def exercise():
from mmtbx.ions import server as s
import iotbx.pdb.hierarchy
import iotbx.pdb
from cctbx.eltbx import chemical_elements
# Assert that valence parameters exist for all common ions with their
# coordinating atoms
for elem in [
"NA", "MG", "K", "CA", "MN", "FE", "NI", "CO", "CU", "ZN", "CD"
]:
params = s.get_metal_parameters(elem)
assert (len(params.allowed_coordinating_atoms) > 0)
assert (params.charge is not None)
for elem2 in params.allowed_coordinating_atoms:
atom1 = iotbx.pdb.hierarchy.atom()
atom1.name = elem
atom1.element = elem
atom1.charge = "+" + str(params.charge)
atom2 = iotbx.pdb.hierarchy.atom()
atom2.name = elem2
atom2.element = elem2
atom2.charge = "{:+}".format(s.get_charge(elem2))
assert (s.get_valence_params(atom1, atom2) != (None, None))
# Make sure we don't crash on any ion residue names
for elem in chemical_elements.proper_upper_list():
s.get_element(elem)
s.get_charge(elem)
# Make sure we don't crash on any common residue names either
from mmtbx import monomer_library
from mmtbx.rotamer.rotamer_eval import mon_lib_query
mon_lib_srv = monomer_library.server.server()
common_residues = [
getattr(iotbx.pdb, i) for i in dir(iotbx.pdb)
if i.startswith("common_residue_names")
and isinstance(getattr(iotbx.pdb, i), list)
]
common_atoms = {
"H": -1,
"C": 4,
"N": -3,
"O": -2,
"S": -2,
}
for common in common_residues:
for resn in common:
mlq = mon_lib_query(resn, mon_lib_srv)
if mlq is None:
continue
for atom in mlq.atom_dict().values():
elem, charge = s._get_charge_params(resname=resn,
element=atom.type_symbol)
from libtbx import group_args
class GAtom(group_args):
def fetch_labels(self):
return group_args(resname=self.resname)
def id_str(self):
return "gatom=\"{} {}\"".format(
self.resname, self.element)
def charge_as_int(self):
return int(self.charge)
gatom = GAtom(
element=atom.type_symbol,
resname=resn,
charge="0",
)
get_charge_val, get_elem_val = s.get_charge(
gatom), s.get_element(gatom)
if elem in common_atoms:
assert charge == common_atoms[elem]
assert get_charge_val == charge
assert get_elem_val == elem
# And we support all waters
for resn in iotbx.pdb.common_residue_names_water:
assert s.get_element(resn) == "O"
assert s.get_charge(resn) == -2
print "OK"
def _is_favorable_halide_environment(
chem_env, scatter_env, assume_hydrogens_all_missing=Auto,
):
assume_hydrogens_all_missing = True
atom = chem_env.atom
binds_amide_hydrogen = False
near_cation = False
near_lys = False
near_hydroxyl = False
xyz = col(atom.xyz)
min_distance_to_cation = None
min_distance_to_hydroxyl = min_distance_to_cation
for contact in chem_env.contacts:
other = contact.atom
resname = contact.resname()
atom_name = contact.atom_name()
element = contact.element
distance = abs(contact)
# XXX need to figure out exactly what this should be - CL has a
# fairly large radius though (1.67A according to ener_lib.cif)
if distance < 2.5:
return False
if not element in ["C", "N", "H", "O", "S"]:
charge = server.get_charge(element)
if charge < 0 and distance <= 3.5:
# Nearby anion that is too close
return False
if charge > 0 and distance <= 3.5:
# Nearby cation
near_cation = True
if min_distance_to_cation is None or \
distance < min_distance_to_cation:
min_distance_to_cation = distance
# Lysine sidechains (can't determine planarity)
elif (atom_name in ["NZ"] and #, "NE", "NH1", "NH2"] and
