def test_rebuild_one_artif_compact_CB(self):
for dmm in range(50):
for i in self.aas:
scm = SCModeler([self.dm(), self.dm(i), self.dm()])
frame, dmm1, dmm2 = self.mk_random_cas()
res = scm.rebuild_one(frame, False)
dist = numpy.linalg.norm(frame[1] - res[1])
prop_dst = numpy.linalg.norm(SIDECNT['ALA'][:3])
self.assertEqual(round(prop_dst, 3), round(dist, 3))
def test_rebuild_one_artif_scatter_CB(self):
for dmm in range(50):
for i in self.aas:
scm = SCModeler([self.dm(), self.dm(i), self.dm()])
frame, dummy1, dummy2 = self.mk_random_cas()
res = scm.rebuild_one(frame, False)
dist = numpy.linalg.norm(frame[1] - res[1])
prop_dst = numpy.linalg.norm(SIDECNT['ALA'][3:])
#~ if round(prop_dst, 3) != round(dist, 3):
#~ scm._calc_rot_mtx(*frame, dbg=True)
self.assertAlmostEqual(round(prop_dst, 3), round(dist, 3))
def mk_cmaps(self, ca_traj, meds, clusts, top1k_inds, thr, plots_dir):
scmodeler = SCModeler(ca_traj.template)
sc_traj_full = scmodeler.calculate_sc_traj(ca_traj.coordinates)
sc_med = scmodeler.calculate_sc_traj(meds.coordinates)
shp = sc_med.shape
sc_med = sc_med.reshape((shp[1], shp[0]) + shp[2:])
cmapdir = os.path.join(self.work_dir, 'contact_maps')
try:
os.mkdir(cmapdir)
except OSError:
pass
return sc_traj_full, sc_med, cmapdir
def test_calc_trig_fnc(self):
for i in range(100):
v1 = self.mk_random_versor((None, None, 0))
rot, ang = self.mk_rot_z_mtx()
v2 = numpy.dot(rot, v1)
cos, sin = SCModeler._calc_trig_fnc(v1, v2, numpy.array((0, 0, 1)))
xx = numpy.linalg.norm(numpy.cross(v1, v2))
self.assertAlmostEqual(sin, numpy.sin(ang))
self.assertAlmostEqual(cos, numpy.cos(ang))
def test_calc_nodes_line(self):
for i in range(100):
v1 = self.mk_random_versor()
rot, ang = self.mk_rot_z_mtx()
v2 = numpy.dot(rot, v1)
nv = SCModeler._calc_nodes_line(v1, v2)
self.assertAlmostEqual(1, numpy.linalg.norm(nv))
self.assertAlmostEqual(0, numpy.dot(nv, v1))
self.assertAlmostEqual(0, numpy.dot(nv, v2))
def test_calc_rot_mtx(self):
for i in range(100):
scm = SCModeler([self.dm(), self.dm(), self.dm()])
frame, vec, rot = self.mk_random_cas()
rot, dist = scm._calc_rot_mtx(*frame)
self.assertEqual(numpy.linalg.norm(frame[0] - frame[2]), dist)
xp = numpy.dot(rot, (1, 0, 0))
yp = numpy.dot(rot, (0, 1, 0))
zp = numpy.dot(rot, (0, 0, 1))
for tv in (xp, yp, zp):
self.assertAlmostEqual(numpy.linalg.norm(tv), 1)
for v in SIDECNT.values():
v1 = v[:3]
v2 = v[3:]
n1 = numpy.linalg.norm(v1)
n2 = numpy.linalg.norm(v2)
n1p = numpy.linalg.norm(numpy.dot(rot, v1))
n2p = numpy.linalg.norm(numpy.dot(rot, v2))
self.assertAlmostEqual(n1, n1p)
self.assertAlmostEqual(n2, n2p)
def test_mk_local_system(self):
mtx = numpy.array([[0., 0., 0.], [3.2, 1.5, 0.],
[6.4, 0., 0.]]) # sample CA positions (scatter)
ang = numpy.pi / 6
rot, ang = self.mk_rot_z_mtx(ang)
c1, c2, c3 = [numpy.dot(rot, i) for i in mtx]
x, y, z, dst = SCModeler._mk_local_system(c1, c2, c3)
self.assertEqual(dst, 6.4)
for i in (x, y, z):
self.assertEqual(1, numpy.linalg.norm(i)) # we expect versors
for j in (x, y, z):
if i is j: continue
self.assertAlmostEqual(numpy.dot(i, j),
0) # versors should be orthogonal
def test_coef(self):
for k, v in SIDECNT.items():
if k == 'GLY': continue
for i in numpy.arange(5, 7, .1):
res = SCModeler._calc_scatter_coef(i)
self.assertGreaterEqual(res, 0)
self.assertLessEqual(res, 1)
v1 = numpy.array(v[:3])
v2 = numpy.array(v[3:])
diff = numpy.linalg.norm(v1 - v2)
av_vec = (v1 * res + v2 * (1 - res))
av_diff1 = numpy.linalg.norm(av_vec - v1)
av_diff2 = numpy.linalg.norm(av_vec - v2)
self.assertLessEqual(av_diff1, diff)
self.assertLessEqual(av_diff2, diff)
def test_init(self):
SCModeler([self.dm(i) for i in self.aas])
SCModeler([self.dm(random.choice(self.aas)) for i in range(100)])