--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_compounds.py	Tue Mar 22 16:06:54 2022 +0000
@@ -0,0 +1,60 @@
+import argparse
+import re
+
+from openbabel import openbabel, pybel
+openbabel.obErrorLog.StopLogging()
+
+
+def parse_command_line():
+    parser = argparse.ArgumentParser()
+    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('-m', '--met', required=False, action='store_true', help='Remove organometallic compounds')
+    parser.add_argument('-a', '--anorg', required=False, action='store_true', help='Remove anorganic compounds')
+    return parser.parse_args()
+
+
+def filter_compounds(args, pattern):
+    print(pattern)
+    with open(args.input, "r") as infile, open(args.output, "w") as outfile:
+        for line in infile:
+            values = line.split('\t', 1)
+
+            # check if input is list of SMILES or indexed table of SMILES
+            if values[0].isnumeric():
+                mol = pybel.readstring('smi', values[1]).write('inchi').split('/')[1] if values[1].strip() else ''
+
+                # check if both organometallic and anorganic filtering passes
+                # write original line if compound is organic without metals
+                if False not in ([bool(re.search(rf'{x}', mol)) for x in pattern]):
+                    outfile.write(line)
+                else:
+                    outfile.write(f'{values[0]}\t{""}\n')
+            else:
+                mol = pybel.readstring('smi', values[0]).write('inchi').split('/')[1]
+                if False not in ([bool(re.search(rf'{x}', mol)) for x in pattern]):
+                    outfile.write(line)
+
+
+def __main__():
+    """
+        Filter organometallics and/or anorganic compounds.
+    """
+    args = parse_command_line()
+
+    # check if user selected something to filter out, if not output file == input file
+    sel_pattern = []
+    if args.met is False and args.anorg is False:
+        print("No filtering selected - user did not specify what to filter out.")
+        sel_pattern = r'^[a-zA-Z]+$'
+    # select patterns for filtering
+    if args.met:
+        sel_pattern.append(r'^(?:C|N|O|P|F|S|I|B|Si|Se|Cl|Br|Li|Na|H|K|[0-9]|\.)+$')
+    if args.anorg:
+        sel_pattern.append(r'[C][^abd-z]')
+
+    filter_compounds(args, sel_pattern)
+
+
+if __name__ == "__main__":
+    __main__()