Finalized changes for version 1.1.9

CHANGELOG.md

 Changes
 =======
 
+1.1.9
+-----
+
+* Improved error handling when loading SDF files that are poorly formatted
+  (e.g., that do not specify charged nitrogen atoms). Gypsum-DL depends on
+  RDKit for SDF loading, and RDKit apparently cannot handle these errors. If
+  you find that Gypsum-DL skips many of your compounds with a `Warning: Could
+  not convert some SDF-formatted files to SMILES...` error, consider using an
+  SMI (SMILES) file instead.
+
 1.1.8
 -----
 

README.md

-# Gypsum-DL 1.1.8
+# Gypsum-DL 1.1.9
 
 Gypsum-DL is a free, open-source program for preparing 3D small-molecule
 models. Beyond simply assigning atomic coordinates, Gypsum-DL accounts for
@@ -51,7 +51,9 @@ Gypsum-DL accepts the following command-line parameters:
                         Overrides all other arguments specified at the
                         commandline.
   --source input.smi, -s input.smi
-                        Name of the source file (e.g., input.smi).
+                        Name of the source file (e.g., input.smi). Note:
+                        support for SMI (SMILES) files is better than support
+                        for SDF files, though Gypsum-DL can handle both.
   --output_folder OUTPUT_FOLDER, -o OUTPUT_FOLDER
                         The path to an existing folder where the Gypsum-DL
                         output file(s) will be saved.

gypsum_dl/Steps/IO/LoadFiles.py

@@ -125,7 +125,7 @@ def load_sdf_file(filename):
         if mol:
             smiles = Chem.MolToSmiles(mol, isomericSmiles=True, canonical=True)
         else:
-            Utils.log("\tWarning: Could not convert some SDF-formatted files to SMILES. Consider using an SMI file instead.")
+            Utils.log("\tWarning: Could not convert some SDF-formatted files to SMILES. Consider using an SMI (SMILES) file instead.")
             continue
 
         try:

run_gypsum_dl.py

@@ -15,7 +15,7 @@
 # limitations under the License.
 
 """
-Gypsum-DL 1.1.8 is a conversion script to transform smiles strings and 2D SDFs
+Gypsum-DL 1.1.9 is a conversion script to transform smiles strings and 2D SDFs
 into 3D models.
 """
 
@@ -73,7 +73,7 @@ from gypsum_dl import Utils
 PARSER = argparse.ArgumentParser(
     formatter_class=argparse.RawDescriptionHelpFormatter,
     description="""
-Gypsum-DL 1.1.8, a free, open-source program for preparing 3D small-molecule
+Gypsum-DL 1.1.9, a free, open-source program for preparing 3D small-molecule
 models. Beyond simply assigning atomic coordinates, Gypsum-DL accounts for
 alternate ionization, tautomeric, chiral, cis/trans isomeric, and
 ring-conformational forms.""",
@@ -159,7 +159,7 @@ PARSER.add_argument(
     "-s",
     type=str,
     metavar="input.smi",
-    help="Name of the source file (e.g., input.smi).",
+    help="Name of the source file (e.g., input.smi). Note: support for SMI (SMILES) files is better than support for SDF files, though Gypsum-DL can handle both.",
 )
 PARSER.add_argument(
     "--output_folder",