sequence data is loaded.
if not count_spins():
raise RelaxNoSequenceError
# Init the data.
mol_names = []
res_nums = []
res_names = []
spin_nums = []
spin_names = []
# Spin loop.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
mol_names.append(mol_name)
res_nums.append(res_num)
res_names.append(res_name)
spin_nums.append(spin.num)
spin_names.append(spin.name)
# Remove unwanted data.
if not mol_name_flag:
mol_names = None
if not res_num_flag:
res_nums = None
if not res_name_flag:
res_names = None
if not spin_num_flag:
spin_nums = None
if not spin_name_flag:
spin_names = None
# Write the data.
write_spin_data(file=file, dir=dir, sep=sep, mol_names=mol_names, res_nums=res_nums, res_names=res_names, spin_nums=spin_nums, spin_names=spin_names, force=force)
def _num_instances_spin(self):
"""Return the number of instances, equal to the number of selected spins.
@return: The number of instances (equal to the number of spins).
@rtype: int
"""
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Return the number of spins.
return count_spins()
def _num_instances_spin(self):
"""Return the number of instances, equal to the number of selected spins.
@return: The number of instances (equal to the number of spins).
@rtype: int
"""
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Return the number of spins.
return count_spins()
def test_pcs_copy_different_spins(self):
"""Test the operation of the pcs.copy user function for two data pipes with different spin system."""
# Data directory.
dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
# Set up two data identical pipes.
pipes = ['orig', 'new']
delete = ['@C2', '@H17']
for i in range(2):
# Create a data pipe.
self.interpreter.pipe.create(pipes[i], 'N-state')
# Load the spins.
self.interpreter.sequence.read(file='pcs.txt', dir=dir, spin_name_col=1)
# Delete the spin.
self.interpreter.spin.delete(delete[i])
self.interpreter.sequence.display()
# Load the PCSs into the first data pipe.
self.interpreter.pipe.switch('orig')
self.interpreter.pcs.read(align_id='tb', file='pcs.txt', dir=dir, spin_name_col=1, data_col=2)
# Copy the PCSs into the second data pipe.
self.interpreter.pcs.copy(pipe_from='orig', pipe_to='new', align_id='tb')
# Checks.
pcs = [
[0.004, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006, 0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054, 0.075, 0.065, None, 0.070, 0.015, 0.098, 0.060, 0.120],
[0.004, 0.008, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006, 0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054, 0.075, 0.065, None, 0.070, 0.015, 0.098, 0.120]
]
for i in range(2):
print("\nChecking data pipe '%s'." % pipes[i])
self.assert_(hasattr(ds[pipes[i]], 'align_ids'))
self.assert_('tb' in ds[pipes[i]].align_ids)
self.assert_(hasattr(ds[pipes[i]], 'pcs_ids'))
self.assert_('tb' in ds[pipes[i]].pcs_ids)
self.assertEqual(count_spins(), 25)
self.assertEqual(len(cdp.interatomic), 0)
j = 0
for spin in spin_loop(pipe=pipes[i]):
# Atom C2 in the 'new' data pipe has no PCSs.
if i == 1 and j == 1:
self.assert_(not hasattr(spin, 'pcs'))
else:
if pcs[i][j] == None:
self.assertEqual(pcs[i][j], spin.pcs['tb'])
else:
self.assertAlmostEqual(pcs[i][j], spin.pcs['tb'])
j += 1
def test_rdc_copy(self):
"""Test the operation of the rdc.copy user function."""
# Create a data pipe.
self.interpreter.pipe.create('orig', 'N-state')
# Data directory.
dir = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'align_data' + sep
# Load the spins.
self.interpreter.sequence.read(file='tb.txt', dir=dir, spin_id_col=1)
self.interpreter.sequence.attach_protons()
self.interpreter.sequence.display()
# Load the RDCs.
self.interpreter.rdc.read(align_id='tb',
file='tb.txt',
dir=dir,
spin_id1_col=1,
spin_id2_col=2,
data_col=3,
error_col=4)
self.interpreter.sequence.display()
# The RDCs.
rdcs = [
-26.2501958629, 9.93081766942, 7.26317614156, -1.24840526981,
5.31803314334, 14.0362909456, 1.33652530397, -1.6021670281
]
# Create a new data pipe by copying the old, then switch to it.
self.interpreter.pipe.copy(pipe_from='orig', pipe_to='new')
self.interpreter.pipe.switch(pipe_name='new')
# Delete the RDC data.
self.interpreter.rdc.delete()
# Copy the RDCs.
self.interpreter.rdc.copy(pipe_from='orig', align_id='tb')
# Checks.
self.assert_(hasattr(cdp, 'align_ids'))
self.assert_('tb' in cdp.align_ids)
self.assert_(hasattr(cdp, 'rdc_ids'))
self.assert_('tb' in cdp.rdc_ids)
self.assertEqual(count_spins(), 16)
self.assertEqual(len(cdp.interatomic), 8)
i = 0
for interatom in interatomic_loop():
self.assertAlmostEqual(rdcs[i], interatom.rdc['tb'])
i += 1
def test_pcs_copy(self):
"""Test the operation of the pcs.copy user function."""
