"""
Hydrogens
=========
Calculations related to hydrogen placement.
"""
import math
import logging
from typing import List, Optional, Tuple, TYPE_CHECKING
from propka.protonate import Protonate
from propka.bonds import BondMaker
from propka.atom import Atom
if TYPE_CHECKING:
from propka.molecular_container import MolecularContainer
_LOGGER = logging.getLogger(__name__)
[docs]
def setup_bonding_and_protonation(molecular_container: "MolecularContainer") -> None:
"""Set up bonding and protonation for a molecule.
Args:
parameters: not used
molecular_container: molecule container.
"""
# make bonds
my_bond_maker = setup_bonding(molecular_container)
# set up ligand atom names
set_ligand_atom_names(molecular_container)
# apply information on pi electrons
my_bond_maker.add_pi_electron_information(molecular_container)
# Protonate atoms
if molecular_container.options.protonate_all:
protonator = Protonate(verbose=False)
protonator.protonate(molecular_container)
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def setup_bonding(molecular_container: "MolecularContainer") -> BondMaker:
"""Set up bonding for a molecular container.
Args:
molecular_container: the molecular container in question
Returns:
BondMaker object
"""
my_bond_maker = BondMaker()
my_bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
return my_bond_maker
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def setup_bonding_and_protonation_30_style(molecular_container: "MolecularContainer") -> BondMaker:
"""Set up bonding for a molecular container.
Args:
molecular_container: the molecular container in question
Returns:
BondMaker object
"""
# Protonate atoms
protonate_30_style(molecular_container)
# make bonds
bond_maker = BondMaker()
bond_maker.find_bonds_for_molecules_using_boxes(molecular_container)
return bond_maker
[docs]
def protonate_30_style(molecular_container: "MolecularContainer") -> None:
"""Protonate the molecule.
Args:
molecular_container: molecule
"""
for name in molecular_container.conformation_names:
_LOGGER.info('Now protonating %s', name)
# split atom into residues
curres = -1000000
residue: List[Atom] = []
o_atom: Optional[Atom] = None
c_atom: Optional[Atom] = None
for atom in molecular_container.conformations[name].atoms:
if atom.res_num != curres:
curres = atom.res_num
if len(residue) > 0:
# backbone
[o_atom, c_atom] = add_backbone_hydrogen(
residue, o_atom, c_atom)
# arginine
if residue[0].res_name == 'ARG':
add_arg_hydrogen(residue)
# histidine
if residue[0].res_name == 'HIS':
add_his_hydrogen(residue)
# tryptophan
if residue[0].res_name == 'TRP':
add_trp_hydrogen(residue)
# amides
if residue[0].res_name in ['GLN', 'ASN']:
add_amd_hydrogen(residue)
residue = []
if atom.type == 'atom':
residue.append(atom)
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def set_ligand_atom_names(molecular_container: "MolecularContainer") -> None:
"""Set names for ligands in molecular container.
Args:
molecular_container: molecular container for ligand names
"""
for name in molecular_container.conformation_names:
molecular_container.conformations[name].set_ligand_atom_names()
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def add_arg_hydrogen(residue: List[Atom]) -> List[Atom]:
"""Adds Arg hydrogen atoms to residues according to the 'old way'.
Args:
residue: arginine residue to protonate
Returns:
list of hydrogen atoms
"""
cd_atom: Optional[Atom] = None
cz_atom: Optional[Atom] = None
ne_atom: Optional[Atom] = None
nh1_atom: Optional[Atom] = None
nh2_atom: Optional[Atom] = None
for atom in residue:
if atom.name == "CD":
cd_atom = atom
elif atom.name == "CZ":
cz_atom = atom
elif atom.name == "NE":
ne_atom = atom
elif atom.name == "NH1":
nh1_atom = atom
elif atom.name == "NH2":
nh2_atom = atom
if (cd_atom is None or cz_atom is None or ne_atom is None or nh1_atom is None
or nh2_atom is None):
raise ValueError("Unable to find all atoms")
h1_atom = protonate_sp2(cd_atom, ne_atom, cz_atom)
h1_atom.name = "HE"
h2_atom = protonate_direction(nh1_atom, ne_atom, cz_atom)
h2_atom.name = "HN1"
h3_atom = protonate_direction(nh1_atom, ne_atom, cd_atom)
h3_atom.name = "HN2"
h4_atom = protonate_direction(nh2_atom, ne_atom, cz_atom)
h4_atom.name = "HN3"
h5_atom = protonate_direction(nh2_atom, ne_atom, h1_atom)
h5_atom.name = "HN4"
return [h1_atom, h2_atom, h3_atom, h4_atom, h5_atom]
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def add_his_hydrogen(residue: List[Atom]) -> None:
"""Adds His hydrogen atoms to residues according to the 'old way'.
