Minor updates.

CHANGES.md

@@ -6,6 +6,9 @@ Changes
 
 * Updated protonation of nitrogen, oxygen, and sulfur atoms to be compatible
   with the latest version of RDKit, which broke backwards compatibility.
+* Added "silent" option to suppress all output.
+* Added code to suppress unnecessary RDKit warnings.
+* Updated copyright to 2020.
 
 1.2.2
 -----

README.md

@@ -35,7 +35,7 @@ usage: dimorphite_dl.py [-h] [--min_ph MIN] [--max_ph MAX]
                         [--label_states] [--test]
 
 Dimorphite 1.2.3: Creates models of appropriately protonated small moleucles.
-Apache 2.0 License. Copyright 2018 Jacob D. Durrant.
+Apache 2.0 License. Copyright 2020 Jacob D. Durrant.
 
 optional arguments:
   -h, --help           show this help message and exit

dimorphite_dl.py

-# Copyright 2018 Jacob D. Durrant
+# Copyright 2020 Jacob D. Durrant
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -30,19 +30,25 @@ except ImportError:
     # Python3
     from io import StringIO
 
-# Always let the user know a help file is available.
-print("\nFor help, use: python dimorphite_dl.py --help")
+def print_header():
+    """Prints out header information."""
+    # Always let the user know a help file is available.
+    print("\nFor help, use: python dimorphite_dl.py --help")
 
-# And always report citation information.
-print("\nIf you use Dimorphite-DL in your research, please cite:")
-print("Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An")
-print("open-source program for enumerating the ionization states of drug-like small")
-print("molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.\n")
+    # And always report citation information.
+    print("\nIf you use Dimorphite-DL in your research, please cite:")
+    print("Ropp PJ, Kaminsky JC, Yablonski S, Durrant JD (2019) Dimorphite-DL: An")
+    print("open-source program for enumerating the ionization states of drug-like small")
+    print("molecules. J Cheminform 11:14. doi:10.1186/s13321-019-0336-9.\n")
 
 try:
     import rdkit
     from rdkit import Chem
     from rdkit.Chem import AllChem
+
+    # Disable the unnecessary RDKit warnings
+    from rdkit import RDLogger
+    RDLogger.DisableLog("rdApp.*")
 except:
     msg = "Dimorphite-DL requires RDKit. See https://www.rdkit.org/"
     print(msg)
@@ -61,6 +67,8 @@ def main(params=None):
 
     parser = ArgParseFuncs.get_args()
     args = vars(parser.parse_args())
+    if not args["silent"]:
+        print_header()
 
     # Add in any parameters in params.
     if params is not None:
@@ -69,6 +77,7 @@ def main(params=None):
 
     # If being run from the command line, print out all parameters.
     if __name__ == "__main__":
+        if not args["silent"]:
             print("\nPARAMETERS:\n")
             for k in sorted(args.keys()):
                 print(k.rjust(13) + ": " + str(args[k]))
@@ -139,7 +148,7 @@ class ArgParseFuncs:
 
         parser = MyParser(description="Dimorphite 1.2.3: Creates models of " +
                                       "appropriately protonated small moleucles. " +
-                                      "Apache 2.0 License. Copyright 2018 Jacob D. " +
+                                      "Apache 2.0 License. Copyright 2020 Jacob D. " +
                                       "Durrant.")
         parser.add_argument('--min_ph', metavar='MIN', type=float, default=6.4,
                             help='minimum pH to consider (default: 6.4)')
@@ -158,6 +167,8 @@ class ArgParseFuncs:
         parser.add_argument('--label_states', action="store_true",
                             help='label protonated SMILES with target state ' + \
                                 '(i.e., "DEPROTONATED", "PROTONATED", or "BOTH").')
+        parser.add_argument('--silent', action="store_true",
+                            help='do not print any messages to the screen')
         parser.add_argument('--test', action="store_true",
                             help='run unit tests (for debugging)')