diff ob_genProp.py @ 0:75d6c2b7907a draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ob_genProp.py	Sat May 20 08:39:17 2017 -0400
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+"""
+    Input: Molecular input file.
+    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 openbabel
+openbabel.obErrorLog.StopLogging()
+import pybel
+import cheminfolib
+
+
+def parse_command_line(argv):
+    parser = argparse.ArgumentParser()
+    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('--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)
+    else:
+        outfile = open(args.output, 'w')
+        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 ] ) )
+
+    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 ]
+                outfile.write(mol)
+            else:
+                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
+    """
+    args = parse_command_line(sys.argv)
+    compute_properties(args)
+
+if __name__ == "__main__" :
+    __main__()