def main():
usage = """
./pdb_rmsd.py pdb_file1 pdb_file2
Extract the largest RNA chain from each file and calculate the rmsd between
all the matching atoms. Matching atoms are those that share a position and name.
I.e. residue 1, atom C1'
"""
num_args= 2
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)
chain1 = cup.load_structure(args[0])
chain2 = cup.load_structure(args[1])
print cup.pdb_rmsd(chain1, chain2)[:2]
def main():
usage = """
./pdb_rmsd.py pdb_file1 pdb_file2
Extract the largest RNA chain from each file and calculate the rmsd between
all the matching atoms. Matching atoms are those that share a position and name.
I.e. residue 1, atom C1'
"""
num_args = 2
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)
chain1 = cup.load_structure(args[0])
chain2 = cup.load_structure(args[1])
print cup.pdb_rmsd(chain1, chain2)[:2]
def main():
usage = """
python burial.py pdb_file
Calculate how buried each nucleotide is in this PDB file.
"""
num_args= 1
parser = OptionParser(usage=usage)
parser.add_option('-r', '--radius', dest='radius', default=5, help="The radius of the search ball", type='float')
parser.add_option('-s', '--step-size', dest='step_size', default=1, help="The size of each step in the depth search", type='float')
#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)
all_directions = np.array(ftuv.GetPointsEquiAngularlyDistancedOnSphere(numberOfPoints = 45))
chain = ftup.load_structure(args[0])
atoms = bpdb.Selection.unfold_entities(chain, 'A')
atom_coords = np.array([a.get_coord() for a in atoms])
kd = bkd.KDTree(3)
kd.set_coords(atom_coords)
for i,r in enumerate(chain.get_list()):
distance = calculate_burial(kd, r["C1'"].get_coord(),
all_directions, radius=options.radius,
step_size = options.step_size)
print "{}:{}".format(i+1, distance)
pass
def main():
usage = """
python burial.py pdb_file
Calculate how buried each nucleotide is in this PDB file.
"""
num_args = 1
parser = OptionParser(usage=usage)
parser.add_option('-r',
'--radius',
dest='radius',
default=5,
help="The radius of the search ball",
type='float')
parser.add_option('-s',
'--step-size',
dest='step_size',
default=1,
help="The size of each step in the depth search",
type='float')
#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)
all_directions = np.array(
ftuv.GetPointsEquiAngularlyDistancedOnSphere(numberOfPoints=45))
chain = ftup.load_structure(args[0])
atoms = bpdb.Selection.unfold_entities(chain, 'A')
atom_coords = np.array([a.get_coord() for a in atoms])
kd = bkd.KDTree(3)
kd.set_coords(atom_coords)
for i, r in enumerate(chain.get_list()):
distance = calculate_burial(kd,
r["C1'"].get_coord(),
all_directions,
radius=options.radius,
step_size=options.step_size)
print "{}:{}".format(i + 1, distance)
pass