# Create a data pipe.
self.interpreter.pipe.create('orig', 'N-state')
# Data directory.
dir = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'align_data' + sep
# Load the spins.
self.interpreter.sequence.read(file='pcs.txt',
dir=dir,
spin_name_col=1)
self.interpreter.sequence.display()
# Load the PCSs.
self.interpreter.pcs.read(align_id='tb',
file='pcs.txt',
dir=dir,
spin_name_col=1,
data_col=2)
self.interpreter.sequence.display()
# The PCSs.
pcs = [
0.004, 0.008, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006,
0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054,
0.075, 0.065, None, 0.070, 0.015, 0.098, 0.060, 0.120
]
# Create a new data pipe by copying the old, then switch to it.
self.interpreter.pipe.copy(pipe_from='orig', pipe_to='new')
self.interpreter.pipe.switch(pipe_name='new')
# Delete the PCS data.
self.interpreter.pcs.delete()
# Copy the PCSs.
self.interpreter.pcs.copy(pipe_from='orig', align_id='tb')
# Checks.
self.assert_(hasattr(cdp, 'align_ids'))
self.assert_('tb' in cdp.align_ids)
self.assert_(hasattr(cdp, 'pcs_ids'))
self.assert_('tb' in cdp.pcs_ids)
self.assertEqual(count_spins(), 26)
self.assertEqual(len(cdp.interatomic), 0)
i = 0
for spin in spin_loop():
self.assertEqual(pcs[i], spin.pcs['tb'])
i += 1
def test_count_no_spins(self):
"""Test that the number of spins (zero) can be properly counted.
The function tested is pipe_control.mol_res_spin.count_spins().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Test the number of spins counted.
self.assertEqual(mol_res_spin.count_spins(), 0)
def test_count_no_spins(self):
"""Test that the number of spins (zero) can be properly counted.
The function tested is pipe_control.mol_res_spin.count_spins().
"""
# Reset relax.
reset()
# Add a data pipe to the data store.
ds.add(pipe_name='orig', pipe_type='mf')
# Test the number of spins counted.
self.assertEqual(mol_res_spin.count_spins(), 0)
def test_rdc_copy(self):
"""Test the operation of the rdc.copy user function."""
# Create a data pipe.
self.interpreter.pipe.create('orig', 'N-state')
# Data directory.
dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
# Load the spins.
self.interpreter.sequence.read(file='tb.txt', dir=dir, spin_id_col=1)
self.interpreter.sequence.attach_protons()
self.interpreter.sequence.display()
# Load the RDCs.
self.interpreter.rdc.read(align_id='tb', file='tb.txt', dir=dir, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
self.interpreter.sequence.display()
# The RDCs.
rdcs = [ -26.2501958629, 9.93081766942, 7.26317614156, -1.24840526981, 5.31803314334, 14.0362909456, 1.33652530397, -1.6021670281]
# Create a new data pipe by copying the old, then switch to it.
self.interpreter.pipe.copy(pipe_from='orig', pipe_to='new')
self.interpreter.pipe.switch(pipe_name='new')
# Delete the RDC data.
self.interpreter.rdc.delete()
# Copy the RDCs.
self.interpreter.rdc.copy(pipe_from='orig', align_id='tb')
# Checks.
self.assert_(hasattr(cdp, 'align_ids'))
self.assert_('tb' in cdp.align_ids)
self.assert_(hasattr(cdp, 'rdc_ids'))
self.assert_('tb' in cdp.rdc_ids)
self.assertEqual(count_spins(), 16)
self.assertEqual(len(cdp.interatomic), 8)
i = 0
for interatom in interatomic_loop():
self.assertAlmostEqual(rdcs[i], interatom.rdc['tb'])
i += 1
def test_pcs_copy(self):
"""Test the operation of the pcs.copy user function."""
# Create a data pipe.
self.interpreter.pipe.create('orig', 'N-state')
# Data directory.
dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
# Load the spins.
self.interpreter.sequence.read(file='pcs.txt', dir=dir, spin_name_col=1)
self.interpreter.sequence.display()
# Load the PCSs.
self.interpreter.pcs.read(align_id='tb', file='pcs.txt', dir=dir, spin_name_col=1, data_col=2)
self.interpreter.sequence.display()
# The PCSs.
pcs = [0.004, 0.008, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006, 0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054, 0.075, 0.065, None, 0.070, 0.015, 0.098, 0.060, 0.120]
# Create a new data pipe by copying the old, then switch to it.
self.interpreter.pipe.copy(pipe_from='orig', pipe_to='new')
self.interpreter.pipe.switch(pipe_name='new')
# Delete the PCS data.
self.interpreter.pcs.delete()
# Copy the PCSs.
self.interpreter.pcs.copy(pipe_from='orig', align_id='tb')
# Checks.
self.assert_(hasattr(cdp, 'align_ids'))
self.assert_('tb' in cdp.align_ids)
self.assert_(hasattr(cdp, 'pcs_ids'))
self.assert_('tb' in cdp.pcs_ids)
self.assertEqual(count_spins(), 26)
self.assertEqual(len(cdp.interatomic), 0)
i = 0
for spin in spin_loop():
self.assertEqual(pcs[i], spin.pcs['tb'])
i += 1
def spin_count(self):
"""Count the number of loaded spins, returning a string formatted as 'xxx spins loaded'.
@return: The number of loaded spins in the format 'xxx spins loaded'.
@rtype: str
"""
# The data pipe.
if hasattr(self.data, 'pipe_name'):
pipe = self.data.pipe_name
else:
pipe = cdp_name()
# The count.
if not has_pipe(pipe):
num = 0
else:
num = count_spins(pipe=pipe)
# Return the formatted string.
return "%s spins loaded and selected" % num
def spin_count(self):
"""Count the number of loaded spins, returning a string formatted as 'xxx spins loaded'.