resname in ["LYS"] and
distance <= 3.5):
near_lys = True
if min_distance_to_cation is None or \
distance < min_distance_to_cation:
min_distance_to_cation = distance
# sidechain amide groups, no hydrogens (except Arg)
# XXX this would be more reliable if we also calculate the expected
# hydrogen positions and use the vector method below
elif (atom_name in ["NZ", "NH1", "NH2", "ND2", "NE2"] and
resname in ["ARG", "ASN", "GLN"] and
(assume_hydrogens_all_missing or resname == "ARG") and
distance <= 3.5):
binds_amide_hydrogen = True
if resname == "ARG" and (
min_distance_to_cation is None or
distance < min_distance_to_cation):
min_distance_to_cation = distance
# hydroxyl groups - note that the orientation of the hydrogen is usually
# arbitrary and we can't determine precise bonding
elif ((atom_name in ["OG1", "OG2", "OH1"]) and
(resname in ["SER", "THR", "TYR"]) and
(distance <= 3.5)):
near_hydroxyl = True
if distance < min_distance_to_hydroxyl:
min_distance_to_hydroxyl = distance
# Backbone amide, implicit H
elif atom_name in ["N"] and assume_hydrogens_all_missing:
binds_amide_hydrogen = True
# xyz_n = col(contact.site_cart)
# bonded_atoms = connectivity[j_seq]
# ca_same = c_prev = None
# for k_seq in bonded_atoms:
# other2 = pdb_atoms[k_seq]
# if other2.name.strip().upper() in ["CA"]:
# ca_same = col(get_site(k_seq))
# elif other2.name.strip().upper() in ["C"]:
# c_prev = col(get_site(k_seq))
# if ca_same is not None and c_prev is not None:
# xyz_cca = (ca_same + c_prev) / 2
# vec_ncca = xyz_n - xyz_cca
# # 0.86 is the backbone N-H bond distance in geostd
# xyz_h = xyz_n + (vec_ncca.normalize() * 0.86)
# vec_nh = xyz_n - xyz_h
# vec_nx = xyz_n - xyz
# angle = abs(vec_nh.angle(vec_nx, deg=True))
# if abs(angle - 180) <= 20:
# binds_amide_hydrogen = True
# now check again for negatively charged sidechain (etc.) atoms (e.g.
# carboxyl groups), but with some leeway if a cation is also nearby.
# backbone carbonyl atoms are also excluded.
for contact in chem_env.contacts:
if contact.altloc() not in ["", "A"]:
continue
resname = contact.resname()
atom_name = contact.atom_name()
distance = abs(contact)
if ((distance < 3.2) and
(min_distance_to_cation is not None and
distance < (min_distance_to_cation + 0.2)) and
halides.is_negatively_charged_oxygen(atom_name, resname)):
return False
return binds_amide_hydrogen or near_cation or near_lys
def exercise () :
from mmtbx.ions import server as s
import iotbx.pdb.hierarchy
import iotbx.pdb
from cctbx.eltbx import chemical_elements
# Assert that valence parameters exist for all common ions with their
# coordinating atoms
for elem in ["NA", "MG", "K", "CA", "MN", "FE", "NI", "CO", "CU", "ZN", "CD"]:
params = s.get_metal_parameters(elem)
assert (len(params.allowed_coordinating_atoms) > 0)
assert (params.charge is not None)
for elem2 in params.allowed_coordinating_atoms :
atom1 = iotbx.pdb.hierarchy.atom()
atom1.name = elem
atom1.element = elem
atom1.charge = "+" + str(params.charge)
atom2 = iotbx.pdb.hierarchy.atom()
atom2.name = elem2
atom2.element = elem2
atom2.charge = "{:+}".format(s.get_charge(elem2))
assert (s.get_valence_params(atom1, atom2) != (None, None))
# Make sure we don't crash on any ion residue names
for elem in chemical_elements.proper_upper_list():
