Updating to 1.2.4.

.gitignore

@@ -1,3 +1,4 @@
 *.pyc
 NOTES.txt
 .DS_Store
+.ipynb_checkpoints

CHANGES.md

@@ -1,11 +1,29 @@
 Changes
 =======
 
-WIP
----
+1.2.4
+-----
 
-site_substructures.smarts can now incldue comments (lines that start with # ignored.)
-Black formatting
+* Dimorphite-DL now better protonates compounds with polyphosphate chains
+  (e.g., ATP). See `site_substructures.smarts` for the rationale behind the
+  added pKa values.
+* Added test cases for ATP and NAD.
+* `site_substructures.smarts` now allows comments (lines that start with `#`).
+* Fixed a bug that affected how Dimorphite-DL deals with new protonation
+    states that yield invalid SMILES strings.
+  * Previously, it simply returned the original input SMILES in these rare
+    cases (better than nothing). Now, it instead returns the last valid SMILES
+    produced, not necessarily the original SMILES.
+  * Consider `O=C(O)N1C=CC=C1` at pH 3.5 as an example.
+    * Dimorphite-DL first deprotonates the carboxyl group, producing
+      `O=C([O-])n1cccc1` (a valid SMILES).
+    * It then attempts to protonate the aromatic nitrogen, producing
+      `O=C([O-])[n+]1cccc1`, an invalid SMILES.
+    * Previously, it would output the original SMILES, `O=C(O)N1C=CC=C1`. Now
+      it outputs the last valid SMILES, `O=C([O-])n1cccc1`.
+* Improved suport for the `--silent` option.
+* Reformatted code per the [*Black* Python code
+  formatter](https://github.com/psf/black).
 
 1.2.3
 -----

README.md

@@ -1,4 +1,4 @@
-Dimorphite-DL 1.2.3
+Dimorphite-DL 1.2.4
 ===================
 
 What is it?
@@ -34,7 +34,7 @@ usage: dimorphite_dl.py [-h] [--min_ph MIN] [--max_ph MAX]
                         [--smiles_file FILE] [--output_file FILE]
                         [--label_states] [--test]
 
-Dimorphite 1.2.3: Creates models of appropriately protonated small moleucles.
+Dimorphite 1.2.4: Creates models of appropriately protonated small moleucles.
 Apache 2.0 License. Copyright 2020 Jacob D. Durrant.
 
 optional arguments: