--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_pubchem_as_smiles.py	Wed May 22 07:44:03 2019 -0400
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+__author__ = 'Bjoern Gruening'
+__version__ = '0.1'
+__date__ = '2012'
+__license__ = 'GLP3+'
+
+import ftplib
+import os, sys
+import argparse
+import subprocess
+from multiprocessing import Pool
+import tempfile
+import shutil
+
+
+def main(output, processors = 4):
+    output_handle = open(output,'w+')
+
+    td = tempfile.mkdtemp()
+    ftp = ftplib.FTP('ftp.ncbi.nih.gov')
+    ftp.login()
+    ftp.cwd('/pubchem/Compound/CURRENT-Full/SDF/')
+    filelist = ftp.nlst()
+    
+    pool = Pool(processes = processors)
+    filenames = zip(filelist, [td]*len(filelist))
+    result = pool.map_async(fetch_convert, filenames)
+    result.get()
+
+    for filename in os.listdir(td):
+        path = os.path.join(td, filename)
+        shutil.copyfileobj(open(path, 'rb'), output_handle)
+
+    output_handle.close()
+    shutil.rmtree(td)
+
+def fetch_convert(args):
+    (filename, td) = args
+    tmp_name = os.path.join( td, filename)
+    subprocess.call( ['wget', '-O', tmp_name, os.path.join('ftp://ftp.ncbi.nih.gov/pubchem/Compound/CURRENT-Full/SDF/', filename)] )
+    output = os.path.join(td, filename) + '.smi'
+    subprocess.call(["obabel", "-isdf", tmp_name, "-ocan", '-O', output])
+    os.remove(tmp_name)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description='Download the whole PubChem and converts it to canonical SMILES on the fly.')
+    parser.add_argument("-o", "--output", dest="output",
+                    required=True,
+                    help="Path to the output file.")
+    parser.add_argument("-p", "--processors", dest="processors",
+                    type=int, default=10,
+                    help="How many processors you want to use.")
+
+    options = parser.parse_args()
+    main( options.output, options.processors )
+