s.get_element(elem)
s.get_charge(elem)
# Make sure we don't crash on any common residue names either
from mmtbx import monomer_library
from mmtbx.rotamer.rotamer_eval import mon_lib_query
mon_lib_srv = monomer_library.server.server()
common_residues = [getattr(iotbx.pdb, i) for i in dir(iotbx.pdb)
if i.startswith("common_residue_names") and
isinstance(getattr(iotbx.pdb, i), list)]
common_atoms = {
"H": -1,
"C": 4,
"N": -3,
"O": -2,
"S": -2,
}
for common in common_residues:
for resn in common:
mlq = mon_lib_query(resn, mon_lib_srv)
if mlq is None:
continue
for atom in mlq.atom_dict().values():
elem, charge = s._get_charge_params(resname = resn,
element = atom.type_symbol)
from libtbx import group_args
class GAtom(group_args):
def fetch_labels(self):
return group_args(resname = self.resname)
def id_str(self):
return "gatom=\"{} {}\"".format(self.resname, self.element)
def charge_as_int(self):
return int(self.charge)
gatom = GAtom(
element = atom.type_symbol,
resname = resn,
charge = "0",
)
get_charge_val, get_elem_val = s.get_charge(gatom), s.get_element(gatom)
if elem in common_atoms:
assert charge == common_atoms[elem]
assert get_charge_val == charge
assert get_elem_val == elem
# And we support all waters
for resn in iotbx.pdb.common_residue_names_water:
assert s.get_element(resn) == "O"
assert s.get_charge(resn) == -2
print "OK"
def is_favorable_halide_environment(i_seq,
contacts,
pdb_atoms,
sites_frac,
connectivity,
unit_cell,
params,
assume_hydrogens_all_missing=Auto):
"""
Detects if an atom's site exists in a favorable environment for a halide
ion. This includes coordinating by a positively charged sidechain or backbone
as well as an absense of negatively charged coordinating groups.
Parameters
----------
i_seq : int
contacts : list of mmtbx.ions.environment.atom_contact
pdb_atoms : iotbx.pdb.hierarchy.af_shared_atom
sites_frac : tuple of float, float, float
connectivity : scitbx.array_family.shared.stl_set_unsigned
unit_cell : uctbx.unit_cell
params : libtbx.phil.scope_extract
assume_hydrogens_all_missing : bool, optional
Returns
-------
bool
"""
if (assume_hydrogens_all_missing in [None, Auto]):
elements = pdb_atoms.extract_element()
assume_hydrogens_all_missing = not ("H" in elements or "D" in elements)
atom = pdb_atoms[i_seq]
binds_amide_hydrogen = False
near_cation = False
near_lys = False
near_hydroxyl = False
xyz = col(atom.xyz)
min_distance_to_cation = max(unit_cell.parameters()[0:3])
min_distance_to_hydroxyl = min_distance_to_cation
for contact in contacts:
# to analyze local geometry, we use the target site mapped to be in the
# same ASU as the interacting site
def get_site(k_seq):
return unit_cell.orthogonalize(site_frac=(contact.rt_mx *
sites_frac[k_seq]))
other = contact.atom
resname = contact.resname()
atom_name = contact.atom_name()
element = contact.element
distance = abs(contact)
j_seq = other.i_seq
# XXX need to figure out exactly what this should be - CL has a
# fairly large radius though (1.67A according to ener_lib.cif)
if (distance < params.min_distance_to_other_sites):
return False
if not element in ["C", "N", "H", "O", "S"]:
charge = server.get_charge(element)
if charge < 0 and distance <= params.min_distance_to_anion:
# Nearby anion that is too close
return False
if charge > 0 and distance <= params.max_distance_to_cation:
