def test_line_segment_distance_parallel(self):
a0 = np.array([0., 0., 1.])
a1 = np.array([0., 0., 10.])
b0 = np.array([0., 0., 11.])
b1 = np.array([0., 0., 20.])
self.assertAlmostEqual(
ftuv.vec_distance(*ftuv.line_segment_distance(a0, a1, b0, b1)), 1.)
def test_line_segment_distance_point_to_line(self):
a0 = np.array([0., 0., 1.])
a1 = np.array([0., 0., 10.])
b0 = np.array([0., -10., 12.])
b1 = np.array([0., 10., 12.])
self.assertAlmostEqual(
ftuv.vec_distance(*ftuv.line_segment_distance(a0, a1, b0, b1)), 2.)
def test_line_segment_distance_windschief(self):
a0 = np.array([0., 0., -10.])
a1 = np.array([0., 0., 10.])
b0 = np.array([5.2, -10., 5.])
b1 = np.array([5.2, 10., 5.])
self.assertAlmostEqual(ftuv.vec_distance(
*ftuv.line_segment_distance(a0, a1, b0, b1)), 5.2)
def test_line_segment_distance_real_world(self):
a0 = np.array([0., 0., 1.])
a1 = np.array([-2.76245752, -6.86976093, 7.54094508])
b0 = np.array([-27.57744115, 6.96488989, -22.47619655])
b1 = np.array([-16.93424799, -4.0631445, -16.19822301])
self.assertLess(ftuv.vec_distance(
*ftuv.line_segment_distance(a0, a1, b0, b1)), 25)
def test_line_segment_distance_point_to_line(self):
a0 = np.array([0., 0., 1.])
a1 = np.array([0., 0., 10.])
b0 = np.array([0., -10., 12.])
b1 = np.array([0., 10., 12.])
self.assertAlmostEqual(ftuv.vec_distance(
*ftuv.line_segment_distance(a0, a1, b0, b1)), 2.)
def test_line_segment_distance_parallel(self):
a0 = np.array([0., 0., 1.])
a1 = np.array([0., 0., 10.])
b0 = np.array([0., 0., 11.])
b1 = np.array([0., 0., 20.])
self.assertAlmostEqual(ftuv.vec_distance(
*ftuv.line_segment_distance(a0, a1, b0, b1)), 1.)
def test_line_segment_distance_real_world(self):
a0 = np.array([0., 0., 1.])
a1 = np.array([-2.76245752, -6.86976093, 7.54094508])
b0 = np.array([-27.57744115, 6.96488989, -22.47619655])
b1 = np.array([-16.93424799, -4.0631445, -16.19822301])
self.assertLess(
ftuv.vec_distance(*ftuv.line_segment_distance(a0, a1, b0, b1)), 25)
def test_line_segment_distance_windschief(self):
a0 = np.array([0., 0., -10.])
a1 = np.array([0., 0., 10.])
b0 = np.array([5.2, -10., 5.])
b1 = np.array([5.2, 10., 5.])
self.assertAlmostEqual(
ftuv.vec_distance(*ftuv.line_segment_distance(a0, a1, b0, b1)),
5.2)
def output_all_distances(bg):
for (key1, key2) in it.permutations(bg.defines.keys(), 2):
if bg.has_connection(key1, key2):
continue
longrange = "N"
if key2 in bg.longrange[key1]:
longrange = "Y"
#point1 = bg.get_point(key1)
#point2 = bg.get_point(key2)
try:
(i1,i2) = cuv.line_segment_distance(bg.coords[key1][0], bg.coords[key1][1],
bg.coords[key2][0], bg.coords[key2][1])
if abs(cuv.magnitude(i2 - i1)) < 0.000001:
continue
vec1 = bg.coords[key1][1] - bg.coords[key1][0]
'''
basis = cuv.create_orthonormal_basis(vec1)
coords2 = cuv.change_basis(i2 - i1, basis, cuv.standard_basis)
(r, u, v) = cuv.spherical_cartesian_to_polar(coords2)
'''
v = cuv.vec_angle(vec1, i2 - i1)
except KeyError as ke:
#print >>sys.stderr, 'Skipping %s or %s.' % (key1, key2)
continue
seq1 = 'x'
seq2 = 'x'
'''
receptor_angle = 0.
