def test_return_residue(self):
"""Test the function for returning the desired residue data container.
The function tested is pipe_control.mol_res_spin.return_residue().
"""
# Ask for a few residues.
res1 = mol_res_spin.return_residue(':1')
res2 = mol_res_spin.return_residue(selection=':2')
res4 = mol_res_spin.return_residue(selection=':4', pipe='orig')
res5 = mol_res_spin.return_residue(selection='#RNA:-5', pipe='orig')
# Test the data of residue 1.
self.assertEqual(res1.num, 1)
self.assertEqual(res1.name, None)
# Test the data of residue 2.
self.assertEqual(res2.num, 2)
self.assertEqual(res2.name, 'Glu')
# Test the data of residue 4.
self.assertEqual(res4.num, 4)
self.assertEqual(res4.name, 'Pro')
# Test the data of the RNA residue -5.
self.assertEqual(res5.num, -5)
self.assertEqual(res5.name, None)
self.assertEqual(res5.spin[1].name, 'N5')
def test_return_residue(self):
"""Test the function for returning the desired residue data container.
The function tested is pipe_control.mol_res_spin.return_residue().
"""
# Ask for a few residues.
res1 = mol_res_spin.return_residue(':1')
res2 = mol_res_spin.return_residue(selection=':2')
res4 = mol_res_spin.return_residue(selection=':4', pipe='orig')
res5 = mol_res_spin.return_residue(selection='#RNA:-5', pipe='orig')
# Test the data of residue 1.
self.assertEqual(res1.num, 1)
self.assertEqual(res1.name, None)
# Test the data of residue 2.
self.assertEqual(res2.num, 2)
self.assertEqual(res2.name, 'Glu')
# Test the data of residue 4.
self.assertEqual(res4.num, 4)
self.assertEqual(res4.name, 'Pro')
# Test the data of the RNA residue -5.
self.assertEqual(res5.num, -5)
self.assertEqual(res5.name, None)
self.assertEqual(res5.spin[1].name, 'N5')
def prune_res(self, mol_branch_id, mol_id):
"""Remove any molecules which have been deleted.
@param mol_branch_id: The molecule branch ID of the wx.TreeCtrl object.
@type mol_branch_id: TreeItemId
@param mol_id: The molecule identification string.
@type mol_id: str
"""
# Find if the molecule has been removed.
prune_list = []
for key in self.tree_ids[mol_branch_id]:
# Get the python data.
info = self.tree.GetItemPyData(key)
# No info.
if info == None or 'id' not in info:
continue
# Get the residue.
res = return_residue(info['id'])
# Add to the prune list if it has been removed or renamed/renumbered.
if res == None or res.name != info['res_name'] or res.num != info['res_num']:
prune_list.append(key)
# Delete the data.
for key in prune_list:
self.tree.Delete(key)
self.tree_ids[mol_branch_id].pop(key)
def prune_res(self, mol_branch_id, mol_id):
"""Remove any molecules which have been deleted.
@param mol_branch_id: The molecule branch ID of the wx.TreeCtrl object.
@type mol_branch_id: TreeItemId
@param mol_id: The molecule identification string.
@type mol_id: str
"""
# Find if the molecule has been removed.
prune_list = []
for key in self.tree_ids[mol_branch_id]:
# Get the python data.
if dep_check.wx_classic:
info = self.tree.GetItemPyData(key)
else:
info = self.tree.GetItemData(key)
# No info.
if info == None or 'id' not in info:
continue
# Get the residue.
res = return_residue(info['id'])
# Add to the prune list if it has been removed or renamed/renumbered.
if res == None or res.name != info['res_name'] or res.num != info[
'res_num']:
prune_list.append(key)
# Delete the data.
for key in prune_list:
self.tree.Delete(key)
self.tree_ids[mol_branch_id].pop(key)
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 sherekhan_input(spin_id=None, force=False, dir='ShereKhan'):
"""Create the ShereKhan input files.
@keyword spin_id: The spin ID string to restrict the file creation to.
@type spin_id: str
@keyword force: A flag which if True will cause all pre-existing files to be overwritten.
