def add_terminal_hydrogens_old(
hierarchy,
geometry_restraints_manager,
terminate_all_N_terminals=False,
terminate_all_C_terminals=False,
use_capping_hydrogens=False,
append_to_end_of_model=False,
verbose=False,
):
ptr = 0 # belt and braces
additional_hydrogens = []
for residue_group, start, end in generate_residue_group_with_start_and_end(
hierarchy,
geometry_restraints_manager,
verbose=verbose,
):
if use_capping_hydrogens:
conditional_add_cys_hg_to_atom_group(geometry_restraints_manager,
residue_group)
if start:
ptr += 1
assert ptr == 1
if is_n_terminal_residue(residue_group):
rc = None
else:
rc = add_n_terminal_hydrogens_to_residue_group(
residue_group,
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
)
if rc: additional_hydrogens.append(rc)
if end:
ptr -= 1
assert ptr == 0
rc = add_c_terminal_oxygens_to_residue_group(
residue_group,
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
)
if rc: additional_hydrogens.append(rc)
else:
pass
print(additional_hydrogens)
def add_terminal_hydrogens_threes(
hierarchy,
geometry_restraints_manager,
terminate_all_N_terminals=False,
terminate_all_C_terminals=False,
use_capping_hydrogens=False,
append_to_end_of_model=False,
verbose=False,
):
from mmtbx.conformation_dependent_library import generate_protein_threes
additional_hydrogens = [] #hierarchy_utils.smart_add_atoms()
for three in generate_protein_threes(
hierarchy,
geometry_restraints_manager,
#include_non_linked=False,
backbone_only=False,
include_linked_via_restraints_manager=True,
verbose=verbose,
):
# print three
#print dir(three)
# print geometry_restraints_manager
#print dir(geometry_restraints_manager)
bond_params_table = geometry_restraints_manager.bond_params_table
# print bond_params_table
#print dir(bond_params_table)
# print 'use_capping_hydrogens',use_capping_hydrogens
def get_bonds():
bonds = {}
for i, a1 in enumerate(residue_group.atoms()):
for j, a2 in enumerate(residue_group.atoms()):
if i >= j: continue
bond = three.bond_params_table.lookup(a1.i_seq, a2.i_seq)
if bond:
bonds[(a1.i_seq, a2.i_seq)] = True
bonds[(a2.i_seq, a1.i_seq)] = True
return bonds
if use_capping_hydrogens:
for i in range(len(three)):
residue_group = three.get_residue_group_from_hierarchy(
hierarchy, i)
rc = conditional_add_cys_hg_to_atom_group(
geometry_restraints_manager, residue_group)
#assert not rc, '%s' % rc
if three.start:
residue_group = three.get_residue_group_from_hierarchy(
hierarchy, 0)
rc = add_n_terminal_hydrogens_to_residue_group(
residue_group,
bonds=get_bonds(),
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
)
if rc: additional_hydrogens.append(rc)
if three.end:
residue_group = three.get_residue_group_from_hierarchy(
hierarchy, 2)
rc = add_c_terminal_oxygens_to_residue_group(
residue_group,
bonds=get_bonds(),
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
)
if rc: additional_hydrogens.append(rc)
return additional_hydrogens
def iterate_using_original(
hierarchy,
geometry_restraints_manager,
original_hierarchy,
use_capping_hydrogens=False,
append_to_end_of_model=False,
):
slots = []
start = 18
assert len(original_hierarchy.models()) == 1
assert len(hierarchy.models()) == 1
for chain in original_hierarchy.chains():
for org in chain.residue_groups():
protein = True
for atom_group in org.atom_groups():
if (get_class(atom_group.resname) not in [
"common_amino_acid",
"modified_amino_acid",
] and atom_group.resname
not in aac.three_letter_l_given_three_letter_d):
protein = False
break
if not protein:
slots.append(False)
continue
org_atom1_quote = org.atoms()[0].quote()[start:]
for rg in hierarchy.residue_groups():
if rg.atoms()[0].quote()[start:] == org_atom1_quote:
slots.append(rg)
break
else:
slots.append(0)
slots.append(None)
ptr = 0
additional_hydrogens = []
for i in range(len(slots)):
start = False
end = False
if slots[i]:
if i == 0: start = True
elif not slots[i - 1]: start = True
if i == len(slots) - 1: end = True
elif not slots[i + 1]: end = True
# does not work for chain ends
else:
continue
rg = slots[i]
conditional_add_cys_hg_to_atom_group(
geometry_restraints_manager,
rg,
append_to_end_of_model=append_to_end_of_model)
if start:
ptr += 1
assert ptr == 1
if hierarchy_utils.is_n_terminal_residue(rg):
rc = None
else:
rc = add_n_terminal_hydrogens_to_residue_group(
rg,
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
)
if rc: additional_hydrogens.append(rc)
if end:
ptr -= 1
assert ptr == 0
rc = add_c_terminal_oxygens_to_residue_group(
rg,
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
)
if rc: additional_hydrogens.append(rc)
else:
pass
return additional_hydrogens
def iterate_over_threes(
hierarchy,
geometry_restraints_manager,
use_capping_hydrogens=False,
append_to_end_of_model=False,
verbose=False,
):
atoms = hierarchy.atoms()
###
def get_residue_group(residue):
for atom in residue.atoms():
atom = atoms[atom.i_seq]
break
return atom.parent().parent()
###
additional_hydrogens = hierarchy_utils.smart_add_atoms()
for three in hierarchy_utils.generate_protein_fragments(
hierarchy,
geometry_restraints_manager,
backbone_only=False,
use_capping_hydrogens=use_capping_hydrogens,
):
if verbose: print(three)
if not len(three): continue
ptr = 0
assert three.are_linked()
if use_capping_hydrogens:
for i in range(len(three)):
rg = get_residue_group(three[i])
rc = conditional_add_cys_hg_to_atom_group(
geometry_restraints_manager,
rg,
append_to_end_of_model=append_to_end_of_model,
)
if rc:
additional_hydrogens.append(rc)
else:
for i in range(len(three)):
rg = get_residue_group(three[i])
conditional_remove_cys_hg_to_atom_group(
geometry_restraints_manager,
rg,
)
# check if N-term residue - FVA
n_term_done = False
if three[0].resname in [
'FVA',
]:
n_term_done = True
ptr += 1
assert ptr == 1, 'ptr (%d) is not 1' % ptr
if three.start and not n_term_done:
ptr += 1
assert ptr == 1, 'ptr (%d) is not 1' % ptr
rg = get_residue_group(three[0])
rc = add_n_terminal_hydrogens_to_residue_group(
rg,
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
)
if rc: additional_hydrogens.append(rc)
#hierarchy.reset_i_seq_if_necessary()
c_term_done = False
if three[-1].resname in [
'ETA',
]:
c_term_done = True
ptr -= 1
assert ptr == 0, 'ptr (%d) is not 0' % ptr
if three.end and not c_term_done:
ptr -= 1
assert ptr == 0, 'ptr (%d) is not 0' % ptr
rg = get_residue_group(three[-1])
rc = add_c_terminal_oxygens_to_residue_group(
rg,
use_capping_hydrogens=use_capping_hydrogens,
append_to_end_of_model=append_to_end_of_model,
)
if rc: additional_hydrogens.append(rc)
#hierarchy.reset_i_seq_if_necessary()
else:
pass
return additional_hydrogens