Args:
residue: histidine residue to protonate
"""
cg_atom: Optional[Atom] = None
nd_atom: Optional[Atom] = None
cd_atom: Optional[Atom] = None
ce_atom: Optional[Atom] = None
ne_atom: Optional[Atom] = None
for atom in residue:
if atom.name == "CG":
cg_atom = atom
elif atom.name == "ND1":
nd_atom = atom
elif atom.name == "CD2":
cd_atom = atom
elif atom.name == "CE1":
ce_atom = atom
elif atom.name == "NE2":
ne_atom = atom
if (cg_atom is None or nd_atom is None or cd_atom is None or ce_atom is None
or ne_atom is None):
raise ValueError("Unable to find all atoms")
hd_atom = protonate_sp2(cg_atom, nd_atom, ce_atom)
hd_atom.name = "HND"
he_atom = protonate_sp2(cd_atom, ne_atom, ce_atom)
he_atom.name = "HNE"
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def add_trp_hydrogen(residue: List[Atom]) -> None:
"""Adds Trp hydrogen atoms to residues according to the 'old way'.
Args:
residue: tryptophan residue to protonate
"""
cd_atom = None
ne_atom = None
ce_atom = None
for atom in residue:
if atom.name == "CD1":
cd_atom = atom
elif atom.name == "NE1":
ne_atom = atom
elif atom.name == "CE2":
ce_atom = atom
if (cd_atom is None) or (ne_atom is None) or (ce_atom is None):
str_ = "Unable to find all atoms for {0:s} {1:s}".format(
residue[0].res_name, residue[0].res_num)
raise ValueError(str_)
he_atom = protonate_sp2(cd_atom, ne_atom, ce_atom)
he_atom.name = "HNE"
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def add_amd_hydrogen(residue: List[Atom]) -> None:
"""Adds Gln & Asn hydrogen atoms to residues according to the 'old way'.
Args:
residue: glutamine or asparagine residue to protonate
"""
c_atom = None
o_atom = None
n_atom = None
for atom in residue:
if ((atom.res_name == "GLN" and atom.name == "CD")
or (atom.res_name == "ASN" and atom.name == "CG")):
c_atom = atom
elif ((atom.res_name == "GLN" and atom.name == "OE1")
or (atom.res_name == "ASN" and atom.name == "OD1")):
o_atom = atom
elif ((atom.res_name == "GLN" and atom.name == "NE2")
or (atom.res_name == "ASN" and atom.name == "ND2")):
n_atom = atom
if (c_atom is None) or (o_atom is None) or (n_atom is None):
str_ = "Unable to find all atoms for {0:s} {1:s}".format(
residue[0].res_name, residue[0].res_num)
raise ValueError(str_)
h1_atom = protonate_direction(n_atom, o_atom, c_atom)
h1_atom.name = "HN1"
h2_atom = protonate_average_direction(n_atom, c_atom, o_atom)
h2_atom.name = "HN2"
[docs]
def add_backbone_hydrogen(residue: List[Atom],
o_atom: Optional[Atom],
c_atom: Optional[Atom]) -> Tuple[Optional[Atom], Optional[Atom]]:
"""Adds hydrogen backbone atoms to residues according to the old way.
dR is wrong for the N-terminus (i.e. first residue) but it doesn't affect
anything at the moment. Could be improved, but works for now.