if bg.get_type(key1) != 's' and bg.get_type(key1) != 'i' and bg.get_length(key1) > 1:
seq1 = bg.get_seq(key1)
if bg.get_type(key2) != 's' and bg.get_type(key2) != 'i'and bg.get_length(key2) > 1:
seq2 = bg.get_seq(key2)
if bg.get_type(key1) == 'l' and bg.get_type(key2) == 's':
receptor_angle = cgg.receptor_angle(bg, key1, key2)
'''
print "%s %s %d %s %s %d %f %s %s %s %f" % (key1,
key1[0],
bg.get_length(key1),
key2,
key2[0],
bg.get_length(key2),
cuv.magnitude(i2-i1),
seq1, seq2, longrange, v)
def get_relative_orientation(cg, l1, l2):
'''
Return how l1 is related to l2 in terms of three parameters. l2 should
be the receptor of a potential A-Minor interaction, whereas l1 should
be the donor.
1. Distance between the closest points of the two elements
2. The angle between l2 and the vector between the two
3. The angle between the minor groove of l2 and the vector between
l1 and l2
'''
(i1, i2) = ftuv.line_segment_distance(cg.coords[l1][0],
cg.coords[l1][1],
cg.coords[l2][0],
cg.coords[l2][1])
'''
angle1 = ftuv.vec_angle(cg.coords[l2][1] - cg.coords[l2][0],
i2 - i1)
'''
angle1 = ftuv.vec_angle(cg.coords[l2][1] - cg.coords[l2][0],
cg.coords[l1][1] - cg.coords[l1][0])
#fud.pv('angle1')
tw = cg.get_twists(l2)
if l2[0] != 's':
angle2 = ftuv.vec_angle((tw[0] + tw[1]) / 2.,
i2 - i1)
else:
stem_len = cg.stem_length(l2)
pos = ftuv.magnitude(i2 - cg.coords[l2][0]) / ftuv.magnitude(cg.coords[l2][1] - cg.coords[l2][0]) * stem_len
vec = ftug.virtual_res_3d_pos_core(cg.coords[l2], cg.twists[l2], pos, stem_len)[1]
angle2 = ftuv.vec_angle(vec,
i2 - i1)
dist = ftug.element_distance(cg, l1, l2)
return (dist, angle1, angle2)
def output_long_range_distances(bg):
for key1 in bg.longrange.keys():
for key2 in bg.longrange[key1]:
if bg.has_connection(key1, key2):
continue
#point1 = bg.get_point(key1)
#point2 = bg.get_point(key2)
(i1,i2) = cuv.line_segment_distance(bg.coords[key1][0], bg.coords[key1][1],
bg.coords[key2][0], bg.coords[key2][1])
vec1 = bg.coords[key1][1] - bg.coords[key2][0]
basis = cuv.create_orthonormal_basis(vec1)
coords2 = cuv.change_basis(i2 - i1, basis, cuv.standard_basis)
(r, u, v) = cuv.spherical_polar_to_cartesian(coords2)
seq1 = 'x'
seq2 = 'x'
'''
if key1[0] != 's' and key[0] != 'i':
seq1 = bg.get_seq(key1)
if key2[0] != 's' and key2[0] != 'i':
seq2 = bg.get_seq(key2)
'''
print "%s %s %d %s %s %d %f %s %s %s %f" % (key1,
key1[0],
bg.get_length(key1),
key2,
key2[0],
bg.get_length(key2),
cuv.magnitude(i2-i1),
seq1, seq2, "Y", v)
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 add_cg(self, cg, labels, color_modifier=1.0):
"""
:param labels: A dictionary with element names as keys
and labels as values.
