diff ob_genProp.py @ 13:e94b2920d4e4 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"

--- a/ob_genProp.py	Tue Jul 28 08:38:01 2020 -0400
+++ b/ob_genProp.py	Mon Oct 19 14:44:19 2020 +0000
@@ -4,23 +4,25 @@
     Output: Physico-chemical properties are computed and stored as metadata in the sdf output file.
     Copyright 2012, Bjoern Gruening and Xavier Lucas
 """
-import sys, os
 import argparse
+import sys
+
+import cheminfolib
 import openbabel
+from openbabel import pybel
 openbabel.obErrorLog.StopLogging()
-import cheminfolib
 
-from openbabel import pybel
 
 def parse_command_line(argv):
     parser = argparse.ArgumentParser()
-    parser.add_argument('--iformat', default='sdf' , help='input file format')
+    parser.add_argument('--iformat', default='sdf', help='input file format')
     parser.add_argument('-i', '--input', required=True, help='input file name')
-    parser.add_argument('--oformat', default='sdf', choices = ['sdf', 'table'] , help='output file format')
+    parser.add_argument('--oformat', default='sdf', choices=['sdf', 'table'], help='output file format')
     parser.add_argument('--header', type=bool, help='Include the header as the first line of the output table')
     parser.add_argument('-o', '--output', required=True, help='output file name')
     return parser.parse_args()
 
+
 def compute_properties(args):
     if args.oformat == 'sdf':
         outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
@@ -29,18 +31,19 @@
         if args.header:
             mol = next(pybel.readfile(args.iformat, args.input))
             metadata = cheminfolib.get_properties_ext(mol)
-            outfile.write( '%s\n' % '\t'.join( [ cheminfolib.ColumnNames[key] for key in metadata ] ) )
+            outfile.write('%s\n' % '\t'.join([cheminfolib.ColumnNames[key] for key in metadata]))
 
     for mol in pybel.readfile(args.iformat, args.input):
         if mol.OBMol.NumHvyAtoms() > 5:
             metadata = cheminfolib.get_properties_ext(mol)
             if args.oformat == 'sdf':
-                [ mol.data.update( { cheminfolib.ColumnNames[key] : metadata[key] } ) for key in metadata ]
+                [mol.data.update({cheminfolib.ColumnNames[key]: metadata[key]}) for key in metadata]
                 outfile.write(mol)
             else:
-                outfile.write( '%s\n' % ('\t'.join( [ str(metadata[key]) for key in metadata ] ) ) )
+                outfile.write('%s\n' % ('\t'.join([str(metadata[key]) for key in metadata])))
     outfile.close()
 
+
 def __main__():
     """
         Physico-chemical properties are computed and stored as metadata in the sdf output file
@@ -48,5 +51,6 @@
     args = parse_command_line(sys.argv)
     compute_properties(args)
 
-if __name__ == "__main__" :
+
+if __name__ == "__main__":
     __main__()