@return: The number of loaded spins in the format 'xxx spins loaded'.
@rtype: str
"""
# The data pipe.
if hasattr(self.data, 'pipe_name'):
pipe = self.data.pipe_name
else:
pipe = cdp_name()
# The count.
if not has_pipe(pipe):
num = 0
else:
num = count_spins(pipe=pipe)
# Return the formatted string.
return "%s spins loaded and selected" % num
def test_pcs_load(self):
"""Test for the loading of some PCS data with the spin ID format."""
# Create a data pipe.
self.interpreter.pipe.create('test', 'N-state')
# Data directory.
dir = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'align_data' + sep
# Load the spins.
self.interpreter.sequence.read(file='pcs.txt',
dir=dir,
spin_name_col=1)
self.interpreter.sequence.display()
# Load the PCSs.
self.interpreter.pcs.read(align_id='tb',
file='pcs.txt',
dir=dir,
spin_name_col=1,
data_col=2)
self.interpreter.sequence.display()
# The PCSs.
pcs = [
0.004, 0.008, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006,
0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054,
0.075, 0.065, None, 0.070, 0.015, 0.098, 0.060, 0.120
]
# Checks.
self.assertEqual(count_spins(), 26)
self.assertEqual(len(cdp.interatomic), 0)
i = 0
for spin in spin_loop():
self.assertEqual(pcs[i], spin.pcs['tb'])
i += 1
def copy(pipe_from=None, pipe_to=None, spin_id1=None, spin_id2=None, verbose=True):
"""Copy the interatomic data from one data pipe to another.
@keyword pipe_from: The data pipe to copy the interatomic data from. This defaults to the current data pipe.
@type pipe_from: str
@keyword pipe_to: The data pipe to copy the interatomic data to. This defaults to the current data pipe.
@type pipe_to: str
@keyword spin_id1: The spin ID string of the first atom.
@type spin_id1: str
@keyword spin_id2: The spin ID string of the second atom.
@type spin_id2: str
@keyword verbose: A flag which if True will cause info about each spin pair to be printed out.
@type verbose: bool
"""
# Defaults.
if pipe_from == None and pipe_to == None:
raise RelaxError("The pipe_from and pipe_to arguments cannot both be set to None.")
elif pipe_from == None:
pipe_from = pipes.cdp_name()
elif pipe_to == None:
pipe_to = pipes.cdp_name()
# Test if the pipe_from and pipe_to data pipes exist.
pipes.test(pipe_from)
pipes.test(pipe_to)
# Check that the spin IDs exist.
if spin_id1:
if count_spins(selection=spin_id1, pipe=pipe_from, skip_desel=False) == 0:
raise RelaxNoSpinError(spin_id1, pipe_from)
if count_spins(selection=spin_id1, pipe=pipe_to, skip_desel=False) == 0:
raise RelaxNoSpinError(spin_id1, pipe_to)
if spin_id2:
if count_spins(selection=spin_id2, pipe=pipe_from, skip_desel=False) == 0:
raise RelaxNoSpinError(spin_id2, pipe_from)
if count_spins(selection=spin_id2, pipe=pipe_to, skip_desel=False) == 0:
raise RelaxNoSpinError(spin_id2, pipe_to)
# Check for the sequence data in the target pipe if no spin IDs are given.
if not spin_id1 and not spin_id2:
for spin, spin_id in spin_loop(pipe=pipe_from, return_id=True):
if not return_spin(spin_id, pipe=pipe_to):
raise RelaxNoSpinError(spin_id, pipe_to)
# Test if pipe_from contains interatomic data (skipping the rest of the function if it is missing).
if not exists_data(pipe_from):
return
# Loop over the interatomic data of the pipe_from data pipe.
ids = []
for interatom in interatomic_loop(selection1=spin_id1, selection2=spin_id2, pipe=pipe_from):
# Create a new container.
new_interatom = create_interatom(spin_id1=interatom.spin_id1, spin_id2=interatom.spin_id2, pipe=pipe_to)
# Duplicate all the objects of the container.
for name in dir(interatom):
# Skip special objects.
if search('^_', name):
continue
# Skip the spin IDs.
if name in ['spin_id1', 'spin_id2']:
continue
# Skip class methods.
if name in list(interatom.__class__.__dict__.keys()):
continue
# Duplicate all other objects.
obj = deepcopy(getattr(interatom, name))
setattr(new_interatom, name, obj)
# Store the IDs for the printout.
ids.append([repr(interatom.spin_id1), repr(interatom.spin_id2)])
# Print out.
if verbose:
write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2"], data=ids)
def test_rdc_copy_back_calc(self):
"""Test the operation of the rdc.copy user function for back-calculated values."""