"""
rna_plotter = PyMolRNA(cg.name, color_modifier)
for key in cg.coords.keys():
if self.only_elements is not None:
if key not in self.only_elements:
continue
(p, n) = cg.coords[key]
color = self.get_element_color(key)
if key[0] == 's':
try:
text = labels[key]
except KeyError:
text = key
self.add_stem_like(rna_plotter, cg, text, key, color=color)
if self.show_bounding_boxes:
self.draw_bounding_boxes(rna_plotter, cg, key)
else:
if key[0] == 'h':
if self.add_loops:
try:
text = labels[key]
except KeyError:
text = key + " " + str(cg.get_length(key))
rna_plotter.add_segment(p, n, color, self.cylinder_width,
text,
key=key)
elif key[0] == 'm':
twists = cg.get_twists(key)
try:
text = labels[key]
except KeyError:
# check if the multiloop is longer than one. If it's not, then
# it has an empty define and its length will be 0
if len(cg.defines[key]) == 0:
text = key + " 0"
else:
text = key + " " + \
str(cg.defines[key][1] -
cg.defines[key][0] + 1)
rna_plotter.add_segment(p, n, color, self.cylinder_width,
text, key=key)
elif key[0] in 'ft':
try:
text = labels[key]
except KeyError:
text = key + " " + \
str(cg.defines[key][1] - cg.defines[key][0] + 1)
if self.visualize_three_and_five_prime:
rna_plotter.add_segment(p, n, color, self.cylinder_width,
text, key=key)
elif key[0] == "i":
try:
text = labels[key]
except KeyError:
text = key
rna_plotter.add_segment(
p, n, color, self.cylinder_width, text, key=key)
if self.display_virtual_residues:
for i in range(1, cg.seq_length + 1):
pos = cg.get_virtual_residue(i, True)
if cg.get_node_from_residue_num(i)[0] == "s":
c = "cyan"
else:
c = "magenta"
rna_plotter.add_sphere(pos, c, 1.)
if self.add_longrange:
for key1 in cg.longrange.keys():
for key2 in cg.longrange[key1]:
if self.only_elements is not None:
if key1 not in self.only_elements or key2 not in self.only_elements:
continue
try:
p = cuv.line_segment_distance(cg.coords[key1][0],
cg.coords[key1][1],
cg.coords[key2][0],
cg.coords[key2][1])
rna_plotter.add_dashed(p[0], p[1])
except:
continue
if self.encompassing_stems:
self.add_encompassing_cylinders(rna_plotter, 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, key=key)
rna_plotter.add_segment(i1, i2, 'cyan', 0.3, key=key)
if self.virtual_atoms or self.sidechain_atoms:
cg.add_all_virtual_residues()
va = ftug.virtual_atoms(cg, sidechain=self.sidechain_atoms)
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')
rna_plotter.add_sphere(va[r][a],
color=cmap(
i / float(len(va.keys()))),
width=atom_width)
else:
d = cg.get_node_from_residue_num(r)
if d[0] == 's':
if a in ftup.nonsidechain_atoms:
rna_plotter.add_sphere(
va[r][a], self.stem_color, width=atom_width)
else:
rna_plotter.add_sphere(
va[r][a], 'forest', width=atom_width)
elif d[0] == 'i':
rna_plotter.add_sphere(
va[r][a], 'yellow', width=atom_width)
elif d[0] == 'm':
rna_plotter.add_sphere(
va[r][a], self.multiloop_color, width=atom_width)
elif d[0] == 'h':
rna_plotter.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)
rna_plotter.add_segment(
origin, origin + 7. * basis[1], 'purple', 0.5, key=key)
self.plotters.append(rna_plotter)
def add_cg(self, cg, labels, color_modifier=1.0):
"""
:param labels: A dictionary with element names as keys
and labels as values.
"""
rna_plotter = PyMolRNA(cg.name, color_modifier)
for key in cg.coords.keys():
if self.only_elements is not None:
if key not in self.only_elements:
continue
(p, n) = cg.coords[key]
color = self.get_element_color(key)
if key[0] == 's':
try:
text = labels[key]
except KeyError:
text = key
self.add_stem_like(rna_plotter, cg, text, key, color=color)
if self.show_bounding_boxes:
self.draw_bounding_boxes(rna_plotter, cg, key)
else:
if key[0] == 'h':
if self.add_loops:
try:
text = labels[key]
except KeyError:
text = key + " " + str(cg.get_length(key))
rna_plotter.add_segment(p,
n,
color,
self.cylinder_width,
text,
key=key)
elif key[0] == 'm':
twists = cg.get_twists(key)
try:
text = labels[key]
except KeyError:
# check if the multiloop is longer than one. If it's not, then
# it has an empty define and its length will be 0
if len(cg.defines[key]) == 0:
text = key + " 0"
else:
text = key + " " + \
str(cg.defines[key][1] -
cg.defines[key][0] + 1)
rna_plotter.add_segment(p,
n,
color,
self.cylinder_width,
text,
key=key)
elif key[0] in 'ft':
try:
text = labels[key]
except KeyError:
text = key + " " + \
str(cg.defines[key][1] - cg.defines[key][0] + 1)
if self.visualize_three_and_five_prime:
rna_plotter.add_segment(p,
n,
color,
self.cylinder_width,
text,
key=key)
elif key[0] == "i":
try:
text = labels[key]
except KeyError:
text = key
rna_plotter.add_segment(p,
n,
color,
self.cylinder_width,
text,
key=key)
if self.display_virtual_residues:
for i in range(1, cg.seq_length + 1):
pos = cg.get_virtual_residue(i, True)
if cg.get_node_from_residue_num(i)[0] == "s":
c = "cyan"
else:
c = "magenta"
rna_plotter.add_sphere(pos, c, 1.)
