def add_n_terminal_hydrogens_to_residue_group(
residue_group,
bonds=None,
use_capping_hydrogens=False,
append_to_end_of_model=False,
):
rc = []
for atom_group, atoms in generate_atom_group_atom_names(residue_group,
['N', 'CA', 'C'],
verbose=False):
if None not in [atom_group, atoms]:
# for ag, (n, ca, c) in generate_atom_group_atom_names(residue_group,
# ['N', 'CA', 'C'],
# ):
tmp = add_n_terminal_hydrogens_to_atom_group(
atom_group,
bonds=bonds,
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
n_ca_c=atoms,
)
assert type(tmp) != type(''), 'not string "%s" %s' % (tmp,
type(tmp))
rc += tmp
return rc
def add_main_chain_atoms_to_protein_three(three):
for ag, (c, ca, n, o) in generate_atom_group_atom_names(
three[1],
['C', 'CA', 'N', 'O'],
return_Nones=True,
):
if o is None:
add_main_chain_o_to_atom_group(
ag,
c_ca_n=[c, ca, n],
)
assert 0
def add_main_chain_atoms_to_residue_group(residue_group):
# I think this needs a three
assert 0
for ag, (c, ca, n, o) in generate_atom_group_atom_names(
residue_group,
['C', 'CA', 'N', 'O'],
return_Nones=True,
):
if o is None:
add_main_chain_o_to_atom_group(
ag,
c_ca_n=[c, ca, n],
)
def add_main_chain_atoms_to_residue_group(residue_group):
# I think this needs a three
assert 0
for ag, (c, ca, n, o) in generate_atom_group_atom_names(
residue_group,
['C', 'CA', 'N', 'O'],
return_Nones=True,
):
# print ag.id_str()
# try: print c.quote(),ca.quote(),n.quote(),o.quote()
# except: print c,ca,n,o
if o is None:
add_main_chain_o_to_atom_group(
ag,
c_ca_n=[c, ca, n],
)
def add_c_terminal_oxygens_to_residue_group(
residue_group,
bonds=None,
use_capping_hydrogens=False,
append_to_end_of_model=False,
):
rc = []
for ag, (c, ca, n) in generate_atom_group_atom_names(
residue_group,
['C', 'CA', 'N'],
):
tmp = add_c_terminal_oxygens_to_atom_group(
ag,
bonds=bonds,
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
c_ca_n=[c, ca, n],
)
rc += tmp
return rc
def add_side_chain_acid_hydrogens_to_residue_group(
residue_group,
configuration_index=0,
element='H',
):
"""Adds hydrogen atoms to side-chain acid.
Args:
residue_group (TYPE): Specific residue group
"""
def _get_atom_names(residue_group):
assert len(residue_group.atom_groups()) == 1
atom_group = residue_group.atom_groups()[0]
lookup = {
'ASP': ['CG', 'OD1', 'OD2'],
'GLU': ['CD', 'OE1', 'OE2'],
}
return lookup.get(atom_group.resname, [])
#
if element == 'H': bond_length = 0.95
elif element == 'D': bond_length = 1.00
else: assert 0
atoms = _get_atom_names(residue_group)
for atom_group, atoms in generate_atom_group_atom_names(
residue_group,
atoms,
):
if atom_group is None: continue
tmp = add_side_chain_acid_hydrogens_to_atom_group(
atom_group,
# append_to_end_of_model=append_to_end_of_model,
anchors=atoms,
configuration_index=configuration_index,
bond_length=bond_length,
element=element,
)
