def add_hydrogens(atom):
existing_bonds = list(atom.iter_bonds())
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
num_hydrogens = self.parameters.num_hydrogens
if len(existing_bonds) == 0:
t = atom.transformation.t + numpy.array([0, bond_length, 0])
H = Atom(name="auto H",
number=1,
transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
existing_bonds.append(bond)
num_hydrogens -= 1
main_direction = numpy.zeros(3, float)
for bond in existing_bonds:
shortest_vector = bond.shortest_vector_relative_to(atom.parent)
if bond.children[1].target == atom:
shortest_vector *= -1
main_direction += shortest_vector
main_direction /= numpy.linalg.norm(main_direction)
normal = random_orthonormal(main_direction)
rotation = Rotation.from_properties(
2 * numpy.pi / float(num_hydrogens), main_direction, False)
h_pos = bond_length * (
main_direction * numpy.cos(self.parameters.valence_angle) +
normal * numpy.sin(self.parameters.valence_angle))
for i in range(num_hydrogens):
t = atom.transformation.t + h_pos
H = Atom(name="auto H",
number=1,
transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation * h_pos
def add_hydrogens(atom):
existing_bonds = list(atom.iter_bonds())
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
num_hydrogens = self.parameters.num_hydrogens
if len(existing_bonds) == 0:
t = atom.transformation.t + numpy.array([0,bond_length,0])
H = Atom(name="auto H", number=1, transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
existing_bonds.append(bond)
num_hydrogens -= 1
main_direction = numpy.zeros(3, float)
for bond in existing_bonds:
shortest_vector = bond.shortest_vector_relative_to(atom.parent)
if bond.children[1].target == atom:
shortest_vector *= -1
main_direction += shortest_vector
main_direction /= numpy.linalg.norm(main_direction)
normal = random_orthonormal(main_direction)
rotation = Rotation.from_properties(2*numpy.pi / float(num_hydrogens), main_direction, False)
h_pos = bond_length*(
main_direction*numpy.cos(self.parameters.valence_angle) +
normal*numpy.sin(self.parameters.valence_angle)
)
for i in range(num_hydrogens):
t = atom.transformation.t + h_pos
H = Atom(name="auto H", number=1, transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation * h_pos
def __init__(self, graph, unit_cell=None):
"""
Argument:
| ``graph`` -- the molecular graph from which the force field terms
are extracted. See
:class:molmod.molecular_graphs.MolecularGraph
Optional argument:
| ``unit_cell`` -- periodic boundry conditions, see
:class:`molmod.unit_cells.UnitCell`
"""
from molmod.bonds import bonds
if unit_cell is None:
self.matrix = None
self.reciprocal = None
else:
self.matrix = unit_cell.matrix
self.reciprocal = unit_cell.reciprocal
self.dm = graph.distances.astype(numpy.int32)
dm = self.dm.astype(float)
self.dm0 = dm**2
self.dmk = (dm+0.1)**(-3)
self.vdw_radii = numpy.array([periodic[number].vdw_radius for number in graph.numbers], dtype=float)
self.covalent_radii = numpy.array([periodic[number].covalent_radius for number in graph.numbers], dtype=float)
bond_edges = []
bond_lengths = []
for i, j in graph.edges:
bond_edges.append((i, j))
bond_lengths.append(bonds.get_length(graph.numbers[i], graph.numbers[j]))
self.bond_edges = numpy.array(bond_edges, numpy.int32)
self.bond_lengths = numpy.array(bond_lengths, float)
special_angles = SpecialAngles()
span_edges = []
span_lengths = []
for i, neighbors in graph.neighbors.iteritems():
number_i = graph.numbers[i]
if (number_i >= 5 and number_i <=8):
valence = len(neighbors) + abs(number_i-6)
elif number_i >= 13 and number_i <= 16:
valence = len(neighbors) + abs(number_i-14)
else:
valence = -1
if valence < 2 or valence > 6:
default_angle = numpy.pi/180.0*115.0
elif valence == 2:
default_angle = numpy.pi
elif valence == 3:
default_angle = numpy.pi/180.0*125.0
elif valence == 4:
default_angle = numpy.pi/180.0*109.0
elif valence == 5:
default_angle = numpy.pi/180.0*100.0
elif valence == 6:
default_angle = numpy.pi/180.0*90.0
for j in neighbors:
number_j = graph.numbers[j]
for k in neighbors:
if j < k and not frozenset([j, k]) in graph.edges:
number_k = graph.numbers[k]
triplet = (
number_j, len(graph.neighbors[j]),
number_i, len(graph.neighbors[i]),
number_k, len(graph.neighbors[k]),
)
angle = special_angles.get_angle(triplet)
if angle is None:
angle = default_angle
dj = bonds.get_length(number_i, number_j)
dk = bonds.get_length(number_i, number_k)
d = numpy.sqrt(dj**2+dk**2-2*dj*dk*numpy.cos(angle))
span_edges.append((j, k))
span_lengths.append(d)
self.span_edges = numpy.array(span_edges, numpy.int32)
self.span_lengths = numpy.array(span_lengths, float)
self.dm_quad = 0.0
self.dm_reci = 0.0
self.bond_quad = 0.0
self.span_quad = 0.0
self.bond_hyper = 0.0
self.bond_hyper_scale = 5.0
def add_hydrogens(atom):
existing_bonds = list(atom.iter_bonds())
num_bonds = len(existing_bonds)
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
if num_bonds == 0:
t = atom.transformation.t + numpy.array([0, bond_length, 0])
H = Atom(name="auto H",
number=1,
transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
existing_bonds.append(bond)
num_bonds = 1
used_valence = 0
oposite_direction = numpy.zeros(3, float)
for bond in existing_bonds:
shortest_vector = bond.shortest_vector_relative_to(atom.parent)
if bond.children[1].target == atom:
shortest_vector *= -1
oposite_direction -= shortest_vector
if bond.bond_type == BOND_SINGLE:
used_valence += 1
elif bond.bond_type == BOND_DOUBLE:
used_valence += 2
elif bond.bond_type == BOND_TRIPLE:
used_valence += 3
oposite_direction /= numpy.linalg.norm(oposite_direction)
num_hydrogens = valence_el(
atom.number) - 2 * lone_pairs(atom.number) - used_valence
if num_hydrogens <= 0:
return
hybride_count = num_hydrogens + lone_pairs(
atom.number) + num_bonds - (used_valence - num_bonds)
num_sites = num_hydrogens + lone_pairs(atom.number)
rotation = Rotation.from_properties(
2 * numpy.pi / float(num_sites), oposite_direction, False)
opening_key = (hybride_count, num_sites)
opening_angle = self.opening_angles.get(opening_key)
if opening_angle is None:
return
if num_bonds == 1:
first_bond = existing_bonds[0]
other_atom = first_bond.children[0].target
if other_atom == atom:
other_atom = first_bond.children[1].target
other_bonds = [
bond for bond in other_atom.iter_bonds()
if bond != first_bond
]
if len(other_bonds) > 0:
normal = other_bonds[0].shortest_vector_relative_to(
atom.parent)
normal -= numpy.dot(normal,
oposite_direction) * oposite_direction
normal /= numpy.linalg.norm(normal)
if other_bonds[0].children[0].target == other_atom:
normal *= -1
else:
normal = random_orthonormal(oposite_direction)
elif num_bonds == 2:
normal = numpy.cross(
oposite_direction,
existing_bonds[0].shortest_vector_relative_to(atom.parent))
normal /= numpy.linalg.norm(normal)
elif num_bonds == 3:
normal = random_orthonormal(oposite_direction)
else:
return
h_pos = bond_length * (oposite_direction * numpy.cos(opening_angle)
+ normal * numpy.sin(opening_angle))
for i in range(num_hydrogens):
t = atom.transformation.t + h_pos
H = Atom(name="auto H",
number=1,
transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation * h_pos
def replace(self, gl_object):
if not gl_object.get_fixed():
new = self.get_new(gl_object.transformation.t)
# select a target object, i.e. the one the will be connected with
# the bonds/vectors/... of the replaced object
if (self.current_object == "Fragment"):
# fragments are inserted as frames
# take atom with index 1 as target
target_object = new.children[1]
else:
target_object = new
# check if all connections to the replaced object are applicable
# to the new object. if not, then do not perform the replacement
# and return early.
for reference in gl_object.references[::-1]:
if not reference.check_target(target_object):
return
# add the new object
parent = gl_object.parent
primitive.Add(new, parent)
if (self.current_object == "Fragment"):
