def test_16_models_stats(self):
if CHKTIME:
t0 = time()
models = load_structuralmodels('models.pick')
# write cmm
models.write_cmm('.', model_num=2)
model = load_impmodel_from_cmm('model.%s.cmm' % models[2]['rand_init'])
# clean
system('rm -f model.*')
# stats
self.assertEqual(200, round(model.distance(2, 3), 0))
self.assertTrue(9 <= round(model.distance(8, 20) / 100, 0) <= 10)
self.assertEqual(round(30, 0), round(model.radius_of_gyration() / 20,
0))
self.assertEqual(400, round(model.contour() / 10, 0))
self.assertTrue(
21 <= round((model.shortest_axe() + model.longest_axe()) /
100, 0) <= 22)
self.assertEqual([15, 16], model.inaccessible_particles(1000))
acc, num, acc_area, tot_area, bypt = model.accessible_surface(
150, superradius=200, nump=150)
self.assertTrue(210 <= acc <= 240)
self.assertTrue(500 <= num <= 600)
self.assertEqual(0.4, round(acc_area, 1))
self.assertEqual(4, round(tot_area, 0))
self.assertEqual(101, len(bypt))
self.assertTrue(19 <= bypt[100][0] <= 22 and 8 <= bypt[100][1] <= 38
and 8 <= bypt[100][2] <= 23)
if CHKTIME:
print '16', time() - t0
def test_16_models_stats(self):
if ONLY and "16" not in ONLY:
return
if CHKTIME:
t0 = time()
models = load_structuralmodels("models.pick")
# write cmm
models.write_cmm(".", model_num=2)
model = load_impmodel_from_cmm("model.%s.cmm" % models[2]["rand_init"])
# clean
system("rm -f model.*")
# stats
self.assertEqual(200, round(model.distance(2, 3), 0))
self.assertTrue(9 <= round(model.distance(8, 20) / 100, 0) <= 10)
self.assertEqual(round(30, 0), round(model.radius_of_gyration() / 20, 0))
self.assertEqual(400, round(model.contour() / 10, 0))
self.assertTrue(21 <= round((model.shortest_axe() + model.longest_axe()) / 100, 0) <= 22)
self.assertEqual([15, 16], model.inaccessible_particles(1000))
acc, num, acc_area, tot_area, bypt = model.accessible_surface(150, superradius=200, nump=150)
self.assertTrue(210 <= acc <= 240)
self.assertTrue(500 <= num <= 600)
self.assertEqual(0.4, round(acc_area, 1))
self.assertEqual(4, round(tot_area, 0))
self.assertEqual(101, len(bypt))
self.assertTrue(19 <= bypt[100][0] <= 22 and 8 <= bypt[100][1] <= 38 and 8 <= bypt[100][2] <= 23)
if CHKTIME:
print "16", time() - t0
def test_16_models_stats(self):
if CHKTIME:
t0 = time()
models = load_structuralmodels('models.pick')
# write cmm
models.write_cmm('.', model_num=2)
model = load_impmodel_from_cmm('model.%s.cmm' % models[2]['rand_init'])
# clean
system('rm -f model.*')
# stats
self.assertEqual(200, round(model.distance(2, 3), 0))
self.assertEqual(11, round(model.distance(8, 20)/100, 0))
self.assertEqual(round(593, 0),
round(model.radius_of_gyration(), 0))
self.assertEqual(400, round(model.contour()/10, 0))
self.assertEqual(21,
round((model.shortest_axe()+model.longest_axe())/100, 0))
self.assertEqual([11, 16], model.inaccessible_particles(1000))
acc, num, acc_area, tot_area, bypt = model.accessible_surface(
150, superradius=200, nump=150)
self.assertEqual(214, acc)
self.assertEqual(502, num)
self.assertEqual(0.4, round(acc_area, 1))
self.assertEqual(4, round(tot_area, 0))
self.assertEqual(101, len(bypt))
self.assertEqual(bypt[100], (21, 11, 8))
if CHKTIME:
print '16', time() - t0
def main():
opts = get_options()
if opts.model_path.endswith('.cmm'):
model = load_impmodel_from_cmm(opts.model_path)
elif opts.model_path.endswith('.xyz'):
model = load_impmodel_from_xyz(opts.model_path)
nump = int(opts.nump)
radius = int(opts.radius)
(accesible_parts,
number_parts,
accessible_area,
total_area, by_part) = model.accessible_surface(
radius, nump=nump, verbose=True, write_cmm_file=opts.outfcmm,
include_edges=opts.slow, superradius=(int(opts.superradius) if
opts.superradius else None))
print '\n GLOBAL STATS:\n -------------\n'
print ' - accesible dots (of the mesh) : %s' % accesible_parts
print ' - total number dots calculated : %s' % number_parts
print ' - proportion of accesible dots : %.2f%%' % (100*float(accesible_parts)/number_parts)
print ' - accessible area : %.4f square micrometers' % accessible_area
print ' - total area (straight chromatin) : %.4f square micrometers' % total_area
print ' - proportion of accesible surface : %.2f%%' % (100*float(accessible_area)/total_area)
print ''
if opts.outf:
out = open(opts.outf, 'w')
else:
out = stdout
for part, acc, ina in by_part:
if opts.burry:
burried = 1 if (100*float(ina) / (acc + ina)) > float(opts.burry) else 0
out.write('%s\t%.2f\n' % (part, burried))
else:
try:
out.write('%s\t%.2f\n' % (part, 100*float(ina) / (acc + ina)))
except ZeroDivisionError:
out.write('%s\t%s\n' % (part, 'nan'))
out.close()
