Question

I’m using the code below to create a folder and then download the assocated PDBs with that protein. The problem I’m having is the PDBs are downloaded into the wrong location. They are downloaded into the loaction with the python script and not into the Cytochrome_C folder.

pdb = [
['Cytochrome_C']
['1giw','TITLE']
['1lc1','TITLE']
['1lc2','TITLE']
]

for pdb in pdbs:

    if str(pdb[0]) == 'Cytochrome_C':
        os.popen('mkdir Cytochrome_C')
        os.popen('cd ./Cytochrome_C')


    if len(pdb) == 2:
        os.popen('wget http://www.pdb.org/pdb/files/%s.pdb' % (str(pdb[0])))

Answer 1

os.popen is unnecessary for every one of those tasks. Use shutil and urllib2:

pdb = [
['Cytochrome_C']
['1giw','TITLE']
['1lc1','TITLE']
['1lc2','TITLE']
]
cwd = os.path.abspath(os.getcwd())

for pdb in pdbs:
    if pdb[0] == 'Cytochrome_C':
        shutil.mkdir(os.path.join(cwd, pdb[0]))

    if len(pdb) == 2:
        s = urllib2.urlopen('http://www.pdb.org/pdb/files/%s.pdb' % pdb[0]).read()
        open(os.path.join(cwd, 'Cytochrome_C', '%s.pdb' % pdb[0]), "w").write(s)