# Data directory.
dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
# Set up two data identical pipes.
pipes = ['orig', 'new']
delete = [':6', ':11']
for i in range(2):
# Create a data pipe.
self.interpreter.pipe.create(pipes[i], 'N-state')
# Load the spins.
self.interpreter.sequence.read(file='tb.txt', dir=dir, spin_id_col=1)
self.interpreter.spin.element('N')
# Delete the residue.
self.interpreter.residue.delete(delete[i])
# Attach protons.
self.interpreter.sequence.attach_protons()
self.interpreter.sequence.display()
# Create the interatomic data containers.
self.interpreter.interatom.define(spin_id1='@N', spin_id2='@H')
# Printout.
print("\n\nInteratomic data containers for the 'orig' data pipe:")
for interatom in interatomic_loop(pipe='orig'):
print("'%s' '%s'" % (interatom.spin_id1, interatom.spin_id2))
print("\nInteratomic data containers for the 'new' data pipe:")
for interatom in interatomic_loop(pipe='new'):
print("'%s' '%s'" % (interatom.spin_id1, interatom.spin_id2))
# Load the RDCs into the first data pipe.
self.interpreter.pipe.switch('orig')
self.interpreter.rdc.read(align_id='tb', file='tb.txt', dir=dir, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
# Create back-calculated RDC values from the real values.
for interatom in interatomic_loop():
if hasattr(interatom, 'rdc'):
if not hasattr(interatom, 'rdc_bc'):
interatom.rdc_bc = {}
interatom.rdc_bc['tb'] = interatom.rdc['tb'] + 1.0
# Copy the RDCs, including back-calculated values, into the second data pipe.
self.interpreter.rdc.copy(pipe_from='orig', pipe_to='new', align_id='tb', back_calc=True)
# Checks.
rdcs = [
[ -26.2501958629, 7.26317614156, -1.24840526981, 5.31803314334, 14.0362909456, 1.33652530397, -1.6021670281],
[ -26.2501958629, 9.93081766942, 7.26317614156, -1.24840526981, 5.31803314334, 14.0362909456, -1.6021670281]
]
for i in range(2):
print("\nChecking data pipe '%s'." % pipes[i])
# Metadata.
self.assert_(hasattr(ds[pipes[i]], 'align_ids'))
self.assert_('tb' in ds[pipes[i]].align_ids)
self.assert_(hasattr(ds[pipes[i]], 'rdc_ids'))
self.assert_('tb' in ds[pipes[i]].rdc_ids)
# Spin data.
self.assertEqual(count_spins(pipe=pipes[i]), 14)
self.assertEqual(len(ds[pipes[i]].interatomic), 7)
j = 0
for interatom in interatomic_loop(pipe=pipes[i]):
# Residue 6 in the 'new' data pipe has no RDCs.
if i == 1 and j == 1:
self.assert_(not hasattr(interatom, 'rdc'))
self.assert_(not hasattr(interatom, 'rdc_data_types'))
self.assert_(not hasattr(interatom, 'absolute_rdc'))
else:
self.assertAlmostEqual(rdcs[i][j], interatom.rdc['tb'])
self.assertAlmostEqual(rdcs[i][j]+1.0, interatom.rdc_bc['tb'])
self.assert_(hasattr(interatom, 'rdc_data_types'))
self.assert_('tb' in interatom.rdc_data_types)
self.assertEqual(interatom.rdc_data_types['tb'], 'D')
self.assert_(hasattr(interatom, 'absolute_rdc'))
self.assert_('tb' in interatom.absolute_rdc)
self.assertEqual(interatom.absolute_rdc['tb'], False)
j += 1
def test_curve_fitting_height_estimate_error(self):
"""Test the relaxation curve fitting C modules and estimate error."""
# Reset
self.interpreter.reset()
# Create pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_fit'
self.interpreter.pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_fit')
# The intensity type.
ds.int_type = 'height'
# Create the data pipe and load the base data.
data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'
# Create the spins
self.interpreter.spectrum.read_spins(file="T2_ncyc1_ave.list", dir=data_path)
# Relaxation times (in seconds).
times = [
0.0176,
0.0176,
0.0352,
0.0704,
0.0704,
0.1056,
0.1584,
0.1584,
0.1936,
0.1936
]
# Spectrum names.
names = [
'T2_ncyc1_ave',
'T2_ncyc1b_ave',
'T2_ncyc2_ave',
'T2_ncyc4_ave',
'T2_ncyc4b_ave',
'T2_ncyc6_ave',
'T2_ncyc9_ave',
'T2_ncyc9b_ave',
'T2_ncyc11_ave',
'T2_ncyc11b_ave'
]
# Loop over Spectrum names.
for i, sname in enumerate(names):
# Get the time.
time = times[i]
# Load the peak intensities.
self.interpreter.spectrum.read_intensities(file=sname+'.list', dir=data_path, spectrum_id=sname, int_method=ds.int_type)
# Set the relaxation times.
self.interpreter.relax_fit.relax_time(time=time, spectrum_id=sname)
self.interpreter.deselect.spin(':3,11,18,19,23,31,42,44,54,66,82,92,94,99,101,113,124,126,136,141,145,147,332,345,346,358,361')
GRID_INC = 11
MC_SIM = 3
results_dir = mkdtemp()
#min_method = 'simplex'
#min_method = 'BFGS'
min_method = 'newton'
# De select one more.
self.interpreter.deselect.spin(':512@ND2')
# Set the relaxation curve type.
self.interpreter.relax_fit.select_model('exp')
# Do automatic
if True:
relax_fit.Relax_fit(pipe_name=pipe_name, pipe_bundle=pipe_bundle, file_root='R2', results_dir=results_dir, grid_inc=GRID_INC, mc_sim_num=MC_SIM, view_plots=False)
else:
