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 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()
