def main(args):
cg = ftmc.CoarseGrainRNA(args.rna)
for stem in cg.stem_iterator():
stem_vec = cg.coords.get_direction(stem)
twist_vec = cg.twists[stem][0]
try:
ftuv.create_orthonormal_basis(stem_vec, twist_vec)
except AssertionError:
cg.twists[stem] = ftuv.vector_rejection(twist_vec, stem_vec), cg.twists[stem][1]
twist_vec = cg.twists[stem][1]
try:
ftuv.create_orthonormal_basis(stem_vec, twist_vec)
except AssertionError:
cg.twists[stem] = cg.twists[stem][0], ftuv.vector_rejection(twist_vec, stem_vec)
try:
cg.add_all_virtual_residues()
except:
assert False
print(cg.to_cg_string())
def main(args):
cg = ftmc.CoarseGrainRNA.from_bg_file(args.rna)
for stem in cg.stem_iterator():
stem_vec = cg.coords.get_direction(stem)
twist_vec = cg.twists[stem][0]
try:
ftuv.create_orthonormal_basis(stem_vec, twist_vec)
except AssertionError:
cg.twists[stem] = ftuv.vector_rejection(
twist_vec, stem_vec), cg.twists[stem][1]
twist_vec = cg.twists[stem][1]
try:
ftuv.create_orthonormal_basis(stem_vec, twist_vec)
except AssertionError:
cg.twists[stem] = cg.twists[stem][0], ftuv.vector_rejection(
twist_vec, stem_vec)
try:
cg.add_all_virtual_residues()
except:
assert False
print(cg.to_cg_string())
def get_twists(self, node):
'''
Get the array of twists for this node. If the node is a stem,
then the twists will simply those stored in the array.
If the node is an interior loop or a junction segment,
then the twists will be the ones that are adjacent to it.
If the node is a hairpin loop or a free end, then the same twist
will be duplicated and returned twice.
@param node: The name of the node
'''
if node[0] == 's':
return self.twists[node]
connections = list(self.edges[node])
(s1b, s1e) = self.get_sides(connections[0], node)
if len(connections) == 1:
vec = ftuv.normalize(ftuv.vector_rejection(
self.twists[connections[0]][s1b],
self.coords[connections[0]][1] -
self.coords[connections[0]][0]))
return (vec,vec)
if len(connections) == 2:
# interior loop or junction segment
(s2b, s2e) = self.get_sides(connections[1], node)
bulge_vec = (self.coords[connections[0]][s1b] -
self.coords[connections[1]][s2b])
return (ftuv.normalize(ftuv.vector_rejection(
self.twists[connections[0]][s1b], bulge_vec)),
ftuv.normalize(ftuv.vector_rejection(self.twists[connections[1]][s2b], bulge_vec)))
# uh oh, this shouldn't happen since every node
# should have either one or two edges
return None
def get_relative_orientation(cg, loop, stem):
'''
Return how loop is related to stem in terms of three parameters.
The stem is the receptor of a potential A-Minor interaction, whereas the
loop is the donor.
The 3 parameters are:
1. Distance between the closest points of the two elements
2. The angle between the stem and the vector between the two
3. The angle between the minor groove of l2 and the projection of
the vector between stem and loop onto the plane normal to the stem
direction.
'''
point_on_stem, point_on_loop = ftuv.line_segment_distance(
cg.coords[stem][0], cg.coords[stem][1], cg.coords[loop][0],
cg.coords[loop][1])
conn_vec = point_on_loop - point_on_stem
dist = ftuv.magnitude(conn_vec)
angle1 = ftuv.vec_angle(cg.coords.get_direction(stem), conn_vec)
# The direction of the stem vector is irrelevant, so
# choose the smaller of the two angles between two lines
if angle1 > np.pi / 2:
angle1 = np.pi - angle1
tw = cg.get_twists(stem)
if dist == 0:
angle2 = float("nan")
else:
if stem[0] != 's':
raise ValueError(
"The receptor needs to be a stem, not {}".format(stem))
else:
stem_len = cg.stem_length(stem)
# Where along the helix our A-residue points to the minor groove.
# This can be between residues. We express it as floating point nucleotide coordinates.
# So 0.0 means at the first basepair, while 1.5 means between the second and the third basepair.
pos = ftuv.magnitude(
point_on_stem - cg.coords[stem][0]) / ftuv.magnitude(
cg.coords.get_direction(stem)) * (stem_len - 1)
# The vector pointing to the minor groove, even if we are not at a virtual residue (pos is a float value)
virt_twist = ftug.virtual_res_3d_pos_core(cg.coords[stem],
cg.twists[stem], pos,
stem_len)[1]
# The projection of the connection vector onto the plane normal to the stem
conn_proj = ftuv.vector_rejection(conn_vec,
cg.coords.get_direction(stem))
try:
# Note: here the directions of both vectors are well defined,
# so angles >90 degrees make sense.
angle2 = ftuv.vec_angle(virt_twist, conn_proj)
except ValueError:
if np.all(virt_twist == 0):
angle2 = float("nan")
else:
raise
# Furthermore, the direction of the second angle is meaningful.
# We call use a positive angle, if the cross-product of the two vectors
# has the same sign as the stem vector and a negative angle otherwise
cr = np.cross(virt_twist, conn_proj)
sign = ftuv.is_almost_parallel(cr, cg.coords.get_direction(stem))
#assert sign != 0, "{} vs {} not (anti) parallel".format(
# cr, cg.coords.get_direction(stem))
angle2 *= sign
return dist, angle1, angle2
def get_relative_orientation(cg, loop, stem):
'''
Return how loop is related to stem in terms of three parameters.
