def diff(self, other_angle, next_stem_length=1):
'''
Calculate the distance between the start and end of the hypothetical
next stem defined by these two angles.
:param other_angle: The other angle stat
:param next_stem_length: the length of the stem that is attached to this angle.
:param return: The distance between the starts and ends of the two hypothetical
next stems defined by this angle and the other angle
'''
this_stem_start = np.array(
ftuv.spherical_polar_to_cartesian([self.r1, self.u1, self.v1]))
this_stem_end = np.array(
ftuv.spherical_polar_to_cartesian(
[next_stem_length, self.u, self.v]))
other_stem_start = np.array(
ftuv.spherical_polar_to_cartesian(
[other_angle.r1, other_angle.u1, other_angle.v1]))
other_stem_end = np.array(
ftuv.spherical_polar_to_cartesian(
[next_stem_length, other_angle.u, other_angle.v]))
return ftuv.vec_distance(this_stem_start,
other_stem_start) + ftuv.vec_distance(
this_stem_start + this_stem_end,
other_stem_start + other_stem_end)
def test_spherical_coordinate_transforms(self):
for vec in [np.array([0,0,1]), np.array([0,2,0]), np.array([3,0,0]), np.array([4,5,0]), np.array([6,0,7]), np.array([8,9,0.4])]:
sphe=ftuv.spherical_cartesian_to_polar(vec)
nptest.assert_allclose(ftuv.spherical_polar_to_cartesian(sphe),vec, atol=0.0000001)
nptest.assert_allclose(ftuv.spherical_polar_to_cartesian([1,0,math.pi/2]), np.array([0,0,1]), atol=0.0000001)
nptest.assert_allclose(ftuv.spherical_polar_to_cartesian([2, math.pi/2, math.pi/4]), np.array([1,1,0])*2/math.sqrt(2), atol=0.0000001)
nptest.assert_allclose(ftuv.spherical_cartesian_to_polar(np.array([0,2,2])/math.sqrt(2)), [2,math.pi/4,math.pi/2], atol=0.0000001)
def get_angle(self):
'''
Return the angle between the two connected stems.
'''
return ftuv.vec_angle(
np.array([-1., 0., 0.]),
ftuv.spherical_polar_to_cartesian([1, self.u, self.v]))
def updateProjection(self, _=None):
direction = ftuv.spherical_polar_to_cartesian(
np.array([
1,
math.radians(self.theta.get()),
math.radians(self.phi.get())
]))
self.proj = fpp.Projection2D(self.cg,
project_virtual_atoms=True,
proj_direction=direction,
project_virtual_residues=list(
range(1,
len(self.cg.seq) + 1)))
self.update()
def deviation_from(self, stat2):
"""
How much does the other stat differ from this stat?
:param stat2: Another AngleStat
:returns: A 4-tuple: The positional deviation in Angstrom, and 3 absolute angular deviations in radians.
The angular deviations are u, v and t
"""
ret = []
pos1 = ftuv.spherical_polar_to_cartesian(self.position_params())
pos2 = ftuv.spherical_polar_to_cartesian(stat2.position_params())
ret.append(ftuv.magnitude(pos1 - pos2))
log.debug("Position difference is %f", ret[-1])
for attr in ["u", "v", "t"]:
raw_diff = getattr(self, attr) - getattr(stat2, attr)
# Map the difference to a value between 0 and pi
raw_diff_on_circle = abs(
(raw_diff + math.pi / 2) % (math.pi) - math.pi / 2)
log.debug("Angular difference for %s is %f, mapped to %f",
attr, raw_diff, raw_diff_on_circle)
ret.append(raw_diff_on_circle)
return tuple(ret)
def deviation_from(self, stat2):
"""
How much does the other stat differ from this stat?
:param stat2: Another AngleStat
:returns: A 4-tuple: The positional deviation in Angstrom, and 3 absolute angular deviations in radians.
