def test_virtual_residue_atoms(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
ftug.add_virtual_residues(cg, 's1')
bases_to_test = []
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's0', 1, 0))
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's0', 2, 1))
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's1', 0, 0))
#Assert that any two atoms of the same base within reasonable distance to each other
#(https://en.wikipedia.org/wiki/Bond_length says than a CH-bond is >= 1.06A)
for va in bases_to_test:
for k1, v1 in va.items():
for k2, v2 in va.items():
dist = ftuv.magnitude(v1 - v2)
self.assertLess(dist,
30,
msg="Nucleotide too big: "
"Distance between {} and {} is {}".format(
k1, k2, dist))
if k1 != k2:
dist = ftuv.magnitude(v1 - v2)
self.assertGreater(
dist,
0.8,
msg="Nucleotide too small: "
"Distance between {} and {} is {}".format(
k1, k2, dist))
def test_virtual_residue_atom_exact_match(self):
#This test serves to detect unwanted changes in the virtual atom calculation algorithm.
#It is allowed to fail, if the virtual atom calculation changes.
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
vres= ftug.virtual_residue_atoms(cg, 's0', 1, 0)
nptest.assert_allclose(vres['C8'], np.array([ 5.60052258, -2.31817798, -2.74075904]))
nptest.assert_allclose(vres['N2'], np.array([ 7.27932017, 2.84403948, -2.83806392]))
def test_virtual_residue_atom_exact_match(self):
#This test serves to detect unwanted changes in the virtual atom calculation algorithm.
#It is allowed to fail, if the virtual atom calculation changes.
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
vres = ftug.virtual_residue_atoms(cg, 's0', 1, 0)
nptest.assert_allclose(vres['C8'],
np.array([5.23455929, -2.9606417, -2.18156476]))
nptest.assert_allclose(vres['N2'],
np.array([6.99285237, 2.32505693, -1.95868568]))
def setUp(self):
self.rs_random_281=ftmc.from_pdb('test/forgi/threedee/data/RS_random_281_S_0.pdb')
for key in self.rs_random_281.defines.keys():
if key[0] =="s":
ftug.add_virtual_residues(self.rs_random_281, key)
self.minimal_multiloop = ftmc.CoarseGrainRNA()
self.minimal_multiloop.from_file('test/forgi/threedee/data/minimal_multiloop.cg')
for key in self.minimal_multiloop.defines.keys():
if key[0] =="s":
ftug.add_virtual_residues(self.minimal_multiloop, key)
def setUp(self):
self.rs_random_281=ftmc.from_pdb('test/forgi/threedee/data/RS_random_281_S_0.pdb')
for key in self.rs_random_281.defines.keys():
if key[0] =="s":
ftug.add_virtual_residues(self.rs_random_281, key)
self.minimal_multiloop = ftmc.CoarseGrainRNA()
self.minimal_multiloop.from_file('test/forgi/threedee/data/minimal_multiloop.cg')
for key in self.minimal_multiloop.defines.keys():
if key[0] =="s":
ftug.add_virtual_residues(self.minimal_multiloop, key)
def setUp(self):
try:
self.rs_random_281, = ftmc.CoarseGrainRNA.from_pdb(
'test/forgi/threedee/data/RS_random_281_S_0.pdb', annotation_tool="MC-Annotate")
except ftmc.AnnotationToolNotInstalled:
self.skipTest("Requires MC-Annotate")
for key in self.rs_random_281.defines.keys():
if key[0] == "s":
ftug.add_virtual_residues(self.rs_random_281, key)
self.minimal_multiloop = ftmc.CoarseGrainRNA.from_bg_file(
'test/forgi/threedee/data/minimal_multiloop.cg')
for key in self.minimal_multiloop.defines.keys():
if key[0] == "s":
ftug.add_virtual_residues(self.minimal_multiloop, key)
def test_basis_transformation_for_virtual_residues(self):
cg, = ftmc.CoarseGrainRNA.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
offset = cg.vposs["s0"][0]
vbasis = cg.vbases["s0"][0]
local_pos = np.array([0, 0, 1])
