def test_cg_from_sg_invalid_subgraph_breaking_m(self):
cg = ftmc.CoarseGrainRNA('test/forgi/threedee/data/3D0U_A.cg')
"""
/s3 --h1
m1 |
/ |
s0 m2
\ |
m0 |
\s1--i0--s2--h0
"""
split_ml = ["s0", "m0", "s1"]
with self.assertRaises(Exception):
ftmc.cg_from_sg(cg, split_ml)
def test_cg_from_sg_invalid_subgraph_breaking_m(self):
cg = ftmc.CoarseGrainRNA.from_bg_file(
'test/forgi/threedee/data/3D0U_A.cg')
"""
/s3 --h1
m1 |
/ |
s0 m2
\ |
m0 |
\s1--i0--s2--h0
"""
split_ml = ["s0", "m0", "s1"]
with self.assertRaises(Exception):
ftmc.cg_from_sg(cg, split_ml)
def cg_from_sg(cg, sg):
'''
Create a coarse-grain structure from a subgraph.
@param cg: The original structure
@param sg: The list of elements that are in the subgraph
'''
new_cg = ftmc.cg_from_sg(cg, sg)
return new_cg
for d in sg:
new_cg.defines[d] = cg.defines[d]
if d in cg.coords.keys():
new_cg.coords[d] = cg.coords[d]
if d in cg.twists.keys():
new_cg.twists[d] = cg.twists[d]
if d in cg.longrange.keys():
new_cg.longrange[d] = cg.longrange[d]
for x in cg.edges[d]:
if x in new_cg.defines.keys():
new_cg.edges[d].add(x)
new_cg.edges[x].add(d)
return new_cg
def main():
usage = """
python create_colinearity_measures.py temp.cg
"""
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')
parser.add_option('-i', '--iterations', dest='iterations', default=1, help="The number of iterations to perform", type='int')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
for arg in args:
cg = ftmc.CoarseGrainRNA(arg)
cie = fbe.CylinderIntersectionEnergy()
for i in range(options.iterations):
sg = cg.random_subgraph()
csg = ftmc.cg_from_sg(cg, sg)
total_length = sum([len(list(cg.define_residue_num_iterator(d))) for d in sg])
cylinder_intersections = cie.calculate_intersection_coverages(csg)
print total_length, " ".join(map("{:.2f}".format, cylinder_intersections.values()))
def cg_from_sg(cg, sg):
'''
Create a coarse-grain structure from a subgraph.
@param cg: The original structure
@param sg: The list of elements that are in the subgraph
'''
new_cg = ftmc.cg_from_sg(cg, sg)
return new_cg
for d in sg:
new_cg.defines[d] = cg.defines[d]
if d in cg.coords.keys():
new_cg.coords[d] = cg.coords[d]
if d in cg.twists.keys():
new_cg.twists[d] = cg.twists[d]
if d in cg.longrange.keys():
new_cg.longrange[d] = cg.longrange[d]
for x in cg.edges[d]:
if x in new_cg.defines.keys():
new_cg.edges[d].add(x)
new_cg.edges[x].add(d)
return new_cg
def test_cg_from_sg_breaking_after_s(self):
cg = ftmc.CoarseGrainRNA('test/forgi/threedee/data/3D0U_A.cg')
"""
/s3 --h1
m1 |
/ |
s0 m2
\ |
m0 |
\s1--i0--s2--h0
"""
split_ml = ["s0", "m0", "s1", "m2", "s3", "m1", "h1"]
sg = ftmc.cg_from_sg(cg, split_ml)
self.check_graph_integrity(sg)
def test_cg_from_sg_breaking_after_s(self):
cg = ftmc.CoarseGrainRNA.from_bg_file(
'test/forgi/threedee/data/3D0U_A.cg')
"""
/s3 --h1
m1 |
/ |
s0 m2
\ |
m0 |
\s1--i0--s2--h0
"""
split_ml = ["s0", "m0", "s1", "m2", "s3", "m1", "h1"]
sg = ftmc.cg_from_sg(cg, split_ml)
self.check_graph_integrity(sg)
def main():
usage = """
python create_colinearity_measures.py temp.cg
"""
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')
parser.add_option('-i',
'--iterations',
dest='iterations',
default=1,
help="The number of iterations to perform",
type='int')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
for arg in args:
cg = ftmc.CoarseGrainRNA(arg)
cie = fbe.CylinderIntersectionEnergy()
for i in range(options.iterations):
sg = cg.random_subgraph()
csg = ftmc.cg_from_sg(cg, sg)
total_length = sum(
[len(list(cg.define_residue_num_iterator(d))) for d in sg])
cylinder_intersections = cie.calculate_intersection_coverages(csg)
print total_length, " ".join(
map("{:.2f}".format, cylinder_intersections.values()))