The angular deviations are u, v and t
"""
ret = []
pos1 = ftuv.spherical_polar_to_cartesian(self.position_params())
pos2 = ftuv.spherical_polar_to_cartesian(stat2.position_params())
ret.append(ftuv.magnitude(pos1 - pos2))
log.debug("Position difference is %f", ret[-1])
for attr in ["u", "v", "t"]:
raw_diff = getattr(self, attr) - getattr(stat2, attr)
#Map the difference to a value between 0 and pi
raw_diff_on_circle = abs((raw_diff + math.pi / 2) % (math.pi) -
math.pi / 2)
log.debug("Angular difference for %s is %f, mapped to %f", attr,
raw_diff, raw_diff_on_circle)
ret.append(raw_diff_on_circle)
return tuple(ret)
def test_spherical_coordinate_transforms(self):
for vec in [
np.array([0, 0, 1]),
np.array([0, 2, 0]),
np.array([3, 0, 0]),
np.array([4, 5, 0]),
np.array([6, 0, 7]),
np.array([8, 9, 0.4])
]:
sphe = ftuv.spherical_cartesian_to_polar(vec)
nptest.assert_allclose(ftuv.spherical_polar_to_cartesian(sphe),
vec,
atol=0.0000001)
nptest.assert_allclose(ftuv.spherical_polar_to_cartesian(
[1, 0, math.pi / 2]),
np.array([0, 0, 1]),
atol=0.0000001)
nptest.assert_allclose(ftuv.spherical_polar_to_cartesian(
[2, math.pi / 2, math.pi / 4]),
np.array([1, 1, 0]) * 2 / math.sqrt(2),
atol=0.0000001)
nptest.assert_allclose(ftuv.spherical_cartesian_to_polar(
np.array([0, 2, 2]) / math.sqrt(2)), [2, math.pi / 4, math.pi / 2],
atol=0.0000001)
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 updateProjection(self, _=None):
direction = ftuv.spherical_polar_to_cartesian(
np.array([1, math.radians(self.theta.get()), math.radians(self.phi.get())]))
self.proj = fpp.Projection2D(self.cg, project_virtual_atoms=True, proj_direction=direction,
project_virtual_residues=list(range(1, len(self.cg.seq) + 1)))
self.update()
parser=generateParser()
if __name__=="__main__":
args = parser.parse_args()
#Get the stats object
conf_stats = ftms.get_conformation_stats(data_file(args.stats_file))
angle_stats = conf_stats.angle_stats
colors = plt.cm.Spectral(np.linspace(0, 1, 10))
colors=np.array(list(colors)*500)
markers="o"*10+"v"*10+"<"*10+">"*10+"."*10+"s"*10+"^"*10+"8"*10+"*"*10+"+"*10
markers=markers*500
for key in angle_stats.keys():
point_to=[]
to_clust=[]
angles=[]
for stat in angle_stats[key]:
stem_start = np.array(ftuv.spherical_polar_to_cartesian([stat.r1, stat.u1, stat.v1]))
#stem_vec = np.array(ftuv.spherical_polar_to_cartesian([1, stat.u, stat.v]))
#point1 = stem_start+stem_vec
stem_vec = np.array(ftuv.spherical_polar_to_cartesian([1, stat.u, stat.v]))
#point2 = stem_start+stem_vec
#stem_vec = np.array(ftuv.spherical_polar_to_cartesian([100, stat.u, stat.v]))/100
#point3 = stem_start+stem_vec
#point_to.append(list(point1)+list(point2)+list(point3))
point_to.append(list(stem_start)+list(stem_vec))
to_clust.append(list(stem_vec))
angles.append([stat.u, stat.v])
point_to=np.array(point_to)
if len(point_to)<10: continue
#db = sklearn.cluster.DBSCAN(eps=args.threshold, min_samples=3).fit(to_clust)
#labels_db = db.labels_
if __name__ == "__main__":
args = parser.parse_args()
#Get the stats object
conf_stats = ftms.get_conformation_stats(data_file(args.stats_file))
angle_stats = conf_stats.angle_stats
colors = plt.cm.Spectral(np.linspace(0, 1, 10))
colors = np.array(list(colors) * 500)
markers = "o" * 10 + "v" * 10 + "<" * 10 + ">" * 10 + "." * 10 + "s" * 10 + "^" * 10 + "8" * 10 + "*" * 10 + "+" * 10
markers = markers * 500
for key in angle_stats.keys():
point_to = []
to_clust = []
angles = []
for stat in angle_stats[key]:
stem_start = np.array(
ftuv.spherical_polar_to_cartesian([stat.r1, stat.u1, stat.v1]))
#stem_vec = np.array(ftuv.spherical_polar_to_cartesian([1, stat.u, stat.v]))
#point1 = stem_start+stem_vec
stem_vec = np.array(
ftuv.spherical_polar_to_cartesian([1, stat.u, stat.v]))
#point2 = stem_start+stem_vec
#stem_vec = np.array(ftuv.spherical_polar_to_cartesian([100, stat.u, stat.v]))/100
#point3 = stem_start+stem_vec
#point_to.append(list(point1)+list(point2)+list(point3))
point_to.append(list(stem_start) + list(stem_vec))
to_clust.append(list(stem_vec))
angles.append([stat.u, stat.v])
point_to = np.array(point_to)
if len(point_to) < 10: continue
#db = sklearn.cluster.DBSCAN(eps=args.threshold, min_samples=3).fit(to_clust)
def get_angle(self):
'''
Return the angle between the two connected stems.