# Fix the rotation and translation of the molecular fragment.
# Rotation
Bond = context.application.plugins.get_node("Bond")
if len(gl_object.references) == 1 and isinstance(
gl_object.references[0].parent, Bond):
bond1 = gl_object.references[0].parent
direction1 = bond1.shortest_vector_relative_to(parent)
if bond1.children[0].target != gl_object:
direction1 *= -1
bond2 = new.children[0].references[0].parent
direction2 = bond2.shortest_vector_relative_to(parent)
if bond2.children[0].target != target_object:
direction2 *= -1
axis = numpy.cross(direction2, direction1)
if numpy.linalg.norm(axis) < 1e-8:
axis = random_orthonormal(direction1)
angle = compute_angle(direction1, direction2)
rotation = Rotation.from_properties(angle, axis, False)
primitive.Transform(new, rotation)
else:
bond1 = None
# Tranlsation
pos_old = new.children[1].get_frame_relative_to(parent).t
pos_new = gl_object.transformation.t
translation = Translation(pos_new - pos_old)
primitive.Transform(new, translation)
if bond1 != None:
# bond length
old_length = numpy.linalg.norm(direction1)
new_length = bonds.get_length(
new.children[1].number,
bond1.get_neighbor(gl_object).number)
translation = Translation(-direction1 / old_length *
(new_length - old_length))
primitive.Transform(new, translation)
# let the references to the replaced object point to the new object
for reference in gl_object.references[::-1]:
try:
primitive.SetTarget(reference, target_object)
except primitive.PrimitiveError:
primitive.Delete(reference.parent)
# delete the replaced object
primitive.Delete(gl_object)
if (self.current_object == "Fragment"):
# Delete the first atom in the fragment
primitive.Delete(new.children[0])
# Unframe the fragment
UnframeAbsolute = context.application.plugins.get_action(
"UnframeAbsolute")
UnframeAbsolute([new])
def replace(self, gl_object):
if not gl_object.get_fixed():
new = self.get_new(gl_object.transformation.t)
# select a target object, i.e. the one the will be connected with
# the bonds/vectors/... of the replaced object
if(self.current_object == "Fragment"):
# fragments are inserted as frames
# take atom with index 1 as target
target_object = new.children[1]
else:
target_object = new
# check if all connections to the replaced object are applicable
# to the new object. if not, then do not perform the replacement
# and return early.
for reference in gl_object.references[::-1]:
if not reference.check_target(target_object):
return
# add the new object
parent = gl_object.parent
primitive.Add(new, parent)
if(self.current_object == "Fragment"):
# Fix the rotation and translation of the molecular fragment.
# Rotation
Bond = context.application.plugins.get_node("Bond")
if len(gl_object.references) == 1 and isinstance(gl_object.references[0].parent, Bond):
bond1 = gl_object.references[0].parent
direction1 = bond1.shortest_vector_relative_to(parent)
if bond1.children[0].target != gl_object:
direction1 *= -1
bond2 = new.children[0].references[0].parent
direction2 = bond2.shortest_vector_relative_to(parent)
if bond2.children[0].target != target_object:
direction2 *= -1
axis = numpy.cross(direction2, direction1)
if numpy.linalg.norm(axis) < 1e-8:
axis = random_orthonormal(direction1)
angle = compute_angle(direction1, direction2)
rotation = Rotation.from_properties(angle, axis, False)
primitive.Transform(new, rotation)
else:
bond1 = None
# Tranlsation
pos_old = new.children[1].get_frame_relative_to(parent).t
pos_new = gl_object.transformation.t
translation = Translation(pos_new - pos_old)
primitive.Transform(new, translation)
if bond1 != None:
# bond length
old_length = numpy.linalg.norm(direction1)
new_length = bonds.get_length(new.children[1].number, bond1.get_neighbor(gl_object).number)
translation = Translation(-direction1/old_length*(new_length-old_length))
primitive.Transform(new, translation)
# let the references to the replaced object point to the new object
for reference in gl_object.references[::-1]:
try:
primitive.SetTarget(reference, target_object)
except primitive.PrimitiveError:
primitive.Delete(reference.parent)
# delete the replaced object
primitive.Delete(gl_object)
if(self.current_object == "Fragment"):
# Delete the first atom in the fragment
primitive.Delete(new.children[0])
# Unframe the fragment
UnframeAbsolute = context.application.plugins.get_action("UnframeAbsolute")
UnframeAbsolute([new])
def __init__(self, graph, unit_cell=None):
"""
Argument:
| ``graph`` -- the molecular graph from which the force field terms
are extracted. See
:class:molmod.molecular_graphs.MolecularGraph
Optional argument:
| ``unit_cell`` -- periodic boundry conditions, see
