import os
import urllib

#Note the %s where the PDB code should go:
src = "http://www.rcsb.org/pdb/downloadFile.do" \
    + "?fileFormat=pdb&compression=NO&structureId=%s"

#Store all the downloads in this subdirectory:
assert os.path.isdir("top500")

input_file = open("top500.tsv","r")
lines = input_file.readlines()
input_file.close()

for line in lines :
    (pdb, chains) = line.split("\t")

    filename = os.path.join("top500", pdb+".pdb")

    if os.path.isfile(filename) :
        print "Already have " + pdb
    else :
        print "Downloading " + pdb
        urllib.urlretrieve(src % pdb, filename)