global_pos = np.dot(vbasis.transpose(), local_pos) + offset
# Checking dimensions of vectors, just in case...
self.assertEqual(len(global_pos), 3)
self.assertEqual(len(vbasis), 3)
self.assertEqual(len(vbasis[0]), 3)
# Analytically true:
self.assertTrue(all(global_pos[x] - vbasis[2][x] - offset[x] < 0.0000001 for x in [0, 1, 2]),
msg="global pos for (0,0,1) should be {}+{}={}, but is {} instead.".format(
vbasis[2], offset, vbasis[2] + offset, global_pos))
def test_basis_transformation_for_virtual_residues(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
offset=cg.vposs["s0"][0]
vbasis=cg.vbases["s0"][0]
local_pos=np.array([0,0,1])
global_pos = np.dot(vbasis.transpose(), local_pos) + offset
#Checking dimensions of vectors, just in case...
self.assertEqual(len(global_pos),3)
self.assertEqual(len(vbasis),3)
self.assertEqual(len(vbasis[0]),3)
#Analytically true:
self.assertTrue(all(global_pos[x]-vbasis[2][x]-offset[x]<0.0000001 for x in [0,1,2]),
msg="global pos for (0,0,1) should be {}+{}={}, but is {} instead.".format(
vbasis[2], offset, vbasis[2]+offset, global_pos))
def setUp(self):
try:
self.rs_random_281, = ftmc.CoarseGrainRNA.from_pdb(
'test/forgi/threedee/data/RS_random_281_S_0.pdb',
annotation_tool="MC-Annotate")
except ftmc.AnnotationToolNotInstalled:
self.skipTest("Requires MC-Annotate")
for key in self.rs_random_281.defines.keys():
if key[0] == "s":
ftug.add_virtual_residues(self.rs_random_281, key)
self.minimal_multiloop = ftmc.CoarseGrainRNA.from_bg_file(
'test/forgi/threedee/data/minimal_multiloop.cg')
for key in self.minimal_multiloop.defines.keys():
if key[0] == "s":
ftug.add_virtual_residues(self.minimal_multiloop, key)
def test_virtual_residue_atom_exact_match(self):
# This test serves to detect unwanted changes in the virtual atom calculation algorithm.
# It is allowed to fail, if the virtual atom calculation changes.
try:
cg, = ftmc.CoarseGrainRNA.from_pdb('test/forgi/threedee/data/1y26.pdb',
annotation_tool="MC-Annotate")
except ftmc.AnnotationToolNotInstalled:
self.skipTest("Requires MC-Annotate")
ftug.add_virtual_residues(cg, 's0')
vres = ftug.virtual_residue_atoms(cg, 's0', 1, 0)
print(vres['C8'])
print(vres['N2'])
nptest.assert_allclose(vres['C8'], np.array(
[5.17130963, -2.93616933, -2.16725865]))
nptest.assert_allclose(vres['N2'], np.array(
[6.91170703, 2.35440312, -1.92080436]))
def test_coordinates_for_add_virtual_residues(self):
try:
cg, = ftmc.CoarseGrainRNA.from_pdb(
'test/forgi/threedee/data/1y26.pdb',
annotation_tool="MC-Annotate")
except ftmc.AnnotationToolNotInstalled:
self.skipTest("This requires MC-Annotate")
ftug.add_virtual_residues(cg, 's0')
# XYZ coordinate for first residue are ok:
self.assertAlmostEqual(
cg.vposs["s0"][0][0],
2.3,
delta=3,
msg="Wrong x-position for virtual residue 0 of stem s0: {}".format(
cg.vposs["s0"][0][0]))
self.assertAlmostEqual(
cg.vposs["s0"][0][1],
1.3,
delta=3,
msg="Wrong y-position for virtual residue 0 of stem s0: {}".format(
cg.vposs["s0"][0][1]))
self.assertAlmostEqual(
cg.vposs["s0"][0][2],
1.0,
delta=3,
msg="Wrong z-position for virtual residue 0 of stem s0: {}".format(
cg.vposs["s0"][0][2]))
last_residue = cg.stem_length("s0") - 1
self.assertAlmostEqual(
cg.vposs["s0"][last_residue][0],
16,
delta=4,
msg="Wrong x-position for virtual residue {} of stem s0: {}".