:class:`molmod.unit_cells.UnitCell`
"""
from molmod.bonds import bonds
if unit_cell is None:
self.matrix = None
self.reciprocal = None
else:
self.matrix = unit_cell.matrix
self.reciprocal = unit_cell.reciprocal
self.dm = graph.distances.astype(int)
dm = self.dm.astype(float)
self.dm0 = dm**2
self.dmk = (dm + 0.1)**(-3)
self.vdw_radii = np.array(
[periodic[number].vdw_radius for number in graph.numbers],
dtype=float)
self.covalent_radii = np.array(
[periodic[number].covalent_radius for number in graph.numbers],
dtype=float)
bond_edges = []
bond_lengths = []
for i, j in graph.edges:
bond_edges.append((i, j))
bond_lengths.append(
bonds.get_length(graph.numbers[i], graph.numbers[j]))
self.bond_edges = np.array(bond_edges, int)
self.bond_lengths = np.array(bond_lengths, float)
special_angles = SpecialAngles()
span_edges = []
span_lengths = []
for i, neighbors in graph.neighbors.items():
number_i = graph.numbers[i]
if (number_i >= 5 and number_i <= 8):
valence = len(neighbors) + abs(number_i - 6)
elif number_i >= 13 and number_i <= 16:
valence = len(neighbors) + abs(number_i - 14)
else:
valence = -1
if valence < 2 or valence > 6:
default_angle = np.pi / 180.0 * 115.0
elif valence == 2:
default_angle = np.pi
elif valence == 3:
default_angle = np.pi / 180.0 * 125.0
elif valence == 4:
default_angle = np.pi / 180.0 * 109.0
elif valence == 5:
default_angle = np.pi / 180.0 * 100.0
elif valence == 6:
default_angle = np.pi / 180.0 * 90.0
for j in neighbors:
number_j = graph.numbers[j]
for k in neighbors:
if j < k and not frozenset([j, k]) in graph.edges:
number_k = graph.numbers[k]
triplet = (
number_j,
len(graph.neighbors[j]),
number_i,
len(graph.neighbors[i]),
number_k,
len(graph.neighbors[k]),
)
angle = special_angles.get_angle(triplet)
if angle is None:
angle = default_angle
dj = bonds.get_length(number_i, number_j)
dk = bonds.get_length(number_i, number_k)
d = np.sqrt(dj**2 + dk**2 -
2 * dj * dk * np.cos(angle))
span_edges.append((j, k))
span_lengths.append(d)
self.span_edges = np.array(span_edges, int)
self.span_lengths = np.array(span_lengths, float)
self.dm_quad = 0.0
self.dm_reci = 0.0
self.bond_quad = 0.0
self.span_quad = 0.0
self.bond_hyper = 0.0
self.bond_hyper_scale = 5.0
def add_hydrogens(atom):
existing_bonds = list(atom.iter_bonds())
num_bonds = len(existing_bonds)
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
if num_bonds == 0:
t = atom.transformation.t + numpy.array([0,bond_length,0])
H = Atom(name="auto H", number=1, transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
existing_bonds.append(bond)
num_bonds = 1
used_valence = 0
oposite_direction = numpy.zeros(3, float)
for bond in existing_bonds:
shortest_vector = bond.shortest_vector_relative_to(atom.parent)
if bond.children[1].target == atom:
shortest_vector *= -1
oposite_direction -= shortest_vector
if bond.bond_type == BOND_SINGLE:
used_valence += 1
elif bond.bond_type == BOND_DOUBLE:
used_valence += 2
elif bond.bond_type == BOND_TRIPLE:
used_valence += 3
oposite_direction /= numpy.linalg.norm(oposite_direction)
num_hydrogens = valence_el(atom.number) - 2*lone_pairs(atom.number) - used_valence
if num_hydrogens <= 0:
return
hybride_count = num_hydrogens + lone_pairs(atom.number) + num_bonds - (used_valence - num_bonds)
num_sites = num_hydrogens + lone_pairs(atom.number)
rotation = Rotation.from_properties(2*numpy.pi / float(num_sites), oposite_direction, False)
opening_key = (hybride_count, num_sites)
opening_angle = self.opening_angles.get(opening_key)
if opening_angle is None:
return
if num_bonds == 1:
first_bond = existing_bonds[0]
other_atom = first_bond.children[0].target
if other_atom == atom:
other_atom = first_bond.children[1].target
other_bonds = [bond for bond in other_atom.iter_bonds() if bond != first_bond]
if len(other_bonds) > 0:
normal = other_bonds[0].shortest_vector_relative_to(atom.parent)
normal -= numpy.dot(normal, oposite_direction) * oposite_direction
normal /= numpy.linalg.norm(normal)
if other_bonds[0].children[0].target == other_atom:
normal *= -1
else:
normal = random_orthonormal(oposite_direction)
elif num_bonds == 2:
normal = numpy.cross(oposite_direction, existing_bonds[0].shortest_vector_relative_to(atom.parent))
normal /= numpy.linalg.norm(normal)
elif num_bonds == 3:
normal = random_orthonormal(oposite_direction)
else:
return
h_pos = bond_length*(oposite_direction*numpy.cos(opening_angle) + normal*numpy.sin(opening_angle))
for i in range(num_hydrogens):
t = atom.transformation.t + h_pos
H = Atom(name="auto H", number=1, transformation=Translation(t))
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation * h_pos