if self.add_longrange:
for key1 in cg.longrange.keys():
for key2 in cg.longrange[key1]:
if self.only_elements is not None:
if key1 not in self.only_elements or key2 not in self.only_elements:
continue
try:
p = cuv.line_segment_distance(cg.coords[key1][0],
cg.coords[key1][1],
cg.coords[key2][0],
cg.coords[key2][1])
rna_plotter.add_dashed(p[0], p[1])
except:
continue
if self.encompassing_stems:
self.add_encompassing_cylinders(rna_plotter, 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, key=key)
rna_plotter.add_segment(i1, i2, 'cyan', 0.3, key=key)
if self.virtual_atoms or self.sidechain_atoms:
cg.add_all_virtual_residues()
va = ftug.virtual_atoms(cg, sidechain=self.sidechain_atoms)
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')
rna_plotter.add_sphere(va[r][a],
color=cmap(
i / float(len(va.keys()))),
width=atom_width)
else:
d = cg.get_node_from_residue_num(r)
if d[0] == 's':
if a in ftup.nonsidechain_atoms:
rna_plotter.add_sphere(va[r][a],
self.stem_color,
width=atom_width)
else:
rna_plotter.add_sphere(va[r][a],
'forest',
width=atom_width)
elif d[0] == 'i':
rna_plotter.add_sphere(va[r][a],
'yellow',
width=atom_width)
elif d[0] == 'm':
rna_plotter.add_sphere(va[r][a],
self.multiloop_color,
width=atom_width)
elif d[0] == 'h':
rna_plotter.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)
rna_plotter.add_segment(origin,
origin + 7. * basis[1],
'purple',
0.5,
key=key)
self.plotters.append(rna_plotter)
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)
'''
def describe_ml_segments(cg):
data = defaultdict(list)
loops = cg.find_mlonly_multiloops()
for loop in it.chain(loops, [[i] for i in cg.iloop_iterator()]):
print(loop)
if loop[0][0] == "i":
description = ["interior_loop"]
else:
description = cg.describe_multiloop(loop)
try:
j3_roles = cg._assign_loop_roles(loop)
except ValueError:
j3_roles = None
if j3_roles:
j3_familyFlat = cg._junction_family_westhof1(j3_roles)
j3_family3D = cg._junction_family_3d(j3_roles)
j3_familyPerp = cg._junction_family_is_perpenticular(j3_roles)
j3_Delta = cg.get_length(j3_roles["J23"]) - cg.get_length(
j3_roles["J31"])
else:
j3_family3D = None
j3_familyFlat = None
j3_familyPerp = None
j3_Delta = None
loop_start = float("inf")
for segment in loop:
if cg.define_a(segment)[0] < loop_start:
loop_start = cg.define_a(segment)[0]
for segment in loop:
if segment[0] not in "mi":
continue
data["loop_start_after"].append(loop_start)
data["segment_start_after"].append(cg.define_a(segment)[0])
data["segment"].append(segment)
data["junction_length"].append(len(loop))
data["segment_length"].append(cg.get_length(segment))
if segment[0] == "i":
dims = list(sorted(cg.get_bulge_dimensions(segment)))
else:
dims = [-1, -1]
data["iloop_length_1"].append(dims[0])
data["iloop_length_2"].append(dims[1])
data["loops_largest_segment_length"].append(
max(cg.get_length(x) for x in loop))
data["loops_shortest_segment_length"].append(
min(cg.get_length(x) for x in loop))
data["sum_of_loops_segment_lengths"].append(
sum(cg.get_length(x) for x in loop))
data["loop_segment_lengths"].append(",".join(
map(str, sorted(cg.get_length(x) for x in loop))))
data["angle_type"].append(
abs(cg.get_angle_type(segment, allow_broken=True)))
s1, s2 = cg.connections(segment)
vec1 = cg.coords.get_direction(s1)
if cg.get_sides(s1, segment) == (1, 0):
vec1 = -vec1
else:
assert cg.get_sides(s1, segment) == (0, 1)
vec2 = cg.coords.get_direction(s2)
if cg.get_sides(s2, segment) == (1, 0):