# Nearby cation
near_cation = True
if (distance < min_distance_to_cation):
min_distance_to_cation = distance
# Lysine sidechains (can't determine planarity)
elif (atom_name in ["NZ"] and #, "NE", "NH1", "NH2"] and
resname in ["LYS"] and
distance <= params.max_distance_to_cation):
near_lys = True
if (distance < min_distance_to_cation):
min_distance_to_cation = distance
# sidechain amide groups, no hydrogens (except Arg)
# XXX this would be more reliable if we also calculate the expected
# hydrogen positions and use the vector method below
elif (atom_name in ["NZ", "NH1", "NH2", "ND2", "NE2"]
and resname in ["ARG", "ASN", "GLN"]
and (assume_hydrogens_all_missing or resname == "ARG")
and distance <= params.max_distance_to_cation):
if (_is_coplanar_with_sidechain(
atom,
other.parent(),
distance_cutoff=params.max_deviation_from_plane)):
binds_amide_hydrogen = True
if (resname == "ARG") and (distance < min_distance_to_cation):
min_distance_to_cation = distance
# hydroxyl groups - note that the orientation of the hydrogen is usually
# arbitrary and we can't determine precise bonding
elif ((atom_name in ["OG1", "OG2", "OH1"])
and (resname in ["SER", "THR", "TYR"])
and (distance <= params.max_distance_to_hydroxyl)):
near_hydroxyl = True
if (distance < min_distance_to_hydroxyl):
min_distance_to_hydroxyl = distance
# Backbone amide, explicit H
elif atom_name in ["H"]:
# TODO make this more general for any amide H?
xyz_h = col(contact.site_cart)
bonded_atoms = connectivity[j_seq]
if (len(bonded_atoms) != 1):
continue
xyz_n = col(get_site(bonded_atoms[0]))
vec_hn = xyz_h - xyz_n
vec_hx = xyz_h - xyz
angle = abs(vec_hn.angle(vec_hx, deg=True))
# If Cl, H, and N line up, Cl binds the amide group
if abs(angle - 180) <= params.delta_amide_h_angle:
binds_amide_hydrogen = True
else:
pass #print "%s N-H-X angle: %s" % (atom.id_str(), angle)
# Backbone amide, implicit H
elif atom_name in ["N"] and assume_hydrogens_all_missing:
xyz_n = col(contact.site_cart)
bonded_atoms = connectivity[j_seq]
ca_same = c_prev = None
for k_seq in bonded_atoms:
other2 = pdb_atoms[k_seq]
if other2.name.strip().upper() in ["CA"]:
ca_same = col(get_site(k_seq))
elif other2.name.strip().upper() in ["C"]:
c_prev = col(get_site(k_seq))
if ca_same is not None and c_prev is not None:
xyz_cca = (ca_same + c_prev) / 2
vec_ncca = xyz_n - xyz_cca
# 0.86 is the backbone N-H bond distance in geostd
xyz_h = xyz_n + (vec_ncca.normalize() * 0.86)
vec_nh = xyz_n - xyz_h
vec_nx = xyz_n - xyz
angle = abs(vec_nh.angle(vec_nx, deg=True))
if abs(angle - 180) <= params.delta_amide_h_angle:
binds_amide_hydrogen = True
# sidechain NH2 groups, explicit H
elif ((atom_name in ["HD1", "HD2"] and resname in ["ASN"])
or (atom_name in ["HE1", "HE2"] and resname in ["GLN"])):
# XXX not doing this for Arg because it can't handle the bidentate
# coordination
#(atom_name in ["HH11","HH12","HH21","HH22"] and resname == "ARG")):
bonded_atoms = connectivity[j_seq]
assert (len(bonded_atoms) == 1)
xyz_n = col(get_site(bonded_atoms[0]))
xyz_h = col(contact.site_cart)
vec_nh = xyz_n - xyz_h
vec_xh = xyz - xyz_h
angle = abs(vec_nh.angle(vec_xh, deg=True))
if abs(angle - 180) <= params.delta_amide_h_angle:
binds_amide_hydrogen = True
else:
pass #print "%s amide angle: %s" % (atom.id_str(), angle)