The stem is the receptor of a potential A-Minor interaction, whereas the
loop is the donor.
The 3 parameters are:
1. Distance between the closest points of the two elements
2. The angle between the stem and the vector between the two
3. The angle between the minor groove of l2 and the projection of
the vector between stem and loop onto the plane normal to the stem
direction.
'''
point_on_stem, point_on_loop = ftuv.line_segment_distance(cg.coords[stem][0],
cg.coords[stem][1],
cg.coords[loop][0],
cg.coords[loop][1])
conn_vec = point_on_loop - point_on_stem
dist = ftuv.magnitude(conn_vec)
angle1 = ftuv.vec_angle(cg.coords.get_direction(stem),
conn_vec)
# The direction of the stem vector is irrelevant, so
# choose the smaller of the two angles between two lines
if angle1 > np.pi / 2:
angle1 = np.pi - angle1
tw = cg.get_twists(stem)
if dist == 0:
angle2 = float("nan")
else:
if stem[0] != 's':
raise ValueError(
"The receptor needs to be a stem, not {}".format(stem))
else:
stem_len = cg.stem_length(stem)
# Where along the helix our A-residue points to the minor groove.
# This can be between residues. We express it as floating point nucleotide coordinates.
# So 0.0 means at the first basepair, while 1.5 means between the second and the third basepair.
pos = ftuv.magnitude(point_on_stem - cg.coords[stem][0]) / ftuv.magnitude(
cg.coords.get_direction(stem)) * (stem_len - 1)
# The vector pointing to the minor groove, even if we are not at a virtual residue (pos is a float value)
virt_twist = ftug.virtual_res_3d_pos_core(
cg.coords[stem], cg.twists[stem], pos, stem_len)[1]
# The projection of the connection vector onto the plane normal to the stem
conn_proj = ftuv.vector_rejection(
conn_vec, cg.coords.get_direction(stem))
try:
# Note: here the directions of both vectors are well defined,
# so angles >90 degrees make sense.
angle2 = ftuv.vec_angle(virt_twist, conn_proj)
except ValueError:
if np.all(virt_twist == 0):
angle2 = float("nan")
else:
raise
# Furthermore, the direction of the second angle is meaningful.
# We call use a positive angle, if the cross-product of the two vectors
# has the same sign as the stem vector and a negative angle otherwise
cr = np.cross(virt_twist, conn_proj)
sign = ftuv.is_almost_parallel(cr, cg.coords.get_direction(stem))
#assert sign != 0, "{} vs {} not (anti) parallel".format(
# cr, cg.coords.get_direction(stem))
angle2 *= sign
return dist, angle1, angle2
def coordinates_to_pymol(self, cg):
loops = list(cg.hloop_iterator())
for key in cg.coords.keys():
if self.constraints is not None:
if key not in self.constraints:
continue
(p, n) = cg.coords[key]
color = self.get_element_color(key)
if key[0] == 's':
self.add_stem_like(cg, key)
self.draw_bounding_boxes(cg, key)
else:
if key[0] == 'h':
if self.add_loops:
if key in loops:
self.add_segment(p, n, color, 1.0,
key + " " + str(cg.get_length(key)))
elif key[0] == 'm':
twists = cg.get_twists(key)
# check if the multiloop is longer than one. If it's not, then
# it has an empty define and we its length will be 1
if len(cg.defines[key]) == 0:
self.add_segment(p, n, color, 1.0,
key + " 1")
else:
self.add_segment(p, n, color, 1.0,
key + " " +
str(cg.defines[key][1] -
cg.defines[key][0] + 1))
self.add_segment(p, p+ 7 * twists[0], 'light gray', 0.3)
self.add_segment(n, n+ 7 * twists[1], 'light gray', 0.3)
x = (p + n) / 2
t = ftuv.normalize((twists[0] + twists[1]) / 2.)