Args:
residue: residue to protonate
o_atom: backbone oxygen atom
c_atom: backbone carbon atom
Returns:
[new backbone oxygen atom, new backbone carbon atom]
"""
new_c_atom = None
new_o_atom = None
n_atom = None
for atom in residue:
if atom.name == "N":
n_atom = atom
if atom.name == "C":
new_c_atom = atom
if atom.name == "O":
new_o_atom = atom
if c_atom is None or o_atom is None or n_atom is None:
return (new_o_atom, new_c_atom)
if n_atom.res_name == "PRO":
# PRO doesn't have an H-atom; do nothing
pass
else:
h_atom = protonate_direction(n_atom, o_atom, c_atom)
h_atom.name = "H"
return (new_o_atom, new_c_atom)
[docs]
def protonate_direction(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) -> Atom:
"""Protonates an atom, x1_atom, given a direction.
New direction for x1_atom proton is (x2_atom -> x3_atom).
Args:
x1_atom: atom to be protonated
x2_atom: atom for direction
x3_atom: other atom for direction
Returns:
new hydrogen atom
"""
dx = (x3_atom.x - x2_atom.x)
dy = (x3_atom.y - x2_atom.y)
dz = (x3_atom.z - x2_atom.z)
length = math.sqrt(dx*dx + dy*dy + dz*dz)
x = x1_atom.x + dx/length
y = x1_atom.y + dy/length
z = x1_atom.z + dz/length
h_atom = make_new_h(x1_atom, x, y, z)
h_atom.name = "H"
return h_atom
[docs]
def protonate_average_direction(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) -> Atom:
"""Protonates an atom, x1_atom, given a direction.
New direction for x1_atom is (x1_atom/x2_atom -> x3_atom).
Note, this one uses the average of x1_atom & x2_atom (N & O) unlike
the previous N - C = O
Args:
x1_atom: atom to be protonated
x2_atom: atom for direction
x3_atom: other atom for direction
Returns:
new hydrogen atom
"""
dx = (x3_atom.x + x1_atom.x)*0.5 - x2_atom.x
dy = (x3_atom.y + x1_atom.y)*0.5 - x2_atom.y
dz = (x3_atom.z + x1_atom.z)*0.5 - x2_atom.z
length = math.sqrt(dx*dx + dy*dy + dz*dz)
x = x1_atom.x + dx/length
y = x1_atom.y + dy/length
z = x1_atom.z + dz/length
h_atom = make_new_h(x1_atom, x, y, z)
h_atom.name = "H"
return h_atom
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def protonate_sp2(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) -> Atom:
"""Protonates a SP2 atom, given a list of atoms
Args:
x1_atom: atom to set direction
x2_atom: atom to be protonated
x3_atom: other atom to set direction
Returns:
new hydrogen atom
"""
dx = (x1_atom.x + x3_atom.x)*0.5 - x2_atom.x
dy = (x1_atom.y + x3_atom.y)*0.5 - x2_atom.y
dz = (x1_atom.z + x3_atom.z)*0.5 - x2_atom.z
length = math.sqrt(dx*dx + dy*dy + dz*dz)
x = x2_atom.x - dx/length
y = x2_atom.y - dy/length
z = x2_atom.z - dz/length
h_atom = make_new_h(x2_atom, x, y, z)
h_atom.name = "H"
return h_atom
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def make_new_h(atom: Atom, x: float, y: float, z: float) -> Atom:
"""Add a new hydrogen to an atom at the specified position.
Args:
atom: atom to protonate
x: x position of hydrogen
y: y position of hydrogen
z: z position of hydrogen
Returns:
new hydrogen atom
"""
new_h = Atom()
new_h.set_property(
numb=None, name='H{0:s}'.format(atom.name[1:]),
res_name=atom.res_name, chain_id=atom.chain_id,
res_num=atom.res_num, x=x, y=y, z=z, occ=None, beta=None)
new_h.element = 'H'
new_h.bonded_atoms = [atom]
new_h.charge = 0
new_h.steric_number = 0
new_h.number_of_lone_pairs = 0
new_h.number_of_protons_to_add = 0
new_h.num_pi_elec_2_3_bonds = 0
atom.bonded_atoms.append(new_h)
assert atom.conformation_container is not None
atom.conformation_container.add_atom(new_h)
return new_h