@type force: bool
@keyword dir: The optional directory to place the files into. If None, then the files will be placed into the current directory.
@type dir: str or None
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Test if the experiment type has been set.
if not hasattr(cdp, 'exp_type'):
raise RelaxError("The relaxation dispersion experiment type has not been specified.")
# Test if the model has been set.
if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been specified.")
# Directory creation.
if dir != None:
mkdir_nofail(dir, verbosity=0)
# Loop over the spin blocks.
cluster_index = 0
for spin_ids in loop_cluster():
# The spin containers.
spins = spin_ids_to_containers(spin_ids)
# Loop over the magnetic fields.
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
# Loop over the time, and count it.
time_i = 0
for time, ti in loop_time(exp_type=exp_type, frq=frq, return_indices=True):
time_i += 1
# Check that not more than one time point is returned.
if time_i > 1:
raise RelaxError("Number of returned time poins is %i. Only 1 time point is expected."%time_i)
# The ShereKhan input file for the spin cluster.
file_name = 'sherekhan_frq%s.in' % (mi+1)
if dir != None:
dir_name = dir + sep + 'cluster%s' % (cluster_index+1)
else:
dir_name = 'cluster%s' % (cluster_index+1)
file = open_write_file(file_name=file_name, dir=dir_name, force=force)
# The B0 field for the nuclei of interest in MHz (must be positive to be accepted by the server).
file.write("%.10f\n" % abs(frq / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio('15N') / 1e6))
# The constant relaxation time for the CPMG experiment in seconds.
file.write("%s\n" % (time))
# The comment line.
file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff (rad/s)", "Error"))
# Loop over the spins of the cluster.
for i in range(len(spins)):
# Get the residue container.
res = return_residue(spin_ids[i])
# Name the residue if needed.
res_name = res.name
if res_name == None:
res_name = 'X'
# Initialise the lines to output (to be able to catch missing data).
lines = []
# The residue ID line.
lines.append("# %s%s\n" % (res_name, res.num))
# Loop over the dispersion points.
for offset, point in loop_offset_point(exp_type=exp_type, frq=frq, skip_ref=True):
# The parameter key.
param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point)
# No data.
if param_key not in spins[i].r2eff:
continue
# Store the data.
lines.append("%20.15g %20.13g %20.13g\n" % (point, spins[i].r2eff[param_key], spins[i].r2eff_err[param_key]))
# No data.
if len(lines) == 1:
continue
# Write out the data.
for line in lines:
file.write(line)
# Close the file.
file.close()
# Increment the cluster index.
cluster_index += 1
def sherekhan_input(spin_id=None, force=False, dir='ShereKhan'):
"""Create the ShereKhan input files.
@keyword spin_id: The spin ID string to restrict the file creation to.
@type spin_id: str
@keyword force: A flag which if True will cause all pre-existing files to be overwritten.
@type force: bool
@keyword dir: The optional directory to place the files into. If None, then the files will be placed into the current directory.
@type dir: str or None
"""
# Test if the current pipe exists.
check_pipe()
# Test if sequence data is loaded.
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
# Test if the experiment type has been set.
if not hasattr(cdp, 'exp_type'):
raise RelaxError("The relaxation dispersion experiment type has not been specified.")
# Test if the model has been set.
if not hasattr(cdp, 'model_type'):
raise RelaxError("The relaxation dispersion model has not been specified.")
# Directory creation.
if dir != None:
mkdir_nofail(dir, verbosity=0)
# Loop over the spin blocks.
cluster_index = 0
for spin_ids in loop_cluster():
# The spin containers.
spins = spin_ids_to_containers(spin_ids)
# Loop over the magnetic fields.
for exp_type, frq, ei, mi in loop_exp_frq(return_indices=True):
# Loop over the time, and count it.
time_i = 0
for time, ti in loop_time(exp_type=exp_type, frq=frq, return_indices=True):
time_i += 1
# Check that not more than one time point is returned.
if time_i > 1:
raise RelaxError("Number of returned time poins is %i. Only 1 time point is expected."%time_i)