format(last_residue, cg.vposs["s0"][last_residue][0]))
self.assertAlmostEqual(
cg.vposs["s0"][last_residue][1],
-13,
delta=4,
msg="Wrong y-position for virtual residue {} of stem s0: {}".
format(last_residue, cg.vposs["s0"][last_residue][1]))
self.assertAlmostEqual(
cg.vposs["s0"][last_residue][2],
8,
delta=4,
msg="Wrong z-position for virtual residue {} of stem s0: {}".
format(last_residue, cg.vposs["s0"][last_residue][2]))
def test_coordinates_for_add_virtual_residues(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
#XYZ coordinate for first residue are ok:
self.assertAlmostEqual(cg.vposs["s0"][0][0], 2.3, delta=3,
msg="Wrong x-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][0]))
self.assertAlmostEqual(cg.vposs["s0"][0][1], 1.3, delta=3,
msg="Wrong y-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][1]))
self.assertAlmostEqual(cg.vposs["s0"][0][2], 1.0, delta=3,
msg="Wrong z-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][2]))
last_residue=cg.stem_length("s0") - 1
self.assertAlmostEqual(cg.vposs["s0"][last_residue][0], 16, delta=4,
msg="Wrong x-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][0]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][1], -13, delta=4,
msg="Wrong y-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][1]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][2], 8, delta=4,
msg="Wrong z-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][2]))
def test_virtual_residue_atom_exact_match(self):
# This test serves to detect unwanted changes in the virtual atom calculation algorithm.
# It is allowed to fail, if the virtual atom calculation changes.
try:
cg, = ftmc.CoarseGrainRNA.from_pdb(
'test/forgi/threedee/data/1y26.pdb',
annotation_tool="MC-Annotate")
except ftmc.AnnotationToolNotInstalled:
self.skipTest("Requires MC-Annotate")
ftug.add_virtual_residues(cg, 's0')
vres = ftug.virtual_residue_atoms(cg, 's0', 1, 0)
print(vres['C8'])
print(vres['N2'])
nptest.assert_allclose(
vres['C8'], np.array([5.17130963, -2.93616933, -2.16725865]))
nptest.assert_allclose(vres['N2'],
np.array([6.91170703, 2.35440312, -1.92080436]))
def test_coordinates_for_add_virtual_residues(self):
cg = ftmc.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
#XYZ coordinate for first residue are ok:
self.assertAlmostEqual(cg.vposs["s0"][0][0], 2.3, delta=3,
msg="Wrong x-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][0]))
self.assertAlmostEqual(cg.vposs["s0"][0][1], 1.3, delta=3,
msg="Wrong y-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][1]))
self.assertAlmostEqual(cg.vposs["s0"][0][2], 1.0, delta=3,
msg="Wrong z-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][2]))
last_residue=cg.stem_length("s0") - 1
self.assertAlmostEqual(cg.vposs["s0"][last_residue][0], 16, delta=4,
msg="Wrong x-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][0]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][1], -13, delta=4,
msg="Wrong y-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][1]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][2], 8, delta=4,
msg="Wrong z-position for virtual residue {} of stem s0: {}".format(last_residue,cg.vposs["s0"][last_residue][2]))
def test_coordinates_for_add_virtual_residues(self):
try:
cg, = ftmc.CoarseGrainRNA.from_pdb('test/forgi/threedee/data/1y26.pdb', annotation_tool="MC-Annotate")
except ftmc.AnnotationToolNotInstalled:
self.skipTest("This requires MC-Annotate")
ftug.add_virtual_residues(cg, 's0')
# XYZ coordinate for first residue are ok:
self.assertAlmostEqual(cg.vposs["s0"][0][0], 2.3, delta=3,
msg="Wrong x-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][0]))
self.assertAlmostEqual(cg.vposs["s0"][0][1], 1.3, delta=3,
msg="Wrong y-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][1]))
self.assertAlmostEqual(cg.vposs["s0"][0][2], 1.0, delta=3,
msg="Wrong z-position for virtual residue 0 of stem s0: {}".format(cg.vposs["s0"][0][2]))
