diff sdf_to_tab.py @ 6:4beb3e026bbb draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit c1d813d3f0fec60ea6efe8a11e59d98bfdc1636f"

--- a/sdf_to_tab.py	Wed Feb 17 13:00:12 2021 +0000
+++ b/sdf_to_tab.py	Sat Dec 04 16:39:05 2021 +0000
@@ -13,36 +13,55 @@
         if mols[n]:
             d = mols[n].GetPropsAsDict()
             # filter dict for desired props
-            if vars.props.strip() == '':  # none specified, return all
-                d = {prop: val for (prop, val) in d.items() if not any(x in str(val) for x in ['\n', '\t'])}  # remove items containing newlines or tabs
+            if vars.props.strip() == "":  # none specified, return all
+                d = {
+                    prop: val
+                    for (prop, val) in d.items()
+                    if not any(x in str(val) for x in ["\n", "\t"])
+                }  # remove items containing newlines or tabs
             else:
-                d = {prop: val for (prop, val) in d.items() if prop in vars.props.replace(' ', '').split(',')}  # remove items not requested via CLI
+                d = {
+                    prop: val
+                    for (prop, val) in d.items()
+                    if prop in vars.props.replace(" ", "").split(",")
+                }  # remove items not requested via CLI
             if vars.name:
-                d['SDFMoleculeName'] = mols[n].GetProp('_Name')
+                d["SDFMoleculeName"] = mols[n].GetProp("_Name")
             if vars.smiles:
-                d['SMILES'] = Chem.MolToSmiles(mols[n], isomericSmiles=False)
-            d['Index'] = int(n)
+                d["SMILES"] = Chem.MolToSmiles(mols[n], isomericSmiles=False)
+            d["Index"] = int(n)
 
             df = df.append(d, ignore_index=True)
         else:
             print("Molecule could not be read - skipped.")
 
-    df = df.astype({'Index': int}).set_index('Index')
+    df = df.astype({"Index": int}).set_index("Index")
     sorted_cols = sorted(df.columns.values.tolist())
-    df.to_csv(vars.out, sep='\t', header=vars.header, columns=sorted_cols)
+    df.to_csv(vars.out, sep="\t", header=vars.header, columns=sorted_cols)
 
 
 def main():
     parser = argparse.ArgumentParser(description="Convert SDF to tabular")
-    parser.add_argument('--inp', '-i', help="The input file", required=True)
-    parser.add_argument('--out', '-o', help="The output file", required=True)
-    parser.add_argument('--props', '-p', help="Properties to filter (leave blank for all)", required=True)
-    parser.add_argument('--header', '-t', action='store_true',
-                        help="Write property name as the first row.")
-    parser.add_argument('--smiles', '-s', action='store_true',
-                        help="Include SMILES in output.")
-    parser.add_argument('--name', '-n', action='store_true',
-                        help="Include molecule name in output.")
+    parser.add_argument("--inp", "-i", help="The input file", required=True)
+    parser.add_argument("--out", "-o", help="The output file", required=True)
+    parser.add_argument(
+        "--props",
+        "-p",
+        help="Properties to filter (leave blank for all)",
+        required=True,
+    )
+    parser.add_argument(
+        "--header",
+        "-t",
+        action="store_true",
+        help="Write property name as the first row.",
+    )
+    parser.add_argument(
+        "--smiles", "-s", action="store_true", help="Include SMILES in output."
+    )
+    parser.add_argument(
+        "--name", "-n", action="store_true", help="Include molecule name in output."
+    )
     sdf_to_tab(parser.parse_args())