def main():
usage = """
python random_subgraph_radius_of_gyration.py file.cg
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
parser.add_option('-i', '--iterations', dest='iterations', default=1, help="The number of iterations to perform", type='int')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
cg = ftmc.CoarseGrainRNA(args[0])
for i in range(options.iterations):
sg = cg.random_subgraph()
stems = [s for s in sg if s[0] == 's']
if len(stems) == 0:
continue
coords = []
for s in stems:
coords += [cg.coords[s][0]]
coords += [cg.coords[s][1]]
rmsd = ftmd.radius_of_gyration(coords)
total_length = sum([len(list(cg.define_residue_num_iterator(d))) for d in sg])
print(total_length, rmsd)
def main():
usage = """
python random_subgraph_radius_of_gyration.py file.cg
"""
num_args= 0
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
parser.add_option('-i', '--iterations', dest='iterations', default=1, help="The number of iterations to perform", type='int')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
cg = ftmc.CoarseGrainRNA(args[0])
for i in range(options.iterations):
sg = cg.random_subgraph()
stems = [s for s in sg if s[0] == 's']
if len(stems) == 0:
continue
coords = []
for s in stems:
coords += [cg.coords[s][0]]
coords += [cg.coords[s][1]]
rmsd = ftmd.radius_of_gyration(coords)
total_length = sum([len(list(cg.define_residue_num_iterator(d))) for d in sg])
print total_length, rmsd
def test_gyration_tensor_vs_rog(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.],
[-2, -2, -2]])
rog = ftmd.radius_of_gyration(a1)
g_tensor = ftmd.gyration_tensor(a1, diagonalize=True)
print(rog, g_tensor)
#the first invariant is the rog
self.assertAlmostEqual(
g_tensor[0, 0] + g_tensor[1, 1] + g_tensor[2, 2], rog**2)
def test_gyration_tensor_vs_rog(self):
a1 = np.array([[1., 1., 1.], [0., 0., 0.],
[-1., -1., -1.], [-2, -2, -2]])
rog = ftmd.radius_of_gyration(a1)
g_tensor = ftmd.gyration_tensor(a1, diagonalize=True)
print(rog, g_tensor)
# the first invariant is the rog
self.assertAlmostEqual(
g_tensor[0, 0] + g_tensor[1, 1] + g_tensor[2, 2], rog**2)
def main():
usage = """
python cg_rmsd.py file1.cg
Calculate the ROG of a coarse grain models.
"""
num_args = 1
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
cg1 = ftmc.CoarseGrainRNA(args[0])
coords = cg1.get_ordered_stem_poss()
print ftmd.radius_of_gyration(coords)
def main():
usage = """
python cg_rmsd.py file1.cg
Calculate the ROG of a coarse grain models.
"""
num_args= 1
parser = OptionParser(usage=usage)
#parser.add_option('-o', '--options', dest='some_option', default='yo', help="Place holder for a real option", type='str')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
cg1 = ftmc.CoarseGrainRNA(args[0])
coords = cg1.get_ordered_stem_poss()
print ftmd.radius_of_gyration(coords)
def _get_descriptor(self, descriptor, domain=None):
"""
:param ensemble: an Ensemble or EnsembleView object
:param descriptor: A STRING. One of AVAILABLE_DESCRIPTORS
:param domain: An iterable of cg element names or None (whole cg)
:returns: A np.array
"""
if descriptor not in self.AVAILABLE_DESCRIPTORS:
raise ValueError("Descriptor {} not available.".format(descriptor))
if descriptor == "rog":
if domain:
return np.array([
ftmd.radius_of_gyration(
cg.get_poss_for_domain(domain, "vres")) for cg in self
])
else:
return np.array([cg.radius_of_gyration() for cg in self])
elif descriptor == "anisotropy":
if domain:
return np.array([
ftmd.anisotropy(cg.get_poss_for_domain(domain, "vres"))
for cg in self
])
else:
return np.array([
ftmd.anisotropy(cg.get_ordered_stem_poss()) for cg in self
])
elif descriptor == "asphericity":
if domain:
return np.array([
ftmd.asphericity(cg.get_poss_for_domain(domain, "vres"))
for cg in self
])
else:
return np.array([
ftmd.asphericity(cg.get_ordered_stem_poss()) for cg in self
])
def _get_descriptor(self, descriptor, domain=None):
"""
:param ensemble: an Ensemble or EnsembleView object
:param descriptor: A STRING. One of AVAILABLE_DESCRIPTORS
:param domain: An iterable of cg element names or None (whole cg)
:returns: A np.array
"""
if descriptor not in self.AVAILABLE_DESCRIPTORS:
raise ValueError("Descriptor {} not available.".format(descriptor))
if descriptor == "rog":
if domain:
return np.array([ftmd.radius_of_gyration(cg.get_poss_for_domain(domain, "vres")) for cg in self])
else:
return np.array([cg.radius_of_gyration() for cg in self])
elif descriptor == "anisotropy":
if domain:
return np.array([ftmd.anisotropy(cg.get_poss_for_domain(domain, "vres")) for cg in self])
else:
return np.array([ftmd.anisotropy(cg.get_ordered_stem_poss()) for cg in self])
elif descriptor == "asphericity":
if domain:
return np.array([ftmd.asphericity(cg.get_poss_for_domain(domain, "vres")) for cg in self])
else:
return np.array([ftmd.asphericity(cg.get_ordered_stem_poss()) for cg in self])
def test_radius_of_gyration(self):
a = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.]])
r = ftmd.radius_of_gyration(a)
self.assertGreater(r, 0)
self.assertAlmostEqual(r, math.sqrt(2))
def update(self, sm, step):
rog = ftur.radius_of_gyration(sm.bg.get_ordered_stem_poss())
self.history[0].append(rog)
return "{:6.2f} A".format(rog)
def update(self, sm, step):
rog=ftur.radius_of_gyration(sm.bg.get_ordered_stem_poss())
self.history[0].append(rog)
return "{:6.2f} A".format(rog)
def test_radius_of_gyration(self):
a = np.array([[1., 1., 1.], [0., 0., 0.], [-1., -1., -1.]])
r = ftmd.radius_of_gyration(a)
self.assertGreater(r, 0)
self.assertAlmostEqual(r, math.sqrt(2))