Mercurial > repos > bgruening > chemical_data_sources
diff get_pubchem/get_pubchem_as_smiles.py @ 3:021f0ef9474f draft
Uploaded
author | bgruening |
---|---|
date | Wed, 18 Sep 2013 09:44:36 -0400 |
parents | b65518a007fa |
children | 7c1f9962ac07 |
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--- a/get_pubchem/get_pubchem_as_smiles.py Sun Sep 08 09:42:57 2013 -0400 +++ b/get_pubchem/get_pubchem_as_smiles.py Wed Sep 18 09:44:36 2013 -0400 @@ -29,7 +29,7 @@ result.get() for filename in os.listdir(td): - path = os.path.join(td, filename) + path = os.path.join(td, filename) + '.smi' shutil.copyfileobj(open(path, 'rb'), output_handle) output_handle.close() @@ -38,9 +38,9 @@ def fetch_convert(args): (filename, td) = args - tmp_name = os.path.join( tempfile.gettempdir(), filename) + 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) + output = os.path.join(td, filename) + '.smi' subprocess.call(["obabel", "-isdf", tmp_name, "-ocan", '-O', output]) os.remove(tmp_name)