self.add_segment(x, x + 7 * t, 'middle gray', 0.3)
elif key[0] == 'f':
if self.visualize_three_and_five_prime:
self.add_segment(p, n, color, 1.0,
key + " " +
str(cg.defines[key][1] -
cg.defines[key][0] + 1) + "")
elif key[0] == 't':
if self.visualize_three_and_five_prime:
self.add_segment(p, n, color, 1.0,
key + " " +
str(cg.defines[key][1] -
cg.defines[key][0]) + "")
else:
#self.add_stem_like(cg, key, "yellow", 1.0)
self.add_segment(p, n, color, 1.0, key)
if self.add_longrange:
for key1 in cg.longrange.keys():
for key2 in cg.longrange[key1]:
try:
p = cuv.line_segment_distance(cg.coords[key1][0],
cg.coords[key1][1],
cg.coords[key2][0],
cg.coords[key2][1])
(point1, point2) = p
#point1 = cg.get_point(key1)
#point2 = cg.get_point(key2)
dash_length = 0.6
gap_length = dash_length * 2
direction = ftuv.normalize(point2 - point1)
num_dashes = ftuv.magnitude(point2 - point1) / (dash_length + gap_length)
fud.pv('num_dashes')
for i in range(int(num_dashes)):
self.add_segment(point1 + i * (dash_length + gap_length) * direction,
point1 + (i * (dash_length + gap_length) + dash_length) * direction, "purple",
0.3, "")
'''
self.add_segment(point1, point2, "purple",
0.3, key1 + " " + key2)
'''
except:
continue
if self.encompassing_stems:
self.add_encompassing_cylinders(cg, 7.)
if self.max_stem_distances > 0:
for (s1, s2) in it.permutations(cg.stem_iterator(), r=2):
(i1, i2) = cuv.line_segment_distance(cg.coords[s1][0],
cg.coords[s1][1],
cg.coords[s2][0],
cg.coords[s2][1])
if cuv.magnitude(i2 - i1) < self.max_stem_distances:
#self.add_segment(i1, i2, 'cyan', 0.3, s1 + " " + s2)
self.add_segment(i1, i2, 'cyan', 0.3)
if self.virtual_atoms:
va = ftug.virtual_atoms(cg, sidechain=False)
atom_width = 0.5
for i,r in enumerate(sorted(va.keys())):
for a in va[r].keys():
if self.rainbow:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
cmap = plt.get_cmap('gist_rainbow')
self.add_sphere(va[r][a],
color_rgb = cmap(i / float(len(va.keys()))),
width=atom_width)
else:
d = cg.get_node_from_residue_num(r)
if d[0] == 's':
self.add_sphere(va[r][a], 'green', width=atom_width)
elif d[0] == 'i':
self.add_sphere(va[r][a], 'yellow', width=atom_width)
elif d[0] == 'm':
self.add_sphere(va[r][a], 'red', width=atom_width)
elif d[0] == 'h':
self.add_sphere(va[r][a], 'blue', width=atom_width)
if self.basis:
for d in cg.defines.keys():
origin, basis = ftug.element_coord_system(cg, d)
self.add_segment(origin, origin + 7. * basis[1], 'purple', 2.)
print >>sys.stderr, "energy_function:", self.energy_function
# print the contributions of the energy function, if one is specified
if self.energy_function is not None:
print >>sys.stderr, "key"
sum_energy = 0.
e_func = self.energy_function
e_func_iter = e_func.interaction_energy_iter(cg, background=False)
int_energies = list(e_func_iter)
max_energy = max(int_energies, key=lambda x: x[1])
print >>sys.stderr, "max_energy:", max_energy
for (interaction, energy) in int_energies:
(p, n) = (cg.get_point(interaction[0]),
cg.get_point(interaction[1]))
scaled_energy = - max_energy[1] + energy
self.add_segment(p, n, 'purple', 3 * np.exp(scaled_energy))
sum_energy += energy
if self.stem_stem_orientations is not None:
for (s1, s2) in it.permutations(cg.stem_iterator(), 2):
'''
if cg.are_adjacent_stems(s1, s2):
continue
'''
if s1 != 's65':
if s2 != 's65':
continue
s1_vec = cg.coords[s1][1] - cg.coords[s1][0]
s2_vec = cg.coords[s2][1] - cg.coords[s2][0]
(i1, i2) = cuv.line_segment_distance(cg.coords[s1][0],
cg.coords[s1][1],
cg.coords[s2][0],
cg.coords[s2][1])
i_vec = i2 - i1
#i_rej will be orthogonal to s1_vec in the direction
#of s2
i_rej = cuv.vector_rejection(i_vec, s1_vec)
#plane_vec will be orthogonal to s1_vec and to the direction
# of s2
plane_vec = np.cross(i_rej, s1_vec)
# s2_proj is in the intersection plane
s2_proj_in = cuv.vector_rejection(s2_vec, plane_vec)
# s2 proj_out is out of the intersection plane
#s2_proj_out = cuv.vector_rejection(s2_vec, i_rej)
start_point = cg.coords[s1][0] + 5 * cg.twists[s1][0]
ortho_offset = cuv.magnitude(i_rej)
dist = cuv.magnitude(i_vec) + 0.0001
lateral_offset = m.sqrt(dist ** 2 - ortho_offset ** 2)
if lateral_offset > 10:
continue
'''
#self.add_segment(start_point,
start_point + 10 * cuv.normalize(s2_vec),
'white', 0.5)
#self.add_segment(start_point,
start_point + 5 * cuv.normalize(plane_vec),
'magenta', 0.5)
#self.add_segment(start_point,
start_point + 5 * cuv.normalize(i_vec),
'cyan', 0.5)
#self.add_segment(i1, i1 + i_rej, 'cyan', 0.5)
'''
self.add_segment(start_point,
start_point + 7 * cuv.normalize(s2_proj_in),
'white', 1.5)
'''