# Prepare for finding dublictes.
# Collect all times, and matching spectrum ID.
all_times = []
all_id = []
for spectrum_id in cdp.relax_times:
all_times.append(cdp.relax_times[spectrum_id])
all_id.append(spectrum_id)
# Get the dublicates.
dublicates = [(val, [i for i in range(len(all_times)) if all_times[i] == val]) for val in all_times]
# Loop over the list of the mapping of times and duplications.
list_dub_mapping = []
for i, dub in enumerate(dublicates):
# Get current spectum id.
cur_spectrum_id = all_id[i]
# Get the tuple of time and indexes of duplications.
time, list_index_occur = dub
# Collect mapping of index to id.
id_list = []
if len(list_index_occur) > 1:
for list_index in list_index_occur:
id_list.append(all_id[list_index])
# Store to list
list_dub_mapping.append((cur_spectrum_id, id_list))
# Assign dublicates.
for spectrum_id, dub_pair in list_dub_mapping:
if len(dub_pair) > 0:
self.interpreter.spectrum.replicated(spectrum_ids=dub_pair)
# Test the number of replicates stored in cdp, is 4.
self.assertEqual(len(cdp.replicates), 4)
# Peak intensity error analysis.
self.interpreter.spectrum.error_analysis()
# Grid search.
self.interpreter.minimise.grid_search(inc=GRID_INC)
# Minimise.
self.interpreter.minimise.execute(min_method, scaling=False, constraints=False)
# Monte Carlo simulations.
self.interpreter.monte_carlo.setup(number=MC_SIM)
self.interpreter.monte_carlo.create_data()
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_method, scaling=False, constraints=False)
self.interpreter.monte_carlo.error_analysis()
# Test seq
tseq = [ [4, 'GLY', ':4@N'],
[5, 'SER', ':5@N'],
[6, 'MET', ':6@N'],
[7, 'ASP', ':7@N'],
[8, 'SER', ':8@N'],
[12, 'GLY', ':12@N']]
# Print spins
i = 0
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
print(resi, resn, spin_id)
self.assertEqual(resi, tseq[i][0])
self.assertEqual(resn, tseq[i][1])
self.assertEqual(spin_id, tseq[i][2])
i += 1
# Test the number of spins.
self.assertEqual(count_spins(), 6)
# Check the curve-fitting results.
self.check_curve_fitting_manual()
# Compare rx errors.
if True:
# Estimate rx and i0 errors.
self.interpreter.error_analysis.covariance_matrix()
# Collect:
i0_est = []
i0_err_est = []
rx_est = []
rx_err_est = []
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
i0_est.append(cur_spin.i0)
i0_err_est.append(cur_spin.i0_err)
rx_est.append(cur_spin.rx)
rx_err_est.append(cur_spin.rx_err)
# Set number of MC simulati0ns
MC_SIM = 200
# Monte Carlo simulations.
self.interpreter.monte_carlo.setup(number=MC_SIM)
self.interpreter.monte_carlo.create_data()
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_method, scaling=False, constraints=False)
self.interpreter.monte_carlo.error_analysis()
# Collect:
i0_mc = []
i0_err_mc = []
rx_mc = []
rx_err_mc = []
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
i0_mc.append(cur_spin.i0)
i0_err_mc.append(cur_spin.i0_err)
rx_mc.append(cur_spin.rx)
rx_err_mc.append(cur_spin.rx_err)
# Now print and compare
i = 0
print("Comparison between error estimation from Jacobian co-variance matrix and Monte-Carlo simulations.")
print("Spin ID: rx_err_diff=est-MC, i0_err_diff=est-MC, rx_err=est/MC, i0_err=est/MC, i0=est/MC, rx=est/MC.")
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
# Extract for estimation.
i0_est_i = i0_est[i]
i0_err_est_i = i0_err_est[i]
rx_est_i = rx_est[i]
rx_err_est_i = rx_err_est[i]
# Extract from monte carlo.
i0_mc_i = i0_mc[i]
i0_err_mc_i = i0_err_mc[i]
rx_mc_i = rx_mc[i]
rx_err_mc_i = rx_err_mc[i]
# Add to counter.
i += 1
# Prepare text.
rx_err_diff = rx_err_est_i - rx_err_mc_i
i0_err_diff = i0_err_est_i - i0_err_mc_i
text = "Spin '%s': rx_err_diff=%3.4f, i0_err_diff=%3.3f, rx_err=%3.4f/%3.4f, i0_err=%3.3f/%3.3f, rx=%3.3f/%3.3f, i0=%3.3f/%3.3f" % (spin_id, rx_err_diff, i0_err_diff, rx_err_est_i, rx_err_mc_i, i0_err_est_i, i0_err_mc_i, rx_est_i, rx_mc_i, i0_est_i, i0_mc_i)
print(text)
def test_curve_fitting_height_estimate_error(self):
"""Test the relaxation curve fitting C modules and estimate error."""
# Reset
self.interpreter.reset()
# Create pipe.
pipe_name = 'base pipe'
pipe_bundle = 'relax_fit'
self.interpreter.pipe.create(pipe_name=pipe_name, bundle=pipe_bundle, pipe_type='relax_fit')
# The intensity type.
ds.int_type = 'height'
# Create the data pipe and load the base data.
data_path = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'curve_fitting'
# Create the spins
self.interpreter.spectrum.read_spins(file="T2_ncyc1_ave.list", dir=data_path)
# Relaxation times (in seconds).
times = [
0.0176,
0.0176,
0.0352,
0.0704,
0.0704,
0.1056,
0.1584,
0.1584,
0.1936,
0.1936
]
# Spectrum names.
names = [
'T2_ncyc1_ave',
'T2_ncyc1b_ave',
'T2_ncyc2_ave',
'T2_ncyc4_ave',
'T2_ncyc4b_ave',
'T2_ncyc6_ave',
'T2_ncyc9_ave',
'T2_ncyc9b_ave',
'T2_ncyc11_ave',
'T2_ncyc11b_ave'
]
