def add_hydrogens(atom):
existing_bonds = list(atom.yield_bonds())
num_bonds = len(existing_bonds)
bond_length = bonds.get_length(atom.number, 1, BOND_SINGLE)
if num_bonds == 0:
H = Atom(name="auto H", number=1)
H.transformation.t = atom.transformation.t + numpy.array([0,bond_length,0])
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()
rotation.set_rotation_properties(2*math.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.yield_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*math.cos(opening_angle) + normal*math.sin(opening_angle))
for i in range(num_hydrogens):
H = Atom(name="auto H", number=1)
H.transformation.t = atom.transformation.t + h_pos
primitive.Add(H, atom.parent)
bond = Bond(name="aut H bond", targets=[atom, H])
primitive.Add(bond, atom.parent)
h_pos = rotation.vector_apply(h_pos)
class Camera(object):
def __init__(self):
# register configuration settings: default camera
from zeobuilder.gui import fields
from zeobuilder.gui.fields_dialogs import DialogFieldInfo
config = context.application.configuration
config.register_setting(
"viewer_distance",
100.0*angstrom,
DialogFieldInfo("Default Viewer", (1, 0), fields.faulty.Length(
label_text="Distance from origin",
attribute_name="viewer_distance",
low=0.0,
low_inclusive=True,
)),
)
config.register_setting(
"opening_angle",
0.0,
DialogFieldInfo("Default Viewer", (1, 1), fields.faulty.MeasureEntry(
measure="Angle",
label_text="Camera opening angle",
attribute_name="opening_angle",
low=0.0,
low_inclusive=True,
high=0.5*numpy.pi,
high_inclusive=False,
show_popup=False,
)),
)
config.register_setting(
"window_size",
25*angstrom,
DialogFieldInfo("Default Viewer", (1, 2), fields.faulty.Length(
label_text="Window size",
attribute_name="window_size",
low=0.0,
low_inclusive=False,
)),
)
config.register_setting(
"window_depth",
200.0*angstrom,
DialogFieldInfo("Default Viewer", (1, 3), fields.faulty.Length(
label_text="Window depth",
attribute_name="window_depth",
low=0.0,
low_inclusive=False,
)),
)
self.reset()
def reset(self):
config = context.application.configuration
self.rotation_center = Translation()
self.rotation = Rotation()
self.eye = Translation()
self.eye.t[2] = config.viewer_distance
self.opening_angle = config.opening_angle
self.window_size = config.window_size
self.window_depth = config.window_depth
def get_znear(self):
if self.opening_angle > 0.0:
return 0.5*self.window_size/numpy.tan(0.5*self.opening_angle)
else:
return 0.0
znear = property(get_znear)
# coordinate transformations
def eye_to_camera(self, vector_e):
tmp = numpy.ones(2, float)
znear = self.znear
if znear > 0:
return -vector_e[:2]/vector_e[2]/self.window_size*znear
else:
return vector_e[:2]/self.window_size
def camera_window_to_eye(self, vector_c):
tmp = numpy.zeros(3, float)
tmp[:2] = vector_c*self.window_size
znear = self.znear
if znear > 0:
tmp[2] = -self.znear
else:
tmp[2] = -self.window_size/3.0
return tmp
def model_to_eye(self, vector_m):
scene = context.application.scene
tmp = scene.model_center.vector_apply_inverse(vector_m)
tmp = self.rotation_center.vector_apply_inverse(tmp)
tmp = self.rotation.vector_apply_inverse(tmp)
tmp[2] -= self.znear
tmp = self.eye.vector_apply_inverse(tmp)
return tmp
def eye_to_model(self, vector_e):
scene = context.application.scene
tmp = self.eye.vector_apply(vector_e)
tmp[2] += self.znear
tmp = self.rotation.vector_apply(tmp)
tmp = self.rotation_center.vector_apply(tmp)
tmp = scene.model_center.vector_apply(tmp)
return tmp
def model_to_camera(self, vector_m):
return self.eye_to_camera(self.model_to_eye(vector_m))
def camera_window_to_model(self, vector_c):
return self.eye_to_model(self.camera_window_to_eye(vector_c))
def object_to_depth(self, gl_object):
result = -self.model_to_eye(gl_object.get_absolute_frame().t)[2]
return result
def object_to_camera(self, gl_object):
return self.eye_to_camera(self.model_to_eye(gl_object.get_absolute_frame().t))
def object_to_eye(self, gl_object):
return self.model_to_eye(gl_object.get_absolute_frame().t)
def object_eye_rotation(self, gl_object):
"""
Returns a matrix that consists of the x, y and z axes of the
eye frame in the coordinates of the parent frame of the given
object.
"""
if hasattr(gl_object, "parent") and \
isinstance(gl_object.parent, GLTransformationMixin):
parent_matrix = gl_object.parent.get_absolute_frame().r
else:
parent_matrix = numpy.identity(3, float)
result = numpy.dot(self.rotation.r.transpose(), parent_matrix).transpose()
return result
def depth_to_scale(self, depth):
""" transforms a depth into a scale (au/camcoords)"""
znear = self.znear
if znear > 0:
return depth/znear*self.window_size
else:
return self.window_size
def vector_in_plane(self, r, p_m):
"""Returns a vector at camera position r in a plane (through p, orthogonal to viewing direction)
Arguments
r -- a two-dimensional vector in camera coordinates
p_m -- a three-dimensional vector in model coordinates
Returns
rp -- a three-dimensional vector in model coordinates that lies
at the intersection of a plane and a line. The plane is
orthogonal to the viewing direction and goes through the
point p. The line connects the eye (eye_m below) with the
point r (r_m below) in the camera window.
"""
eye_m = self.eye_to_model(numpy.zeros(3, float))
r_m = self.camera_window_to_model(r)
center_m = self.camera_window_to_model(numpy.zeros(2, float))
normal = (eye_m - center_m)
normal /= numpy.linalg.norm(normal)
if self.znear > 0:
# the line is defined as r = eye_m + d*t, where t = -infinity ... infinity
d = eye_m - r_m
# t at the intersection:
t = -numpy.dot(eye_m - p_m, normal)/numpy.dot(d, normal)
return eye_m + d*t
else:
# the line is defined as r = r_m + d*t, where t = -infinity ... infinity
d = normal
# t at the intersection:
t = -numpy.dot(r_m - p_m, normal)/numpy.dot(d, normal)
return r_m + d*t