diff ob_remIons.py @ 15:7b6fd1c273cd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

--- a/ob_remIons.py	Tue Nov 10 20:36:42 2020 +0000
+++ b/ob_remIons.py	Thu Aug 15 11:03:49 2024 +0000
@@ -8,37 +8,43 @@
 import argparse
 
 from openbabel import openbabel, pybel
+
 openbabel.obErrorLog.StopLogging()
 
 
 def parse_command_line():
     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('-o', '--output', required=True, help='output file name')
-    parser.add_argument('-idx', default=False, action='store_true', help='should output be an indexed text table? works only for inchi/smiles, otherwise is ignored')
+    parser.add_argument("-iformat", default="sdf", help="input file format")
+    parser.add_argument("-i", "--input", required=True, help="input file name")
+    parser.add_argument("-o", "--output", required=True, help="output file name")
+    parser.add_argument(
+        "-idx",
+        default=False,
+        action="store_true",
+        help="should output be an indexed text table? works only for inchi/smiles, otherwise is ignored",
+    )
     return parser.parse_args()
 
 
 def remove_ions(args):
-    with open(args.output, 'w') as outfile:
+    with open(args.output, "w") as outfile:
         for index, mol in enumerate(pybel.readfile(args.iformat, args.input)):
             if mol.OBMol.NumHvyAtoms() > 5:
                 mol.OBMol.StripSalts(0)
-                if 'inchi' in mol.data:
-                    del mol.data['inchi']  # remove inchi cache so modified mol is saved
+                if "inchi" in mol.data:
+                    del mol.data["inchi"]  # remove inchi cache so modified mol is saved
 
-            mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else '\n'
+            mol = mol.write(args.iformat) if mol.OBMol.NumHvyAtoms() > 5 else "\n"
 
-            if args.idx and args.iformat in ['inchi', 'smi']:
-                outfile.write(f'{index}\t{mol}')
-            elif mol != '\n':
-                outfile.write(f'{mol}')
+            if args.idx and args.iformat in ["inchi", "smi"]:
+                outfile.write(f"{index}\t{mol}")
+            elif mol != "\n":
+                outfile.write(f"{mol}")
 
 
 def __main__():
     """
-        Remove any counterion and delete any fragment but the largest one for each molecule.
+    Remove any counterion and delete any fragment but the largest one for each molecule.
     """
     args = parse_command_line()
     remove_ions(args)