# Loop over Spectrum names.
for i, sname in enumerate(names):
# Get the time.
time = times[i]
# Load the peak intensities.
self.interpreter.spectrum.read_intensities(file=sname+'.list', dir=data_path, spectrum_id=sname, int_method=ds.int_type)
# Set the relaxation times.
self.interpreter.relax_fit.relax_time(time=time, spectrum_id=sname)
self.interpreter.deselect.spin(':3,11,18,19,23,31,42,44,54,66,82,92,94,99,101,113,124,126,136,141,145,147,332,345,346,358,361')
GRID_INC = 11
MC_SIM = 3
results_dir = mkdtemp()
#min_method = 'simplex'
#min_method = 'BFGS'
min_method = 'newton'
# De select one more.
self.interpreter.deselect.spin(':512@ND2')
# Set the relaxation curve type.
self.interpreter.relax_fit.select_model('exp')
# Do automatic
if True:
relax_fit.Relax_fit(pipe_name=pipe_name, pipe_bundle=pipe_bundle, file_root='R2', results_dir=results_dir, grid_inc=GRID_INC, mc_sim_num=MC_SIM, view_plots=False)
else:
# Prepare for finding dublictes.
# Collect all times, and matching spectrum ID.
all_times = []
all_id = []
for spectrum_id in cdp.relax_times:
all_times.append(cdp.relax_times[spectrum_id])
all_id.append(spectrum_id)
# Get the dublicates.
dublicates = [(val, [i for i in range(len(all_times)) if all_times[i] == val]) for val in all_times]
# Loop over the list of the mapping of times and duplications.
list_dub_mapping = []
for i, dub in enumerate(dublicates):
# Get current spectum id.
cur_spectrum_id = all_id[i]
# Get the tuple of time and indexes of duplications.
time, list_index_occur = dub
# Collect mapping of index to id.
id_list = []
if len(list_index_occur) > 1:
for list_index in list_index_occur:
id_list.append(all_id[list_index])
# Store to list
list_dub_mapping.append((cur_spectrum_id, id_list))
# Assign dublicates.
for spectrum_id, dub_pair in list_dub_mapping:
if len(dub_pair) > 0:
self.interpreter.spectrum.replicated(spectrum_ids=dub_pair)
# Test the number of replicates stored in cdp, is 4.
self.assertEqual(len(cdp.replicates), 4)
# Peak intensity error analysis.
self.interpreter.spectrum.error_analysis()
# Grid search.
self.interpreter.minimise.grid_search(inc=GRID_INC)
# Minimise.
self.interpreter.minimise.execute(min_method, scaling=False, constraints=False)
# Monte Carlo simulations.
self.interpreter.monte_carlo.setup(number=MC_SIM)
self.interpreter.monte_carlo.create_data()
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_method, scaling=False, constraints=False)
self.interpreter.monte_carlo.error_analysis()
# Test seq
tseq = [ [4, 'GLY', ':4@N'],
[5, 'SER', ':5@N'],
[6, 'MET', ':6@N'],
[7, 'ASP', ':7@N'],
[8, 'SER', ':8@N'],
[12, 'GLY', ':12@N']]
# Print spins
i = 0
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
print(resi, resn, spin_id)
self.assertEqual(resi, tseq[i][0])
self.assertEqual(resn, tseq[i][1])
self.assertEqual(spin_id, tseq[i][2])
i += 1
# Test the number of spins.
self.assertEqual(count_spins(), 6)
# Check the curve-fitting results.
self.check_curve_fitting_manual()
# Compare rx errors.
if True:
# Estimate rx and i0 errors.
self.interpreter.error_analysis.covariance_matrix()
# Collect:
i0_est = []
i0_err_est = []
rx_est = []
rx_err_est = []
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
i0_est.append(cur_spin.i0)
i0_err_est.append(cur_spin.i0_err)
rx_est.append(cur_spin.rx)
rx_err_est.append(cur_spin.rx_err)
# Set number of MC simulati0ns
MC_SIM = 200
# Monte Carlo simulations.
self.interpreter.monte_carlo.setup(number=MC_SIM)
self.interpreter.monte_carlo.create_data()
self.interpreter.monte_carlo.initial_values()
self.interpreter.minimise.execute(min_method, scaling=False, constraints=False)
self.interpreter.monte_carlo.error_analysis()
# Collect:
i0_mc = []
i0_err_mc = []
rx_mc = []
rx_err_mc = []
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
i0_mc.append(cur_spin.i0)
i0_err_mc.append(cur_spin.i0_err)
rx_mc.append(cur_spin.rx)
rx_err_mc.append(cur_spin.rx_err)
# Now print and compare
i = 0
print("Comparison between error estimation from Jacobian co-variance matrix and Monte-Carlo simulations.")
print("Spin ID: rx_err_diff=est-MC, i0_err_diff=est-MC, rx_err=est/MC, i0_err=est/MC, i0=est/MC, rx=est/MC.")
