Added documentation and typo fixes

README.md

@@ -21,9 +21,9 @@ Usage
 ```
 usage: protonate.py [-h] [--min_ph MIN] [--max_ph MAX] [--st_dev STD]
                     [--smiles SMILES] [--smiles_file SMILES_FILE]
-                    [--output_file OUTPUT_FILE]
+                    [--output_file OUTPUT_FILE] [--label_states]
 
-Protonates small moleucles.
+Protonates small molecules.
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -35,6 +35,8 @@ optional arguments:
                         File which contains SMILES strings to protonate.
   --output_file OUTPUT_FILE
                         File to write protonated SMILES. (Optional)
+  --label_states        Label protonated SMILES with target state 
+                        ("DEPROTONATED", "PROTONATED", or "BOTH").
 ```
 
 The default pH range is 6.4 to 8.4, considered biologically relevant pH.
@@ -54,6 +56,10 @@ python protonate.py --smiles "CCC(=O)O" --min_ph -3 --max_ph -2
 python protonate.py --smiles "CCCN" --min_ph -3 --max_ph -2 --output_file output.smi
 ```
 
+```
+python protonate.py --smiles_file sample_molecules.smi --st_dev 2.0 --label_states
+```
+
 Authors and Contacts
 --------------------
 

protonation_functions.py

@@ -54,14 +54,16 @@ def protonate(args):
         # in (not the one it IS in per the SMILES string). It's calculated
         # based on the probablistic distributions obtained during training.
         sites = get_prot_sites_and_target_states(smi, subs)
-        states = '\t'.join([x[1] for x in sites])
         new_smis = [smi]
         for site in sites:
             # Make a new smiles with the correct protonation state. Note that
             # new_smis is a growing list. This is how multiple protonation
             # sites are handled.
             new_smis = protonate_site(new_smis, site)
+        # If the user wants to see the target states, add those
+        # to the ends of each line.
         if args["label_states"]:
+            states = '\t'.join([x[1] for x in sites])
             new_lines = [x + "\t" + tag + "\t" + states for x in new_smis]
         else:
             new_lines = [x + "\t" + tag for x in new_smis]