Create setup.py for GitHub-based installation using pip

CHANGELOG.md

@@ -1,6 +1,15 @@
 Changes
 =======
 
+
+1.2.2 (Unreleased)
+-----
+* Added the ability to install `gypsum_dl` in a flexible way using
+  `pip install git+https://github.com/durrantlab/gypsum_dl.git`
+* Replaced the local copy of the `dimorphite_dl` repository with one
+  installed automatically using
+  `pip install git+https://github.com/durrantlab/dimorphite_dl.git`.
+
 1.2.1
 -----
 
@@ -150,7 +159,7 @@ RDKit.
 -----
 
 * Updated Dimorphite-DL dependency from version 1.0.0 to version 1.2.0. See
-  `$PATH/gypsum_dl/gypsum_dl/Steps/SMILES/dimorphite_dl/CHANGES.md` for more
+  `https://github.com/durrantlab/dimorphite_dl/CHANGES.md` for more
   information.
 * Updated MolVS dependency from version v0.1.0 to v0.1.1 2019 release. See
   `$PATH/gypsum_dl/gypsum_dl/molvs/CHANGELOG.md` for more information.

CONTRIBUTORS.md

@@ -8,3 +8,4 @@ Contributors in Alphabetical Order
 * Patrick Ropp
 * Jacob Spigel
 * Jennifer Walker
+* Alex Morehead

README.md

@@ -280,8 +280,10 @@ methods allow users to exclude other potentially problematic forms:
    parameters if Gypsum-DL is producing compounds with undesired protonation
    states. Alternatively, you can delete specific protonation rules by
    modifying the
-   `gypsum_dl/Steps/SMILES/dimorphite_dl/site_substructures.smarts` file.
-3. Add to the Durrant-Lab filters if there is a specific substructure you
+   `site_substructures.smarts` file in your local `dimorphite_dl`
+   installation directory
+   (e.g., `.../site-packages/dimorphite_dl/site_substructures.smarts`).
+4. Add to the Durrant-Lab filters if there is a specific substructure you
    would like to avoid (e.g., imidic acid due to amide/imidic-acid
    tautomerization). Simplify modify the
    `gypsum_dl/Steps/SMILES/DurrantLabFilter.py` file.

gypsum_dl/Steps/SMILES/AddHydrogens.py

@@ -25,7 +25,7 @@
 import gypsum_dl.MyMol as MyMol
 import gypsum_dl.MolContainer as MolCont
 
-from gypsum_dl.Steps.SMILES.dimorphite_dl.dimorphite_dl import Protonate
+from dimorphite_dl.dimorphite_dl import Protonate
 
 
 def add_hydrogens(