for cur_spin, mol_name, resi, resn, spin_id in spin_loop(full_info=True, return_id=True, skip_desel=True):
# Extract for estimation.
i0_est_i = i0_est[i]
i0_err_est_i = i0_err_est[i]
rx_est_i = rx_est[i]
rx_err_est_i = rx_err_est[i]
# Extract from monte carlo.
i0_mc_i = i0_mc[i]
i0_err_mc_i = i0_err_mc[i]
rx_mc_i = rx_mc[i]
rx_err_mc_i = rx_err_mc[i]
# Add to counter.
i += 1
# Prepare text.
rx_err_diff = rx_err_est_i - rx_err_mc_i
i0_err_diff = i0_err_est_i - i0_err_mc_i
text = "Spin '%s': rx_err_diff=%3.4f, i0_err_diff=%3.3f, rx_err=%3.4f/%3.4f, i0_err=%3.3f/%3.3f, rx=%3.3f/%3.3f, i0=%3.3f/%3.3f" % (spin_id, rx_err_diff, i0_err_diff, rx_err_est_i, rx_err_mc_i, i0_err_est_i, i0_err_mc_i, rx_est_i, rx_mc_i, i0_est_i, i0_mc_i)
print(text)
def test_pcs_copy_back_calc(self):
"""Test the operation of the pcs.copy user function for back-calculated values."""
# Data directory.
dir = status.install_path + sep + 'test_suite' + sep + 'shared_data' + sep + 'align_data' + sep
# Set up two data identical pipes.
pipes = ['orig', 'new']
delete = ['@C2', '@H17']
for i in range(2):
# Create a data pipe.
self.interpreter.pipe.create(pipes[i], 'N-state')
# Load the spins.
self.interpreter.sequence.read(file='pcs.txt',
dir=dir,
spin_name_col=1)
# Delete the spin.
self.interpreter.spin.delete(delete[i])
self.interpreter.sequence.display()
# Load the PCSs into the first data pipe.
self.interpreter.pipe.switch('orig')
self.interpreter.pcs.read(align_id='tb',
file='pcs.txt',
dir=dir,
spin_name_col=1,
data_col=2)
# Create back-calculated PCS values from the real values.
for spin in spin_loop():
if hasattr(spin, 'pcs'):
if not hasattr(spin, 'pcs_bc'):
spin.pcs_bc = {}
spin.pcs_bc['tb'] = spin.pcs['tb']
if spin.pcs_bc['tb'] != None:
spin.pcs_bc['tb'] += 1.0
# Copy the PCSs into the second data pipe.
self.interpreter.pcs.copy(pipe_from='orig',
pipe_to='new',
align_id='tb',
back_calc=True)
# Checks.
pcs = [[
0.004, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003, 0.006, 0.003,
0.007, 0.005, 0.001, 0.070, None, 0.025, 0.098, 0.054, 0.075,
0.065, None, 0.070, 0.015, 0.098, 0.060, 0.120
],
[
0.004, 0.008, 0.021, 0.029, 0.016, 0.010, 0.008, 0.003,
0.006, 0.003, 0.007, 0.005, 0.001, 0.070, None, 0.025,
0.098, 0.054, 0.075, 0.065, None, 0.070, 0.015, 0.098, 0.120
]]
for i in range(2):
print("\nChecking data pipe '%s'." % pipes[i])
self.assert_(hasattr(ds[pipes[i]], 'align_ids'))
self.assert_('tb' in ds[pipes[i]].align_ids)
self.assert_(hasattr(ds[pipes[i]], 'pcs_ids'))
self.assert_('tb' in ds[pipes[i]].pcs_ids)
self.assertEqual(count_spins(), 25)
self.assertEqual(len(cdp.interatomic), 0)
j = 0
for spin in spin_loop(pipe=pipes[i]):
# Atom C2 in the 'new' data pipe has no PCSs.
if i == 1 and j == 1:
self.assert_(not hasattr(spin, 'pcs'))
else:
if pcs[i][j] == None:
self.assertEqual(None, spin.pcs['tb'])
self.assertEqual(None, spin.pcs_bc['tb'])
else:
self.assertAlmostEqual(pcs[i][j], spin.pcs['tb'])
self.assertAlmostEqual(pcs[i][j] + 1.0,
spin.pcs_bc['tb'])
j += 1
def copy(pipe_from=None, pipe_to=None, spin_id1=None, spin_id2=None, verbose=True):
"""Copy the interatomic data from one data pipe to another.
@keyword pipe_from: The data pipe to copy the interatomic data from. This defaults to the current data pipe.
@type pipe_from: str
@keyword pipe_to: The data pipe to copy the interatomic data to. This defaults to the current data pipe.
@type pipe_to: str
@keyword spin_id1: The spin ID string of the first atom.
@type spin_id1: str
@keyword spin_id2: The spin ID string of the second atom.
@type spin_id2: str
@keyword verbose: A flag which if True will cause info about each spin pair to be printed out.
@type verbose: bool
"""
# Defaults.
if pipe_from == None and pipe_to == None:
raise RelaxError("The pipe_from and pipe_to arguments cannot both be set to None.")
