def apply_glyco_link_using_proxies_and_atoms(atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji,
link_carbon_dist=2.0,
):
def _add_bond(i_seqs,
bond_params_table,
bond_asu_table,
value,
esd,
rt_mx_ji,
):
proxy = geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs,
distance_ideal=value,
weight=1/esd**2)
bond_params_table.update(i_seq=i_seqs[0],
j_seq=i_seqs[1],
params=proxy)
bond_asu_table.add_pair(
i_seq=i_seqs[0],
j_seq=i_seqs[1],
rt_mx_ji=rt_mx_ji,
)
#
def _add_angle(i_seqs, geometry_proxy_registries, value, esd):
proxy = geometry_restraints.angle_proxy(
i_seqs=i_seqs,
angle_ideal=value,
weight=1/esd**2)
geometry_proxy_registries.angle.add_if_not_duplicated(proxy=proxy)
#
def _add_chiral(i_seqs, geometry_proxy_registries, value, esd, both_signs=False):
proxy = geometry_restraints.chirality_proxy(
i_seqs=i_seqs,
volume_ideal=value,
both_signs=both_signs,
weight=1/esd**2,
)
geometry_proxy_registries.chirality.add_if_not_duplicated(proxy=proxy)
def atom_group_output(atom_group):
outl = ""
for atom in atom_group.atoms():
outl += "%s%s\n" % (' '*10, atom.quote())
return outl
########
from mmtbx.monomer_library import glyco_utils
# anomeric_carbon, link_oxygen, ring_oxygen, ring_carbon, link_carbon, anomeric_hydrogen = \
# glyco_utils.get_glyco_link_atoms(atom_group1, atom_group2)
gla = glyco_utils.get_glyco_link_atoms(atom_group1,
atom_group2,
link_carbon_dist=link_carbon_dist,
)
# checks
if gla and not gla.is_correct():
gla = glyco_utils.get_glyco_link_atoms(atom_group2,
atom_group1,
link_carbon_dist=link_carbon_dist,
)
if gla and not gla.is_correct():
raise Sorry("""Failed to get all the atoms needed for glycosidic bond
between
group 1
%s
group 2
%s
""" % (atom_group_output(atom_group1), atom_group_output(atom_group2)
)
)
if gla is None:
raise Sorry("""Unspecified problem with carbohydrate groups. Could be that
the linking oxygen is on the linking residue instead of the docking residue.
group 1
%s
group 2
%s
""" % (atom_group_output(atom_group1), atom_group_output(atom_group2)
)
)
if not gla.anomeric_carbon_linking:
raise Sorry("""The linking carbohydrate unit has the oxygen attached to the
anomeric carbon.
Consider replacing oxygen %s
with an oxygen linked to %s in the same residue
%s""" % (gla.link_oxygen.quote(),
gla.link_carbon.quote(),
gla)
)
i_seqs = [gla.anomeric_carbon.i_seq, gla.link_oxygen.i_seq]
bond_i_seqs = i_seqs
# bonds
_add_bond(i_seqs, bond_params_table, bond_asu_table, 1.439, 0.02, rt_mx_ji)
# angles
for i_atoms, value, esd in [
[[gla.link_carbon, gla.link_oxygen, gla.anomeric_carbon], 108.7, 3.],
[[gla.link_oxygen, gla.anomeric_carbon, gla.ring_oxygen], 112.3, 3.],
[[gla.link_oxygen, gla.anomeric_carbon, gla.ring_carbon], 109.47, 3.],
[[gla.link_oxygen, gla.anomeric_carbon, gla.anomeric_hydrogen], 109.47, 3.],
]:
if None in i_atoms: continue
i_seqs = [atom.i_seq for atom in i_atoms]
_add_angle(i_seqs, geometry_proxy_registries, value, esd)
# chiral
i_seqs = gla.get_chiral_i_seqs()
if i_seqs is None:
raise Sorry("""Unable to determine the linking chiral atoms for atom groups
group 1
%s
group 2
%s
""" % (atom_group_output(atom_group1), atom_group_output(atom_group2)
)
)
value = get_chiral_sign(gla.anomeric_carbon.parent().resname)
if value:
esd = 0.02
_add_chiral(i_seqs, geometry_proxy_registries, value, esd)
return gla.get_isomer(), gla.as_cif(), bond_i_seqs