vec2 = -vec2
else:
assert cg.get_sides(s2, segment) == (0, 1)
data["angle_between_stems"].append(ftuv.vec_angle(vec1, vec2))
data["offset1"].append(
ftuv.point_line_distance(
cg.coords[s1][cg.get_sides(s1, segment)[0]],
cg.coords[s2][0], cg.coords.get_direction(s2)))
data["offset2"].append(
ftuv.point_line_distance(
cg.coords[s2][cg.get_sides(s2, segment)[0]],
cg.coords[s1][0], cg.coords.get_direction(s1)))
closer1, far1 = cg.coords[s1][cg.get_sides(
s1, segment)[0]], cg.coords[s1][cg.get_sides(s1, segment)[1]]
closer2, far2 = cg.coords[s2][cg.get_sides(
s2, segment)[0]], cg.coords[s2][cg.get_sides(s2, segment)[1]]
data["offset"].append(
ftuv.vec_distance(*ftuv.line_segment_distance(
closer1, closer1 +
(closer1 - far1) * 100000, closer2, closer2 +
(closer2 - far2) * 100000)))
data["junction_va_distance"].append(
ftug.junction_virtual_atom_distance(cg, segment))
data["is_external_multiloop"].append("open" in description)
data["is_pseudoknotted_multiloop"].append(
"pseudoknot" in description)
data["is_regular_multiloop"].append(
"regular_multiloop" in description)
data["is_interior_loop"].append("interior_loop" in description)
if j3_roles is not None:
elem_role, = [
x[0] for x in j3_roles.items() if x[1] == segment
]
else:
elem_role = "?"
data["j3_role"].append(elem_role)
data["j3_familyFlat"].append(j3_familyFlat)
data["j3_family3D"].append(j3_family3D)
data["j3_familyPerp"].append(j3_familyPerp)
data["j3_Delta_j23_j31"].append(j3_Delta)
dssr_stacking = False
if "dssr_stacks" in cg.infos:
if segment in cg.infos["dssr_stacks"]:
dssr_stacking = True
data["dssr_stacking"].append(dssr_stacking)
kh_stem_angle = float("nan")
if abs(cg.get_angle_type(segment, allow_broken=True)) == 5:
next_ml = cg.get_next_ml_segment(segment)
if isinstance(next_ml, str) and next_ml[0] == "m" and abs(
cg.get_angle_type(next_ml, allow_broken=True)) == 5:
stems1 = cg.edges[segment]
stems2 = cg.edges[next_ml]
try:
s1, s2 = (stems1 | stems2) - (stems1 & stems2)
except ValueError:
pass
else:
vec1 = cg.coords.get_direction(s1)
vec2 = cg.coords.get_direction(s2)
angle = ftuv.vec_angle(vec1, vec2)
if angle > math.pi / 2:
angle = math.pi - angle
kh_stem_angle = angle
data["kh_stem_angle"].append(kh_stem_angle)
if data:
data["pk_number"] = number_by(data, "loop_start_after",
"is_pseudoknotted_multiloop")
data["loop_number"] = number_by(data, "loop_start_after", None)
data["reguler_multiloop_number"] = number_by(data, "loop_start_after",
"is_regular_multiloop")
return data
def describe_ml_segments(cg):
data = defaultdict(list)
loops = cg.find_mlonly_multiloops()
for loop in it.chain(loops, [[i] for i in cg.iloop_iterator()]):
print(loop)
if loop[0][0] == "i":
description = ["interior_loop"]
else:
description = cg.describe_multiloop(loop)
try:
j3_roles = cg._assign_loop_roles(loop)
except ValueError:
j3_roles = None
if j3_roles:
j3_familyFlat = cg._junction_family_westhof1(j3_roles)
j3_family3D = cg._junction_family_3d(j3_roles)
j3_familyPerp = cg._junction_family_is_perpenticular(j3_roles)
j3_Delta = cg.get_length(
j3_roles["J23"]) - cg.get_length(j3_roles["J31"])
else:
j3_family3D = None
j3_familyFlat = None
j3_familyPerp = None
j3_Delta = None
loop_start = float("inf")
for segment in loop:
if cg.define_a(segment)[0] < loop_start:
loop_start = cg.define_a(segment)[0]
for segment in loop:
if segment[0] not in "mi":
continue
data["loop_start_after"].append(loop_start)
data["segment_start_after"].append(cg.define_a(segment)[0])