elif pipe_from == None:
pipe_from = pipes.cdp_name()
elif pipe_to == None:
pipe_to = pipes.cdp_name()
# Test if the pipe_from and pipe_to data pipes exist.
check_pipe(pipe_from)
check_pipe(pipe_to)
# Check that the spin IDs exist.
if spin_id1:
if count_spins(selection=spin_id1, pipe=pipe_from, skip_desel=False) == 0:
raise RelaxNoSpinError(spin_id1, pipe_from)
if count_spins(selection=spin_id1, pipe=pipe_to, skip_desel=False) == 0:
raise RelaxNoSpinError(spin_id1, pipe_to)
if spin_id2:
if count_spins(selection=spin_id2, pipe=pipe_from, skip_desel=False) == 0:
raise RelaxNoSpinError(spin_id2, pipe_from)
if count_spins(selection=spin_id2, pipe=pipe_to, skip_desel=False) == 0:
raise RelaxNoSpinError(spin_id2, pipe_to)
# Check for the sequence data in the target pipe if no spin IDs are given.
if not spin_id1 and not spin_id2:
for spin, spin_id in spin_loop(pipe=pipe_from, return_id=True):
if not return_spin(spin_id=spin_id, pipe=pipe_to):
raise RelaxNoSpinError(spin_id, pipe_to)
# Test if pipe_from contains interatomic data (skipping the rest of the function if it is missing).
if not exists_data(pipe_from):
return
# Loop over the interatomic data of the pipe_from data pipe.
ids = []
for interatom in interatomic_loop(selection1=spin_id1, selection2=spin_id2, pipe=pipe_from):
# Create a new container.
new_interatom = create_interatom(spin_id1=interatom.spin_id1, spin_id2=interatom.spin_id2, pipe=pipe_to)
# Duplicate all the objects of the container.
for name in dir(interatom):
# Skip special objects.
if search('^_', name):
continue
# Skip the spin IDs.
if name in ['spin_id1', 'spin_id2']:
continue
# Skip class methods.
if name in interatom.__class__.__dict__:
continue
# Duplicate all other objects.
obj = deepcopy(getattr(interatom, name))
setattr(new_interatom, name, obj)
# Store the IDs for the printout.
ids.append([repr(interatom.spin_id1), repr(interatom.spin_id2)])
# Reconfigure the spin hashes.
hash_update(interatom=new_interatom, pipe=pipe_to)
# Print out.
if verbose:
write_data(out=sys.stdout, headings=["Spin_ID_1", "Spin_ID_2"], data=ids)
def test_rdc_copy_back_calc(self):
"""Test the operation of the rdc.copy user function for back-calculated values."""
# Data directory.
dir = status.install_path + sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
# Set up two data identical pipes.
pipes = ['orig', 'new']
delete = [':6', ':11']
for i in range(2):
# Create a data pipe.
self.interpreter.pipe.create(pipes[i], 'N-state')
# Load the spins.
self.interpreter.sequence.read(file='tb.txt', dir=dir, spin_id_col=1)
self.interpreter.spin.element('N')
# Delete the residue.
self.interpreter.residue.delete(delete[i])
# Attach protons.
self.interpreter.sequence.attach_protons()
self.interpreter.sequence.display()
# Create the interatomic data containers.
self.interpreter.interatom.define(spin_id1='@N', spin_id2='@H')
# Printout.
print("\n\nInteratomic data containers for the 'orig' data pipe:")
for interatom in interatomic_loop(pipe='orig'):
print("'%s' '%s'" % (interatom.spin_id1, interatom.spin_id2))
print("\nInteratomic data containers for the 'new' data pipe:")
for interatom in interatomic_loop(pipe='new'):
print("'%s' '%s'" % (interatom.spin_id1, interatom.spin_id2))
# Load the RDCs into the first data pipe.
self.interpreter.pipe.switch('orig')
self.interpreter.rdc.read(align_id='tb', file='tb.txt', dir=dir, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
# Create back-calculated RDC values from the real values.
for interatom in interatomic_loop():
if hasattr(interatom, 'rdc'):
if not hasattr(interatom, 'rdc_bc'):
interatom.rdc_bc = {}
interatom.rdc_bc['tb'] = interatom.rdc['tb'] + 1.0
# Copy the RDCs, including back-calculated values, into the second data pipe.
self.interpreter.rdc.copy(pipe_from='orig', pipe_to='new', align_id='tb', back_calc=True)
# Checks.
rdcs = [
[ -26.2501958629, 7.26317614156, -1.24840526981, 5.31803314334, 14.0362909456, 1.33652530397, -1.6021670281],
[ -26.2501958629, 9.93081766942, 7.26317614156, -1.24840526981, 5.31803314334, 14.0362909456, -1.6021670281]
]
for i in range(2):
print("\nChecking data pipe '%s'." % pipes[i])
# Metadata.
self.assert_(hasattr(ds[pipes[i]], 'align_ids'))
self.assert_('tb' in ds[pipes[i]].align_ids)
self.assert_(hasattr(ds[pipes[i]], 'rdc_ids'))
self.assert_('tb' in ds[pipes[i]].rdc_ids)
# Spin data.
self.assertEqual(count_spins(pipe=pipes[i]), 14)
self.assertEqual(len(ds[pipes[i]].interatomic), 7)
j = 0
for interatom in interatomic_loop(pipe=pipes[i]):
# Residue 6 in the 'new' data pipe has no RDCs.
if i == 1 and j == 1:
self.assert_(not hasattr(interatom, 'rdc'))
self.assert_(not hasattr(interatom, 'rdc_data_types'))
self.assert_(not hasattr(interatom, 'absolute_rdc'))
else:
self.assertAlmostEqual(rdcs[i][j], interatom.rdc['tb'])
self.assertAlmostEqual(rdcs[i][j]+1.0, interatom.rdc_bc['tb'])
self.assert_(hasattr(interatom, 'rdc_data_types'))
self.assert_('tb' in interatom.rdc_data_types)
self.assertEqual(interatom.rdc_data_types['tb'], 'D')
self.assert_(hasattr(interatom, 'absolute_rdc'))
self.assert_('tb' in interatom.absolute_rdc)
self.assertEqual(interatom.absolute_rdc['tb'], False)
j += 1