last_residue = cg.stem_length("s0") - 1
self.assertAlmostEqual(cg.vposs["s0"][last_residue][0], 16, delta=4,
msg="Wrong x-position for virtual residue {} of stem s0: {}".format(last_residue, cg.vposs["s0"][last_residue][0]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][1], -13, delta=4,
msg="Wrong y-position for virtual residue {} of stem s0: {}".format(last_residue, cg.vposs["s0"][last_residue][1]))
self.assertAlmostEqual(cg.vposs["s0"][last_residue][2], 8, delta=4,
msg="Wrong z-position for virtual residue {} of stem s0: {}".format(last_residue, cg.vposs["s0"][last_residue][2]))
def test_virtual_residue_atoms(self):
cg, = ftmc.CoarseGrainRNA.from_pdb('test/forgi/threedee/data/1y26.pdb')
ftug.add_virtual_residues(cg, 's0')
ftug.add_virtual_residues(cg, 's1')
bases_to_test = []
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's0', 1, 0))
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's0', 2, 1))
bases_to_test.append(ftug.virtual_residue_atoms(cg, 's1', 0, 0))
# Assert that any two atoms of the same base within reasonable distance to each other
#(https://en.wikipedia.org/wiki/Bond_length says than a CH-bond is >= 1.06A)
for va in bases_to_test:
for k1, v1 in va.items():
for k2, v2 in va.items():
dist = ftuv.magnitude(v1 - v2)
self.assertLess(dist, 30, msg="Nucleotide too big: "
"Distance between {} and {} is {}".format(k1, k2, dist))
if k1 != k2:
dist = ftuv.magnitude(v1 - v2)
self.assertGreater(dist, 0.8, msg="Nucleotide too small: "
"Distance between {} and {} is {}".format(k1, k2, dist))
def predict(bg, energies_to_sample, options):
fud.pv('energies_to_sample[0].energies')
if options.cheating:
sm = fbm.SpatialModel(bg)
#energies_to_sample += [fbe.CombinedEnergy([], [fbe.CheatingEnergy(sm.bg)])]
energies_to_sample = [fbe.CheatingEnergy(sm.bg)]
if not os.path.exists(options.output_dir):
os.makedirs(options.output_dir)
if options.output_file == None or options.output_file == sys.stdout:
options.output_file = sys.stdout
else:
options.output_file = open(options.output_file, 'w')
cbc.Configuration.sampling_output_dir = op.join(options.output_dir, bg.name)
if options.output_dir_suffix != None:
cbc.Configuration.sampling_output_dir = op.join(cbc.Configuration.sampling_output_dir, options.output_dir_suffix)
if not os.path.exists(cbc.Configuration.sampling_output_dir):
os.makedirs(cbc.Configuration.sampling_output_dir)
if options.fix_all_loops:
options.fix_loop = ','.join([d for d in bg.defines if d[0] == 'i'])
if options.jared_dir is not None:
# run the jar3d_annotate script to get a list of potential statistics for each interior loop
jared_script = op.join(options.jared_dir, 'scripts/annotate_structure.py')
jared_data = op.join(options.jared_dir, 'JAR3D')
filtered_stats_fn = op.join(cbc.Configuration.sampling_output_dir,
'filtered.stats')
cmd = ['python', jared_script, options.bg_filename, '-o', jared_data,
'-m', '-e', '-d', jared_data]
fud.pv('cmd')
p = spr.Popen(cmd, stdout=spr.PIPE)
out, err = p.communicate()
with open(filtered_stats_fn, 'w') as filtered_out:
filtered_out.write(out)
filtered_stats = ftms.FilteredConformationStats(stats_file=options.stats_file,
filter_filename=filtered_stats_fn)
ftms.set_conformation_stats(filtered_stats)
print >>sys.stderr, "Using JAR3D filtered stats"
elif options.filtered_stats_file is not None:
filtered_stats = ftms.FilteredConformationStats(stats_file=options.stats_file,
filter_filename=options.filtered_stats_file)
ftms.set_conformation_stats(filtered_stats)
elif options.fix_loop is not None:
filtered_stats = ftms.FilteredConformationStats(stats_file=options.stats_file)
filtered_stats.filtered_stats = col.defaultdict(list)
for element_to_fix in options.fix_loop.split(','):
print >>sys.stderr, "fixing loop", element_to_fix
if element_to_fix[0] != 'i' and element_to_fix[0] != 'm':
print >>sys.stderr, "Cannot fix non-interior loop or multi-loop stats, yet!"