'''
return ftuv.vec_angle(np.array([-1., 0., 0.]), ftuv.spherical_polar_to_cartesian([1, self.u, self.v]))
def main():
parser = OptionParser()
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
parser.add_option('-l', '--loops', dest='loops', default=True, action='store_false', help='Toggle loop reconstruction')
parser.add_option('','--drop-into-debugger', dest='drop_into_debugger', default=False, action='store_true')
parser.add_option('-f', '--fragments', dest='fragments', default=False, action='store_true', help='Reconstruct using fragments.')
parser.add_option('', '--output-file', dest='output_file', default='out.pdb', type='str')
parser.add_option('-s', '--samples', dest='samples', default=10, type='int', help='The number of samples to get from Barnacle')
parser.add_option('-a', '--average_atoms', dest='average_atoms', default=False, action='store_true', help='Reconstruct using the positions of the average atoms')
parser.add_option('', '--fr', dest='fruchterman_reingold', default=False, action='store_true', help='Use the Fruchterman Reingold graph layout instead of CCD to close loops')
(options, args) = parser.parse_args()
if len(args) < 1:
print >>sys.stderr, "Usage: ./reconstruct.py temp.comp"
print >>sys.stderr, "Reconstruct a spatial model to full-atom accuracy."
sys.exit(1)
#print >>sys.stderr, "reconstructing model:", args[0]
sm = models.SpatialModel(ftmc.CoarseGrainRNA(args[0]))
sm.sample_native_stems()
sm.create_native_stem_models()
if not options.average_atoms:
chain = rtor.reconstruct_stems(sm)
if options.loops:
if options.average_atoms:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
chain = rtor.reconstruct_from_average(sm)
rtor.output_chain(chain, 'temp.pdb')
return
elif options.fragments:
sm.sampled_from_bg()
sampled_bulges = sm.get_sampled_bulges()
'''
rtor.reconstruct_bulge_with_fragment(chain, sm, 'x2')
rtor.output_chain(chain, options.output_file)
sys.exit(1)
'''
'''
for b in it.chain(sm.bg.iloop_iterator(), sm.bg.mloop_iterator(),
sm.bg.hloop_iterator()):
'''
for b in it.chain(sm.bg.floop_iterator(),
sm.bg.tloop_iterator(),
sm.bg.iloop_iterator(),
sm.bg.mloop_iterator(),
sm.bg.hloop_iterator()):
if b not in sm.bg.sampled.keys():
print >>sys.stderr, "interpolating... %s" % (b)
(as1, as2) = sm.bg.get_bulge_angle_stats(b)
bulge_vec = np.array(cuv.spherical_polar_to_cartesian((as1.r1, as1.u1, as1.v1)))
#bulge_vec = np.array(cuv.spherical_polar_to_cartesian((as2.r1, as2.u1, as2.v1)))
size = sm.bg.get_bulge_dimensions(b)
best_bv_dist = 1000000.
best_bv = None
connections = list(sm.bg.edges[b])
ang_type = sm.bg.connection_type(b, connections)
for ang_s in cbs.get_angle_stats()[(size[0], size[1], ang_type)]:
pot_bulge_vec = np.array(cuv.spherical_polar_to_cartesian((ang_s.r1, ang_s.u1, ang_s.v1)))
pot_bv_dist = cuv.magnitude(bulge_vec - pot_bulge_vec)
if pot_bv_dist < best_bv_dist:
best_bv_dist = pot_bv_dist
best_bv_ang_s = ang_s
best_bv = pot_bulge_vec
sm.angle_defs[b][ang_type] = best_bv_ang_s
rtor.reconstruct_with_fragment(chain, sm, b, move_all_angles=True,
close_loop=not options.fruchterman_reingold)
continue
rtor.reconstruct_with_fragment(chain, sm, b,
close_loop=not options.fruchterman_reingold)
else:
try:
rtor.replace_bases(chain, sm.bg)
rtor.output_chain(chain, options.output_file)
#rtor.reconstruct_loop(chain, sm, 'b1', 0, samples=options.samples, consider_contacts=False)
rtor.reconstruct_loops(chain, sm, samples=options.samples, consider_contacts=False)
except Exception as e:
if options.drop_into_debugger:
pdb.post_mortem()
else:
raise
#rtor.reconstruct_loops(chain, sm)
chain = rtor.reorder_residues(chain, sm.bg)
rtor.replace_bases(chain, sm.bg)
rtor.output_chain(chain, 'out_pre.pdb')
if options.fruchterman_reingold:
import fruchterman_reingold.smooth_fragments as frs
frs.smooth_fragments(chain, sm.bg, iterations=20)
rtor.output_chain(chain, options.output_file)