# now check again for negatively charged sidechain (etc.) atoms (e.g.
# carboxyl groups), but with some leeway if a cation is also nearby.
# backbone carbonyl atoms are also excluded.
for contact in contacts:
if (contact.altloc() not in ["", "A"]):
continue
resname = contact.resname()
atom_name = contact.atom_name()
distance = abs(contact)
if ((distance < 3.2) and (distance < (min_distance_to_cation + 0.2))
and is_negatively_charged_oxygen(atom_name, resname)):
#print contact.id_str(), distance
return False
return (binds_amide_hydrogen or near_cation or near_lys)
def is_favorable_halide_environment (
i_seq,
contacts,
pdb_atoms,
sites_frac,
connectivity,
unit_cell,
params,
assume_hydrogens_all_missing=Auto) :
"""
Detects if an atom's site exists in a favorable environment for a halide
ion. This includes coordinating by a positively charged sidechain or backbone
as well as an absense of negatively charged coordinating groups.
Parameters
----------
i_seq : int
contacts : list of mmtbx.ions.environment.atom_contact
pdb_atoms : iotbx.pdb.hierarchy.af_shared_atom
sites_frac : tuple of float, float, float
connectivity : scitbx.array_family.shared.stl_set_unsigned
unit_cell : uctbx.unit_cell
params : libtbx.phil.scope_extract
assume_hydrogens_all_missing : bool, optional
Returns
-------
bool
"""
if (assume_hydrogens_all_missing in [None, Auto]) :
elements = pdb_atoms.extract_element()
assume_hydrogens_all_missing = not ("H" in elements or "D" in elements)
atom = pdb_atoms[i_seq]
binds_amide_hydrogen = False
near_cation = False
near_lys = False
near_hydroxyl = False
xyz = col(atom.xyz)
min_distance_to_cation = max(unit_cell.parameters()[0:3])
min_distance_to_hydroxyl = min_distance_to_cation
for contact in contacts :
# to analyze local geometry, we use the target site mapped to be in the
# same ASU as the interacting site
def get_site (k_seq) :
return unit_cell.orthogonalize(
site_frac = (contact.rt_mx * sites_frac[k_seq]))
other = contact.atom
resname = contact.resname()
atom_name = contact.atom_name()
element = contact.element
distance = abs(contact)
j_seq = other.i_seq
# XXX need to figure out exactly what this should be - CL has a
# fairly large radius though (1.67A according to ener_lib.cif)
if (distance < params.min_distance_to_other_sites) :
return False
if not element in ["C", "N", "H", "O", "S"]:
charge = server.get_charge(element)
if charge < 0 and distance <= params.min_distance_to_anion:
# Nearby anion that is too close
return False
if charge > 0 and distance <= params.max_distance_to_cation:
# Nearby cation
near_cation = True
if (distance < min_distance_to_cation) :
min_distance_to_cation = distance
# Lysine sidechains (can't determine planarity)
elif (atom_name in ["NZ"] and #, "NE", "NH1", "NH2"] and
resname in ["LYS"] and
distance <= params.max_distance_to_cation):
near_lys = True
if (distance < min_distance_to_cation) :
min_distance_to_cation = distance
# sidechain amide groups, no hydrogens (except Arg)
# XXX this would be more reliable if we also calculate the expected
# hydrogen positions and use the vector method below
elif (atom_name in ["NZ","NH1","NH2","ND2","NE2"] and
resname in ["ARG","ASN","GLN"] and
(assume_hydrogens_all_missing or resname == "ARG") and
distance <= params.max_distance_to_cation) :
if (_is_coplanar_with_sidechain(atom, other.parent(),
distance_cutoff = params.max_deviation_from_plane)) :
binds_amide_hydrogen = True
if (resname == "ARG") and (distance < min_distance_to_cation) :
min_distance_to_cation = distance
# hydroxyl groups - note that the orientation of the hydrogen is usually
# arbitrary and we can't determine precise bonding
elif ((atom_name in ["OG1", "OG2", "OH1"]) and
(resname in ["SER", "THR", "TYR"]) and
(distance <= params.max_distance_to_hydroxyl)) :
near_hydroxyl = True
if (distance < min_distance_to_hydroxyl) :
min_distance_to_hydroxyl = distance
# Backbone amide, explicit H
elif atom_name in ["H"]:
# TODO make this more general for any amide H?
xyz_h = col(contact.site_cart)
bonded_atoms = connectivity[j_seq]
if (len(bonded_atoms) != 1) :
continue
xyz_n = col(get_site(bonded_atoms[0]))
vec_hn = xyz_h - xyz_n
vec_hx = xyz_h - xyz
angle = abs(vec_hn.angle(vec_hx, deg = True))
# If Cl, H, and N line up, Cl binds the amide group
if abs(angle - 180) <= params.delta_amide_h_angle:
binds_amide_hydrogen = True
else :
pass #print "%s N-H-X angle: %s" % (atom.id_str(), angle)
# Backbone amide, implicit H
elif atom_name in ["N"] and assume_hydrogens_all_missing:
xyz_n = col(contact.site_cart)
bonded_atoms = connectivity[j_seq]
ca_same = c_prev = None
for k_seq in bonded_atoms :
other2 = pdb_atoms[k_seq]
if other2.name.strip().upper() in ["CA"]:
ca_same = col(get_site(k_seq))
elif other2.name.strip().upper() in ["C"]:
c_prev = col(get_site(k_seq))
if ca_same is not None and c_prev is not None:
xyz_cca = (ca_same + c_prev) / 2
vec_ncca = xyz_n - xyz_cca
# 0.86 is the backbone N-H bond distance in geostd
xyz_h = xyz_n + (vec_ncca.normalize() * 0.86)
vec_nh = xyz_n - xyz_h
vec_nx = xyz_n - xyz
angle = abs(vec_nh.angle(vec_nx, deg = True))
if abs(angle - 180) <= params.delta_amide_h_angle:
binds_amide_hydrogen = True
# sidechain NH2 groups, explicit H
elif ((atom_name in ["HD1","HD2"] and resname in ["ASN"]) or
(atom_name in ["HE1","HE2"] and resname in ["GLN"])) :
# XXX not doing this for Arg because it can't handle the bidentate
# coordination
#(atom_name in ["HH11","HH12","HH21","HH22"] and resname == "ARG")):
bonded_atoms = connectivity[j_seq]
assert (len(bonded_atoms) == 1)
xyz_n = col(get_site(bonded_atoms[0]))
xyz_h = col(contact.site_cart)
vec_nh = xyz_n - xyz_h
vec_xh = xyz - xyz_h
angle = abs(vec_nh.angle(vec_xh, deg = True))
if abs(angle - 180) <= params.delta_amide_h_angle:
binds_amide_hydrogen = True
else :
pass #print "%s amide angle: %s" % (atom.id_str(), angle)
