def get_pdbs_with_ftp(*pdbs):
"""
Fetches PDB files using FTP from a list of pdb-codes/text-files.
"""
pdbs = expand_pdbs(*pdbs)
entries = ['pdb%s.ent.gz' % pdb for pdb in pdbs]
mget_scripts = ["get %s" % entry for entry in entries]
substitutions = {
'host': 'ftp.wwpdb.org',
'mget_str': '\n'.join(mget_scripts),
}
ftp_script = template % substitutions
open('ftp.sh', 'w').write(ftp_script)
util.run_with_output('chmod +x ftp.sh')
util.run_with_output('./ftp.sh')
for pdb, entry in zip(pdbs, entries):
fname = pdb + '.pdb'
if os.path.isfile(entry):
out_f = open(fname, 'w')
for line in gzip.open(entry):
out_f.write(line)
util.clean_fname(entry)
print fname
else:
print "Failed: %s" % fname
util.clean_fname('ftp.sh')
def get_pdbs_with_ftp(*pdbs):
"""
Fetches PDB files using FTP from a list of pdb-codes/text-files.
"""
pdbs = expand_pdbs(*pdbs)
entries = ['pdb%s.ent.gz' % pdb for pdb in pdbs]
mget_scripts = ["get %s" % entry for entry in entries]
substitutions = {
'host': 'ftp.wwpdb.org',
'mget_str': '\n'.join(mget_scripts),
}
ftp_script = template % substitutions
open('ftp.sh', 'w').write(ftp_script)
util.run_with_output('chmod +x ftp.sh')
util.run_with_output('./ftp.sh')
for pdb, entry in zip(pdbs, entries):
fname = pdb + '.pdb'
if os.path.isfile(entry):
out_f = open(fname, 'w')
for line in gzip.open(entry):
out_f.write(line)
util.clean_fname(entry)
print fname
else:
print "Failed: %s" % fname
util.clean_fname('ftp.sh')
def check_dcd_byte_order(dcd):
if sys.byteorder in 'big':
option = '-B'
elif sys.byteorder in 'little':
option = '-L'
else:
raise "Couldn't find o.s. byte order %s" % sys.byteorder
util.run_with_output('flipdcd %s %s' % (option, dcd))
def run_pymol_script(pml, width=500, height=500):
is_quit = 'quit' in util.words_in_file(pml)
if is_quit:
pymol_batch = data.binary("pymol_batch")
cmd = pymol_batch + ' -c '
else:
pymol = data.binary("pymol")
cmd = pymol + " -q " # no splash screen
cmd += " -W %d -H %d " % (width, height)
cmd += pml
util.run_with_output(cmd)
