def generate_sequence(N=0, spin_ids=None, spin_nums=None, spin_names=None, res_nums=None, res_names=None, mol_names=None, isotopes=None, elements=None):
"""Generate the sequence data from the BRMB information.
@keyword N: The number of spins.
@type N: int
@keyword spin_ids: The list of spin IDs.
@type spin_ids: list of str
@keyword spin_nums: The list of spin numbers.
@type spin_nums: list of int or None
@keyword spin_names: The list of spin names.
@type spin_names: list of str or None
@keyword res_nums: The list of residue numbers.
@type res_nums: list of int or None
@keyword res_names: The list of residue names.
@type res_names: list of str or None
@keyword mol_names: The list of molecule names.
@type mol_names: list of str or None
@keyword isotopes: The optional list of isotope types.
@type isotopes: list of str or None
@keyword elements: The optional list of element types.
@type elements: list of str or None
"""
# The blank data.
if not spin_nums:
spin_nums = [None] * N
if not spin_names:
spin_names = [None] * N
if not res_nums:
res_nums = [None] * N
if not res_names:
res_names = [None] * N
if not mol_names:
mol_names = [None] * N
# Generate the spin IDs.
spin_ids = []
for i in range(N):
spin_ids.append(generate_spin_id(mol_name=mol_names[i], res_num=res_nums[i], spin_name=spin_names[i]))
# Loop over the spin data.
for i in range(N):
# The spin already exists.
spin = return_spin(spin_ids[i])
if spin:
continue
# Create the spin.
spin = create_spin(spin_num=spin_nums[i], spin_name=spin_names[i], res_num=res_nums[i], res_name=res_names[i], mol_name=mol_names[i])
# Set the spin isotope and element.
spin_id = spin._spin_ids[0]
if elements:
set_spin_element(spin_id=spin_id, element=elements[i], force=True)
if isotopes and elements:
isotope = "%s%s" % (isotopes[i], elements[i])
set_spin_isotope(spin_id=spin_id, isotope=isotope, force=True)
# Clean up the spin metadata.
metadata_cleanup()
def ellipsoid_frame():
"""Calculate the spherical angles of the bond vector in the ellipsoid frame."""
# Get the unit vectors Dx, Dy, and Dz of the diffusion tensor axes.
Dx, Dy, Dz = diffusion_tensor.unit_axes()
# Spin loop.
for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
# Test if the vector exists.
if not hasattr(spin, 'xh_vect'):
# Get the spin id string.
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)
# Throw a warning.
warn(RelaxWarning("No angles could be calculated for the spin " + repr(spin_id) + "."))
# Skip the spin.
continue
# dz and dx direction cosines.
dz = dot(Dz, spin.xh_vect)
dx = dot(Dx, spin.xh_vect)
# Calculate the polar angle theta.
spin.theta = acos(dz)
# Calculate the azimuthal angle phi.
spin.phi = acos(dx / sin(spin.theta))
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 attach_protons():
"""Attach a single proton to all heteronuclei."""
# Loop over all spins.
mol_names = []
res_nums = []
res_names = []
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True):
# The spin is already a proton.
if hasattr(spin, 'element') and spin.element == 'H':
continue
# Get the interatomic data container.
interatoms = return_interatom_list(spin_id)
proton_found = False
if len(interatoms):
for i in range(len(interatoms)):
# Get the attached spin.
spin_attached = return_spin(interatoms[i].spin_id1)
if id(spin_attached) == id(spin):
spin_attached = return_spin(interatoms[i].spin_id2)
# Is it a proton?
if hasattr(spin_attached, 'element') and spin_attached.element == 'H' or spin.name == 'H':
proton_found = True
break
# Attached proton found.
if proton_found:
continue
# Store the sequence info.
mol_names.append(mol_name)
res_nums.append(res_num)
res_names.append(res_name)
# Create all protons (this must be done out of the spin loop, as it affects the looping!).
ids = []
for i in range(len(mol_names)):
# Create the spin container.
spin = create_spin(spin_name='H', res_name=res_names[i], res_num=res_nums[i], mol_name=mol_names[i])
ids.append(generate_spin_id(mol_name=mol_names[i], res_num=res_nums[i], res_name=res_names[i], spin_name='H'))
print("Creating the spins %s." % ids)
# Set the element and spin type.
set_spin_element(spin_id='@H', element='H')
set_spin_isotope(spin_id='@H', isotope='1H')
def attach_protons():
"""Attach a single proton to all heteronuclei."""
# Loop over all spins.
mol_names = []
res_nums = []
res_names = []
for spin, mol_name, res_num, res_name, spin_id in spin_loop(full_info=True, return_id=True):
# The spin is already a proton.
if hasattr(spin, 'element') and spin.element == 'H':
continue
# Get the interatomic data container.
interatoms = return_interatom_list(spin_hash=spin._hash)
proton_found = False
if len(interatoms):
for i in range(len(interatoms)):
# Get the attached spin.
spin_attached = return_spin(spin_hash=interatoms[i]._spin_hash1)
if id(spin_attached) == id(spin):
spin_attached = return_spin(spin_hash=interatoms[i]._spin_hash2)
# Is it a proton?
if hasattr(spin_attached, 'element') and spin_attached.element == 'H' or spin.name == 'H':
proton_found = True
break
# Attached proton found.
if proton_found:
continue
# Store the sequence info.
mol_names.append(mol_name)
res_nums.append(res_num)
res_names.append(res_name)
# Create all protons (this must be done out of the spin loop, as it affects the looping!).
ids = []
for i in range(len(mol_names)):
# Create the spin container.
spin = create_spin(spin_name='H', res_name=res_names[i], res_num=res_nums[i], mol_name=mol_names[i])[0]
ids.append(generate_spin_id(mol_name=mol_names[i], res_num=res_nums[i], res_name=res_names[i], spin_name='H'))
print("Creating the spins %s." % ids)
# Set the element and spin type.
set_spin_element(spin_id='@H', element='H')
set_spin_isotope(spin_id='@H', isotope='1H')
def generate_sequence(N=0,
spin_ids=None,
spin_nums=None,
spin_names=None,
res_nums=None,
res_names=None,
mol_names=None,
isotopes=None,
elements=None):
"""Generate the sequence data from the BRMB information.
@keyword N: The number of spins.
@type N: int
@keyword spin_ids: The list of spin IDs.
@type spin_ids: list of str
@keyword spin_nums: The list of spin numbers.
@type spin_nums: list of int or None
@keyword spin_names: The list of spin names.
@type spin_names: list of str or None
@keyword res_nums: The list of residue numbers.
@type res_nums: list of int or None
@keyword res_names: The list of residue names.
@type res_names: list of str or None
@keyword mol_names: The list of molecule names.
@type mol_names: list of str or None
@keyword isotopes: The optional list of isotope types.
@type isotopes: list of str or None
@keyword elements: The optional list of element types.
@type elements: list of str or None
"""
# The blank data.
if not spin_nums:
spin_nums = [None] * N
if not spin_names:
spin_names = [None] * N
if not res_nums:
res_nums = [None] * N
if not res_names:
res_names = [None] * N
if not mol_names:
mol_names = [None] * N
# Generate the spin IDs.
spin_ids = []
for i in range(N):
spin_ids.append(
generate_spin_id(mol_name=mol_names[i],
res_num=res_nums[i],
spin_name=spin_names[i]))
# Loop over the spin data.
for i in range(N):
# The spin already exists.
spin = return_spin(spin_id=spin_ids[i])
if spin:
continue
# Create the spin.
spin = create_spin(spin_num=spin_nums[i],
spin_name=spin_names[i],
res_num=res_nums[i],
res_name=res_names[i],
mol_name=mol_names[i])[0]
# Set the spin isotope and element.
spin_id = spin._spin_ids[0]
if elements:
set_spin_element(spin_id=spin_id, element=elements[i], force=True)
if isotopes and elements:
isotope = "%s%s" % (isotopes[i], elements[i])
set_spin_isotope(spin_id=spin_id, isotope=isotope, force=True)
# Clean up the spin metadata.
metadata_cleanup()
# Unit vector.
r_hat = r / norm(r)
# The PCS (in ppm).
pcs = 1.0 / (4.0 * pi * norm(r)**3) * dot(transpose(r_hat), dot(chi_tensor, r_hat))
pcs = pcs * 1e6
# Write the PCS.
pcs_file.write("%20s%10s%10s%10s%10s%30.11g%30.11g\n" % (mol, res_num, res_name, spin.num, spin.name, pcs, 1e-10))
# RDC time, so skip protons now.
if spin.name == "H":
continue
# Get the interatomic data container.
spin_id1 = generate_spin_id(res_num=res_num, res_name=res_name, spin_num=spin.num, spin_name=spin.name)
spin_id2 = generate_spin_id(res_num=res_num, res_name=res_name, spin_name='H')
interatom = return_interatom(spin_id1, spin_id2)
# Skip interatoms without vectors.
if not hasattr(interatom, 'vector'):
continue
# Calculate and write the RDC.
rdc = dip_const * dot(transpose(interatom.vector), dot(tensor, interatom.vector))
rdc_file.write("%-10s %-10s %20.11f %20.11g\n" % (repr(spin_id1), repr(spin_id2), rdc, 1e-10))
# Print outs.
print("\nAlignment tensor (A):\n" + repr(tensor))
print("Eigenvalues: " + repr(eigvals(tensor)))
print("Dipolar constant: " + repr(dip_const))
# The PCS (in ppm).
pcs = 1.0 / (4.0 * pi * norm(r)**3) * dot(transpose(r_hat),
dot(chi_tensor, r_hat))
pcs = pcs * 1e6
# Write the PCS.
pcs_file.write("%20s%10s%10s%10s%10s%30.11g\n" %
(mol, res_num, res_name, spin.num, spin.name, pcs))
# RDC time, so skip protons now.
if spin.name == "H":
continue
# Get the interatomic data container.
spin_id1 = generate_spin_id(res_num=res_num,
res_name=res_name,
spin_num=spin.num,
spin_name=spin.name)
spin_id2 = generate_spin_id(res_num=res_num,
res_name=res_name,
spin_name='H')
spin2 = return_spin(spin_id=spin_id2)
interatom = return_interatom(spin_hash1=spin._hash, spin_hash2=spin2._hash)
# Skip interatoms without vectors.
if not hasattr(interatom, 'vector'):
continue
# Calculate and write the RDC.
rdc = dip_const * dot(transpose(interatom.vector),
dot(tensor, interatom.vector))
rdc_file.write("%-10s %-10s %20.11f\n" %