# now check again for negatively charged sidechain (etc.) atoms (e.g.
# carboxyl groups), but with some leeway if a cation is also nearby.
# backbone carbonyl atoms are also excluded.
for contact in contacts :
if (contact.altloc() not in ["", "A"]) :
continue
resname = contact.resname()
atom_name = contact.atom_name()
distance = abs(contact)
if ((distance < 3.2) and
(distance < (min_distance_to_cation + 0.2)) and
is_negatively_charged_oxygen(atom_name, resname)) :
#print contact.id_str(), distance
return False
return (binds_amide_hydrogen or near_cation or near_lys)
def _is_favorable_halide_environment(
chem_env,
scatter_env,
assume_hydrogens_all_missing=Auto,
):
assume_hydrogens_all_missing = True
atom = chem_env.atom
binds_amide_hydrogen = False
near_cation = False
near_lys = False
near_hydroxyl = False
xyz = col(atom.xyz)
min_distance_to_cation = None
min_distance_to_hydroxyl = min_distance_to_cation
for contact in chem_env.contacts:
other = contact.atom
resname = contact.resname()
atom_name = contact.atom_name()
element = contact.element
distance = abs(contact)
# XXX need to figure out exactly what this should be - CL has a
# fairly large radius though (1.67A according to ener_lib.cif)
if distance < 2.5:
return False
if not element in ["C", "N", "H", "O", "S"]:
charge = server.get_charge(element)
if charge < 0 and distance <= 3.5:
# Nearby anion that is too close
return False
if charge > 0 and distance <= 3.5:
# Nearby cation
near_cation = True
if min_distance_to_cation is None or \
distance < min_distance_to_cation:
min_distance_to_cation = distance
# Lysine sidechains (can't determine planarity)
elif (atom_name in ["NZ"] and #, "NE", "NH1", "NH2"] and
resname in ["LYS"] and distance <= 3.5):
near_lys = True
if min_distance_to_cation is None or \
distance < min_distance_to_cation:
min_distance_to_cation = distance
# sidechain amide groups, no hydrogens (except Arg)
# XXX this would be more reliable if we also calculate the expected
# hydrogen positions and use the vector method below
elif (atom_name in ["NZ", "NH1", "NH2", "ND2", "NE2"]
and resname in ["ARG", "ASN", "GLN"]
and (assume_hydrogens_all_missing or resname == "ARG")
and distance <= 3.5):
binds_amide_hydrogen = True
if resname == "ARG" and (min_distance_to_cation is None
or distance < min_distance_to_cation):
min_distance_to_cation = distance
# hydroxyl groups - note that the orientation of the hydrogen is usually
# arbitrary and we can't determine precise bonding
elif ((atom_name in ["OG1", "OG2", "OH1"])
and (resname in ["SER", "THR", "TYR"]) and (distance <= 3.5)):
near_hydroxyl = True
if distance < min_distance_to_hydroxyl:
min_distance_to_hydroxyl = distance
# Backbone amide, implicit H
elif atom_name in ["N"] and assume_hydrogens_all_missing:
binds_amide_hydrogen = True
# xyz_n = col(contact.site_cart)
# bonded_atoms = connectivity[j_seq]
# ca_same = c_prev = None
# for k_seq in bonded_atoms:
# other2 = pdb_atoms[k_seq]
# if other2.name.strip().upper() in ["CA"]:
# ca_same = col(get_site(k_seq))
# elif other2.name.strip().upper() in ["C"]:
# c_prev = col(get_site(k_seq))
# if ca_same is not None and c_prev is not None:
# xyz_cca = (ca_same + c_prev) / 2
# vec_ncca = xyz_n - xyz_cca
# # 0.86 is the backbone N-H bond distance in geostd
# xyz_h = xyz_n + (vec_ncca.normalize() * 0.86)
# vec_nh = xyz_n - xyz_h
# vec_nx = xyz_n - xyz
# angle = abs(vec_nh.angle(vec_nx, deg=True))
# if abs(angle - 180) <= 20:
# binds_amide_hydrogen = True
# now check again for negatively charged sidechain (etc.) atoms (e.g.
# carboxyl groups), but with some leeway if a cation is also nearby.
# backbone carbonyl atoms are also excluded.
for contact in chem_env.contacts:
if contact.altloc() not in ["", "A"]:
continue
resname = contact.resname()
atom_name = contact.atom_name()
distance = abs(contact)
if ((distance < 3.2)
and (min_distance_to_cation is not None and distance <
(min_distance_to_cation + 0.2))
and halides.is_negatively_charged_oxygen(atom_name, resname)):
return False
return binds_amide_hydrogen or near_cation or near_lys