data["segment"].append(segment)
data["junction_length"].append(len(loop))
data["segment_length"].append(cg.get_length(segment))
if segment[0] == "i":
dims = list(sorted(cg.get_bulge_dimensions(segment)))
else:
dims = [-1, -1]
data["iloop_length_1"].append(dims[0])
data["iloop_length_2"].append(dims[1])
data["loops_largest_segment_length"].append(
max(cg.get_length(x) for x in loop))
data["loops_shortest_segment_length"].append(
min(cg.get_length(x) for x in loop))
data["sum_of_loops_segment_lengths"].append(
sum(cg.get_length(x) for x in loop))
data["loop_segment_lengths"].append(
",".join(map(str, sorted(cg.get_length(x) for x in loop))))
data["angle_type"].append(
abs(cg.get_angle_type(segment, allow_broken=True)))
s1, s2 = cg.connections(segment)
vec1 = cg.coords.get_direction(s1)
if cg.get_sides(s1, segment) == (1, 0):
vec1 = -vec1
else:
assert cg.get_sides(s1, segment) == (0, 1)
vec2 = cg.coords.get_direction(s2)
if cg.get_sides(s2, segment) == (1, 0):
vec2 = -vec2
else:
assert cg.get_sides(s2, segment) == (0, 1)
data["angle_between_stems"].append(ftuv.vec_angle(vec1, vec2))
data["offset1"].append(ftuv.point_line_distance(cg.coords[s1][cg.get_sides(s1, segment)[0]],
cg.coords[s2][0], cg.coords.get_direction(
s2)
))
data["offset2"].append(ftuv.point_line_distance(cg.coords[s2][cg.get_sides(s2, segment)[0]],
cg.coords[s1][0], cg.coords.get_direction(
s1)
))
closer1, far1 = cg.coords[s1][cg.get_sides(
s1, segment)[0]], cg.coords[s1][cg.get_sides(s1, segment)[1]]
closer2, far2 = cg.coords[s2][cg.get_sides(
s2, segment)[0]], cg.coords[s2][cg.get_sides(s2, segment)[1]]
data["offset"].append(ftuv.vec_distance(*ftuv.line_segment_distance(closer1, closer1 + (closer1 - far1) * 100000,
closer2, closer2 + (closer2 - far2) * 100000)))
data["junction_va_distance"].append(
ftug.junction_virtual_atom_distance(cg, segment))
data["is_external_multiloop"].append("open" in description)
data["is_pseudoknotted_multiloop"].append(
"pseudoknot" in description)
data["is_regular_multiloop"].append(
"regular_multiloop" in description)
data["is_interior_loop"].append("interior_loop" in description)
if j3_roles is not None:
elem_role, = [x[0]
for x in j3_roles.items() if x[1] == segment]
else:
elem_role = "?"
data["j3_role"].append(elem_role)
data["j3_familyFlat"].append(j3_familyFlat)
data["j3_family3D"].append(j3_family3D)
data["j3_familyPerp"].append(j3_familyPerp)
data["j3_Delta_j23_j31"].append(j3_Delta)
dssr_stacking = False
if "dssr_stacks" in cg.infos:
if segment in cg.infos["dssr_stacks"]:
dssr_stacking = True
data["dssr_stacking"].append(dssr_stacking)
kh_stem_angle = float("nan")
if abs(cg.get_angle_type(segment, allow_broken=True)) == 5:
next_ml = cg.get_next_ml_segment(segment)
if isinstance(next_ml, str) and next_ml[0] == "m" and abs(cg.get_angle_type(next_ml, allow_broken=True)) == 5:
stems1 = cg.edges[segment]
stems2 = cg.edges[next_ml]
try:
s1, s2 = (stems1 | stems2) - (stems1 & stems2)
except ValueError:
pass
else:
vec1 = cg.coords.get_direction(s1)
vec2 = cg.coords.get_direction(s2)
angle = ftuv.vec_angle(vec1, vec2)
if angle > math.pi / 2:
angle = math.pi - angle
kh_stem_angle = angle
data["kh_stem_angle"].append(kh_stem_angle)
if data:
data["pk_number"] = number_by(data, "loop_start_after",
"is_pseudoknotted_multiloop")
data["loop_number"] = number_by(data, "loop_start_after", None)
data["reguler_multiloop_number"] = number_by(data, "loop_start_after",
"is_regular_multiloop")
return data