def trigonal(self, atom):
"""Add hydrogens in trigonal geometry.
Args:
atom: atom to protonate
"""
_LOGGER.debug(
'TRIGONAL - {0:d} bonded atoms'.format(len(atom.bonded_atoms))
)
rot_angle = math.radians(120.0)
cvec = Vector(atom1=atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
avec = Vector(atom1=atom, atom2=atom.bonded_atoms[0])
# use plane of bonded trigonal atom - e.g. arg
self.set_steric_number_and_lone_pairs(atom.bonded_atoms[0])
if (atom.bonded_atoms[0].steric_number == 3
and len(atom.bonded_atoms[0].bonded_atoms) > 1):
# use other atoms bonded to the neighbour to establish the
# plane, if possible
other_atom_indices = []
for i, bonded_atom in enumerate(
atom.bonded_atoms[0].bonded_atoms):
if bonded_atom != atom:
other_atom_indices.append(i)
vec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0])
vec2 = Vector(atom1=atom.bonded_atoms[0],
atom2=atom.bonded_atoms[0]
.bonded_atoms[other_atom_indices[0]])
axis = vec1**vec2
# this is a trick to make sure that the order of atoms doesn't
# influence the final postions of added protons
if len(other_atom_indices) > 1:
vec3 = Vector(atom1=atom.bonded_atoms[0],
atom2=atom.bonded_atoms[0]
.bonded_atoms[other_atom_indices[1]])
axis2 = vec1**vec3
if axis*axis2 > 0:
axis = axis+axis2
else:
axis = axis-axis2
else:
axis = avec.orthogonal()
avec = rotate_vector_around_an_axis(rot_angle, axis, avec)
avec = self.set_bond_distance(avec, atom.element)
self.add_proton(atom, cvec+avec)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
avec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
avec2 = Vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
new_a = -avec1 - avec2
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, cvec+new_a)
def are_atoms_planar(atoms):
"""Test whether a group of atoms are planar.
Args:
atoms: list of atoms
Returns:
Boolean
"""
if len(atoms) == 0:
return False
if len(atoms) < 4:
return False
vec1 = Vector(atom1=atoms[0], atom2=atoms[1])
vec2 = Vector(atom1=atoms[0], atom2=atoms[2])
norm = (vec1**vec2).rescale(1.0)
margin = PLANARITY_MARGIN
for atom in atoms[3:]:
vec = Vector(atom1=atoms[0], atom2=atom).rescale(1.0)
if abs(vec * norm) > margin:
return False
return True
def tetrahedral(self, atom):
"""Protonate atom in tetrahedral geometry.
Args:
atom: atom to protonate.
"""
debug('TETRAHEDRAL - {0:d} bonded atoms'.format(len(
atom.bonded_atoms)))
# TODO - might be good to move tetrahedral angle to constant
rot_angle = math.radians(109.5)
cvec = Vector(atom1=atom)
# 0 bonds
if len(atom.bonded_atoms) == 0:
pass
# 1 bond
if len(atom.bonded_atoms) == 1 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first one
avec = Vector(atom1=atom, atom2=atom.bonded_atoms[0])
axis = avec.orthogonal()
avec = rotate_vector_around_an_axis(rot_angle, axis, avec)
avec = self.set_bond_distance(avec, atom.element)
self.add_proton(atom, cvec + avec)
# 2 bonds
if len(atom.bonded_atoms) == 2 and atom.number_of_protons_to_add > 0:
# Add another atom with the right angle to the first two
avec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
avec2 = Vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
axis = avec1 + avec2
new_a = rotate_vector_around_an_axis(math.radians(90), axis,
-avec1)
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, cvec + new_a)
# 3 bonds
if len(atom.bonded_atoms) == 3 and atom.number_of_protons_to_add > 0:
avec1 = Vector(atom1=atom, atom2=atom.bonded_atoms[0]).rescale(1.0)
avec2 = Vector(atom1=atom, atom2=atom.bonded_atoms[1]).rescale(1.0)
avec3 = Vector(atom1=atom, atom2=atom.bonded_atoms[2]).rescale(1.0)
new_a = -avec1 - avec2 - avec3
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, cvec + new_a)