# The ShereKhan input file for the spin cluster.
file_name = 'sherekhan_frq%s.in' % (mi+1)
if dir != None:
dir_name = dir + sep + 'cluster%s' % (cluster_index+1)
else:
dir_name = 'cluster%s' % (cluster_index+1)
file = open_write_file(file_name=file_name, dir=dir_name, force=force)
# The B0 field for the nuclei of interest in MHz (must be positive to be accepted by the server).
file.write("%.10f\n" % abs(frq / periodic_table.gyromagnetic_ratio('1H') * periodic_table.gyromagnetic_ratio('15N') / 1e6))
# The constant relaxation time for the CPMG experiment in seconds.
file.write("%s\n" % (time))
# The comment line.
file.write("# %-18s %-20s %-20s\n" % ("nu_cpmg (Hz)", "R2eff (rad/s)", "Error"))
# Loop over the spins of the cluster.
for i in range(len(spins)):
# Get the residue container.
res = return_residue(spin_ids[i])
# Name the residue if needed.
res_name = res.name
if res_name == None:
res_name = 'X'
# Initialise the lines to output (to be able to catch missing data).
lines = []
# The residue ID line.
lines.append("# %s%s\n" % (res_name, res.num))
# Loop over the dispersion points.
for offset, point in loop_offset_point(exp_type=exp_type, frq=frq, skip_ref=True):
# The parameter key.
param_key = return_param_key_from_data(exp_type=exp_type, frq=frq, offset=offset, point=point)
# No data.
if param_key not in spins[i].r2eff:
continue
# Store the data.
lines.append("%20.15g %20.13g %20.13g\n" % (point, spins[i].r2eff[param_key], spins[i].r2eff_err[param_key]))
# No data.
if len(lines) == 1:
continue
# Write out the data.
for line in lines:
file.write(line)
# Close the file.
file.close()
# Increment the cluster index.
cluster_index += 1
def pipe_centre_of_mass(atom_id=None, model=None, return_mass=False, verbosity=1):
"""Calculate and return the centre of mass of the structures in the current data pipe.
@keyword atom_id: The molecule, residue, and atom identifier string. Only atoms matching this selection will be used.
@type atom_id: str or None
@keyword model: Only use a specific model.
@type model: int or None
@keyword return_mass: A flag which if False will cause only the centre of mass to be returned, but if True will cause the centre of mass and the mass itself to be returned as a tuple.
@type return_mass: bool
@keyword verbosity: The amount of text to print out. 0 results in no printouts, 1 the full amount.
@type verbosity: int
@return: The centre of mass vector, and additionally the mass.
@rtype: list of 3 floats (or tuple of a list of 3 floats and one float)
"""
# Test if a structure has been loaded.
if not hasattr(cdp, 'structure'):
raise RelaxNoPdbError
# Loop over all atoms.
coord = []
element_list = []
for mol_name, res_num, res_name, atom_num, atom_name, element, pos in cdp.structure.atom_loop(atom_id=atom_id, model_num=model, mol_name_flag=True, res_num_flag=True, res_name_flag=True, atom_num_flag=True, atom_name_flag=True, element_flag=True, pos_flag=True, ave=True):
# Initialise the spin id string.
id = ''
# Get the corresponding molecule container.
if mol_name == None:
mol_cont = cdp.mol[0]
else:
id = id + '#' + mol_name
mol_cont = return_molecule(id)
# Get the corresponding residue container.
if res_name == None and res_num == None:
res_cont = mol_cont.res[0]
else:
id = id + ':' + repr(res_num)
res_cont = return_residue(id)
# Get the corresponding spin container.
if atom_name == None and atom_num == None:
spin_cont = res_cont.spin[0]
else:
id = id + '@' + repr(atom_num)
spin_cont = return_spin(id)
# Deselected spins.
if spin_cont and not spin_cont.select:
continue
# No element?
if element == None:
warn(RelaxWarning("Skipping the atom '%s' as the element type cannot be determined." % id))
continue
# Store the position and element.
coord.append(pos)
element_list.append(element)
# Calculate the CoM.
com, mass = centre_of_mass(pos=coord, elements=element_list)
# Return the centre of mass.
if return_mass:
return com, mass
else:
return com
