def main():
progname = os.path.basename(sys.argv[0])
usage = (
progname
+ """ [options] <pdb1, pdb2>
Output pdb1, whose bfactor is replaced by CA deviation between pdb1 and pdb2.
"""
)
args_def = {}
parser = argparse.ArgumentParser()
parser.add_argument("pdb", nargs="*", help="specify two aligned pdb files")
args = parser.parse_args()
if len(sys.argv) == 1:
print "usage: " + usage
print "Please run '" + progname + " -h' for detailed options."
sys.exit(1)
# get default values
for i in args_def:
if args.__dict__[i] == None:
args.__dict__[i] = args_def[i]
#
if len(args.pdb) != 2:
sys.exit("Please input two pdb files!")
pdb1, pdb2 = args.pdb
pdb1_CA, pdb1_CA27 = p3p.pdb_CA(pdb1)
pdb2_CA, pdb2_CA27 = p3p.pdb_CA(pdb2)
pdb_same = set(pdb1_CA27).intersection(pdb2_CA27)
basename1 = os.path.basename(os.path.splitext(pdb1)[0])
basename2 = os.path.basename(os.path.splitext(pdb2)[0])
with open(basename1 + "_dev_" + basename2 + ".pdb", "w") as w_pdb:
for i in pdb1_CA:
if i[:27] in pdb_same:
for j in pdb2_CA:
if j[:27] == i[:27]:
break
(x1, y1, z1), (x2, y2, z2) = p3p.get_coord(i), p3p.get_coord(j)
dev = math.sqrt((x1 - x2) ** 2 + (y1 - y2) ** 2 + (z1 - z2) ** 2)
i = list(i)
i[60:66] = "{:6.2f}".format(dev)
w_pdb.write("".join(i))
def main():
progname = os.path.basename(sys.argv[0])
usage = progname + """ [options] <localres.mrc>
Get local resolution from localres.mrc and transfer to bfactors in pdb.
"""
args_def = {'apix':1.25, 'pdb':''}
parser = argparse.ArgumentParser()
parser.add_argument("mrc", nargs='*', help="specify localres.mrc to be processed")
parser.add_argument("-a", "--apix", type=float, help="specify apix, by default {}".format(args_def['apix']))
parser.add_argument("-p", "--pdb", type=str, help="specify the pdb, by default {}".format(args_def['pdb']))
args = parser.parse_args()
if len(sys.argv) == 1:
print "usage: " + usage
print "Please run '" + progname + " -h' for detailed options."
sys.exit(1)
# get default values
for i in args_def:
if args.__dict__[i] == None:
args.__dict__[i] = args_def[i]
# read the pdb
with open(args.pdb) as p:
lines = p.readlines()
ATM = []
for i in lines:
if i[:6].strip() in ['ATOM', 'HETATM']:
ATM += [i]
basename = os.path.basename(os.path.splitext(args.pdb)[0])
a = args.apix
with open(basename + '_locres2bf.pdb', 'w') as w_pdb:
d = EMData(args.mrc[0])
for i in ATM:
(x, y, z) = p3p.get_coord(i)
x, y, z = int(x/a), int(y/a), int(z/a)
res = d.get_value_at(x, y, z)
i = list(i)
i[60:66] = '{:6.2f}'.format(res)
w_pdb.write(''.join(i))