def apply_glyco_link_using_proxies_and_atoms(
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji,
link_carbon_dist=2.0,
):
def _add_bond(
i_seqs,
bond_params_table,
bond_asu_table,
value,
esd,
rt_mx_ji,
):
proxy = geometry_restraints.bond_simple_proxy(i_seqs=i_seqs,
distance_ideal=value,
weight=1 / esd**2)
bond_params_table.update(i_seq=i_seqs[0],
j_seq=i_seqs[1],
params=proxy)
bond_asu_table.add_pair(
i_seq=i_seqs[0],
j_seq=i_seqs[1],
rt_mx_ji=rt_mx_ji,
)
#
def _add_angle(i_seqs, geometry_proxy_registries, value, esd):
proxy = geometry_restraints.angle_proxy(i_seqs=i_seqs,
angle_ideal=value,
weight=1 / esd**2)
geometry_proxy_registries.angle.add_if_not_duplicated(proxy=proxy)
#
def _add_chiral(i_seqs,
geometry_proxy_registries,
value,
esd,
both_signs=False):
proxy = geometry_restraints.chirality_proxy(
i_seqs=i_seqs,
volume_ideal=value,
both_signs=both_signs,
weight=1 / esd**2,
)
geometry_proxy_registries.chirality.add_if_not_duplicated(proxy=proxy)
def atom_group_output(atom_group):
outl = ""
for atom in atom_group.atoms():
outl += "%s%s\n" % (' ' * 10, atom.quote())
return outl
########
from mmtbx.monomer_library import glyco_utils
# anomeric_carbon, link_oxygen, ring_oxygen, ring_carbon, link_carbon, anomeric_hydrogen = \
# glyco_utils.get_glyco_link_atoms(atom_group1, atom_group2)
gla = glyco_utils.get_glyco_link_atoms(
atom_group1,
atom_group2,
link_carbon_dist=link_carbon_dist,
)
# checks
if gla and not gla.is_correct():
gla = glyco_utils.get_glyco_link_atoms(
atom_group2,
atom_group1,
link_carbon_dist=link_carbon_dist,
)
if gla and not gla.is_correct():
raise Sorry("""Failed to get all the atoms needed for glycosidic bond
between
group 1
%s
group 2
%s
""" % (atom_group_output(atom_group1), atom_group_output(atom_group2)))
if gla is None:
raise Sorry(
"""Unspecified problem with carbohydrate groups. Could be that
the linking oxygen is on the linking residue instead of the docking residue.
group 1
%s
group 2
%s
""" % (atom_group_output(atom_group1), atom_group_output(atom_group2)))
if not gla.anomeric_carbon_linking:
raise Sorry(
"""The linking carbohydrate unit has the oxygen attached to the
anomeric carbon.
Consider replacing oxygen %s
with an oxygen linked to %s in the same residue
%s""" % (gla.link_oxygen.quote(), gla.link_carbon.quote(), gla))
i_seqs = [gla.anomeric_carbon.i_seq, gla.link_oxygen.i_seq]
bond_i_seqs = i_seqs
# bonds
_add_bond(i_seqs, bond_params_table, bond_asu_table, 1.439, 0.02, rt_mx_ji)
# angles
for i_atoms, value, esd in [
[[gla.link_carbon, gla.link_oxygen, gla.anomeric_carbon], 108.7, 3.],
[[gla.link_oxygen, gla.anomeric_carbon, gla.ring_oxygen], 112.3, 3.],
[[gla.link_oxygen, gla.anomeric_carbon, gla.ring_carbon], 109.47, 3.],
[[gla.link_oxygen, gla.anomeric_carbon, gla.anomeric_hydrogen], 109.47,
3.],
]:
if None in i_atoms: continue
i_seqs = [atom.i_seq for atom in i_atoms]
_add_angle(i_seqs, geometry_proxy_registries, value, esd)
# chiral
i_seqs = gla.get_chiral_i_seqs()
if i_seqs is None:
raise Sorry(
"""Unable to determine the linking chiral atoms for atom groups
group 1
%s
group 2
%s
""" % (atom_group_output(atom_group1), atom_group_output(atom_group2)))
value = get_chiral_sign(gla.anomeric_carbon.parent().resname)
if value:
esd = 0.02
_add_chiral(i_seqs, geometry_proxy_registries, value, esd)
return gla.get_isomer(), gla.as_cif(), bond_i_seqs