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