sys.exit(1)
as1, as2 = bg.get_bulge_angle_stats(element_to_fix)
filtered_stats.filtered_stats[(element_to_fix, as1.ang_type)] += [as1]
filtered_stats.filtered_stats[(element_to_fix, as2.ang_type)] += [as2]
ftms.set_conformation_stats(filtered_stats)
fud.pv('element_to_fix')
elif options.stats_file is not None:
cbc.Configuration.stats_file = options.stats_file
print >>sys.stderr, "1"
ftms.set_conformation_stats(ftms.ConformationStats(options.stats_file))
sm = fbm.SpatialModel(bg)
if options.log_to_file:
options.output_file = open(op.join(cbc.Configuration.sampling_output_dir, 'log.txt'), 'w')
if options.eval_energy:
for s in sm.bg.stem_iterator():
cgg.add_virtual_residues(sm.bg, s)
for energy in energies_to_sample:
fud.pv('energy.eval_energy(sm, verbose=True, background=False)')
sys.exit(1)
if options.plot:
plotter = fbs.StatisticsPlotter()
else:
plotter = None
colors = ['g','y','r']
samplers = []
# parse the distances that we want to keep track of
to_track_dists = []
if options.dists is not None:
for distance_pair in options.dists.split(':'):
to_track_dists += [map(int, distance_pair.split(','))]
# only samples from the first energy will be saved
silent = False
for color,energy in zip(colors, energies_to_sample):
fud.pv('options.no_rmsd')
stat = fbs.SamplingStatistics(sm, plotter, color, silent=silent,
output_file=options.output_file,
save_n_best = options.save_n_best,
dists = to_track_dists,
save_iterative_cg_measures=options.save_iterative_cg_measures,
no_rmsd = options.no_rmsd)
stat.step_save = options.step_save
fud.pv('options.mcmc_sampler')
if options.mcmc_sampler:
sm = fbm.SpatialModel(copy.deepcopy(bg))
sm.constraint_energy = fbe.CombinedEnergy([])
sm.junction_constraint_energy = fbe.CombinedEnergy([])
if not (options.cheating or options.no_constraint):
sm.constraint_energy = fbe.CombinedEnergy([fbe.CoarseStemClashEnergy(), fbe.StemVirtualResClashEnergy()])
sm.junction_constraint_energy = fbe.RoughJunctionClosureEnergy()
else:
sm.constraint_energy = None
sm.junction_constraint_energy = None
#sm.constraint_energy = fbe.CombinedEnergy([fbe.RoughJunctionClosureEnergy()])
#sm.constraint_energy = fbe.CombinedEnergy([fbe.StemVirtualResClashEnergy()])
#sm.constraint_energy = fbe.CombinedEnergy([fbe.StemVirtualResClashEnergy(), fbe.RoughJunctionClosureEnergy()])
if options.track_energies:
energies_to_track = [fbe.RadiusOfGyrationEnergy()]
fud.pv('len(list(bg.hloop_iterator()))')
if len(list(bg.hloop_iterator())) > 1:
energies_to_track += [fbe.ShortestLoopDistanceEnergy()]
for h in bg.hloop_iterator():
energies_to_track += [fbe.ShortestLoopDistancePerLoop(h)]
energies_to_track += [fbe.AMinorEnergy(loop_type='h')]
#energies_to_track += [fbe.AMinorEnergy(loop_type='i')]
else:
energies_to_track = []
fud.pv('energies_to_track')
fud.pv('energy')
sampler = fbs.MCMCSampler(sm, energy, stat, options.stats_type, options.no_rmsd, energies_to_track=energies_to_track)
sampler.dump_measures = options.dump_energies
samplers += [sampler]
else:
sm = fbm.SpatialModel(copy.deepcopy(bg))
sm.constraint_energy = fbe.StemVirtualResClashEnergy()
samplers += [fbs.GibbsBGSampler(sm, energy, stat)]
silent = True
fud.pv('samplers')
for i in range(options.iterations):
if options.single_sampler:
samplers[0].step()
else:
for s in samplers:
s.step()
#stats.print_final_stats(energy_function)
#stats.save_top()
if plotter:
plotter.finish()
#plotter.plt.ioff()
#plt.show()
pass