Forces user to choose -ss or -rmsd

and fixes -cc option and logging.

clusttraj/classify.py

@@ -58,17 +58,17 @@ def classify_structures_silhouette(
             t_opt = t
             labels_opt = hcl_labels
 
-    Logger.logger.info(f"Highest silhouette score: {ss_opt}")
+    Logger.logger.info(f"Highest silhouette score: {ss_opt}\n")
 
     if t_opt.size > 1:
         t_opt_str = ", ".join([str(t) for t in t_opt])
         Logger.logger.info(
-            f"The following RMSD threshold values yielded the same optimial silhouette score: {t_opt_str}"
+            f"The following RMSD threshold values yielded the same optimial silhouette score: {t_opt_str}\n"
         )
-        Logger.logger.info(f"The smallest RMSD of {t_opt[0]} has been adopted")
+        Logger.logger.info(f"The smallest RMSD of {t_opt[0]} has been adopted\n")
         clusters = labels_opt[0]
     else:
-        Logger.logger.info(f"Optimal RMSD threshold value: {t_opt}")
+        Logger.logger.info(f"Optimal RMSD threshold value: {t_opt}\n")
         clusters = labels_opt
 
     clust_opt.update({"optimal_cut": t_opt})

clusttraj/io.py

@@ -205,11 +205,6 @@ def configure_runtime(args_in: List[str]) -> ClustOptions:
         type=extant_file,
         help="path to the trajectory containing the conformations to be classified",
     )
-    parser.add_argument(
-        "min_rmsd",
-        type=float,
-        help="value of RMSD used to classify structures as similar",
-    )
     parser.add_argument(
         "-f",
         "--force-overwrite",
@@ -296,12 +291,6 @@ def configure_runtime(args_in: List[str]) -> ClustOptions:
         action="store_true",
         help="force a final Kabsch rotation before the RMSD computation (effect only when using -ns and -e)",
     )
-    parser.add_argument(
-        "-ss",
-        "--silhouette-score",
-        action="store_true",
-        help="use the silhouette score to determine the optimal number of clusters",
-    )
     parser.add_argument(
         "--log",
         type=str,
@@ -310,6 +299,21 @@ def configure_runtime(args_in: List[str]) -> ClustOptions:
         help="log file (default: clusttraj.log)",
     )
 
+    rmsd_criterion = parser.add_mutually_exclusive_group(required=True)
+
+    rmsd_criterion.add_argument(
+        "-ss",
+        "--silhouette-score",
+        action="store_true",
+        help="use the silhouette to determine the criterion to classify structures",
+    )
+    rmsd_criterion.add_argument(
+        "-rmsd",
+        "--min-rmsd",
+        type=float,
+        help="value of RMSD used to classify structures as similar",
+    )
+
     io_group = parser.add_mutually_exclusive_group()
     io_group.add_argument(
         "-i",

clusttraj/main.py

@@ -53,7 +53,6 @@ def main(args: list = None) -> None:
             clust_opt.out_conf_fmt,
             clust_opt.reorder_excl,
             clust_opt.final_kabsch,
-            clust_opt.silhouette_score,
             clust_opt.overwrite,
         )
 

test/test_io.py

@@ -114,7 +114,7 @@ def test_parse_args():
 
 
 def test_configure_runtime(caplog):
-    clust_opt = configure_runtime(["test/ref/testtraj.xyz", "1.0", "-np", "1"])
+    clust_opt = configure_runtime(["test/ref/testtraj.xyz", "--min-rmsd", "1.0", "-np", "1"])
 
     assert clust_opt.trajfile == "test/ref/testtraj.xyz"
     assert clust_opt.min_rmsd == pytest.approx(1.0, abs=1e-8)
@@ -123,22 +123,22 @@ def test_configure_runtime(caplog):
 
     with pytest.raises(SystemExit):
         clust_opt = configure_runtime(
-            ["test/ref/testtraj.xyz", "1.0", "-m", "nonexistent-method"]
+            ["test/ref/testtraj.xyz", "--min-rmsd", "1.0", "-m", "nonexistent-method"]
         )
 
     with pytest.raises(SystemExit):
         clust_opt = configure_runtime(
-            ["test/ref/testtraj.xyz", "1.0", "--reorder-alg", "nonexistent-method"]
+            ["test/ref/testtraj.xyz", "--min-rmsd", "1.0", "--reorder-alg", "nonexistent-method"]
         )
 
     with pytest.raises(SystemExit):
         clust_opt = configure_runtime(
-            ["test/ref/testtraj.xyz", "1.0", "-cc", "nonexistent-extension"]
+            ["test/ref/testtraj.xyz", "--min-rmsd", "1.0", "-cc", "nonexistent-extension"]
         )
 
     with pytest.raises(SystemExit):
         clust_opt = configure_runtime(
-            ["test/ref/testtraj.xyz", "1.0", "-n", "-eex", "1"]
+            ["test/ref/testtraj.xyz", "--min-rmsd", "1.0", "-n", "-eex", "1"]
         )
 
 

test/test_main.py

@@ -6,6 +6,7 @@ def test_main(tmp_path):
     main(
         [
             "test/ref/testtraj.xyz",
+            "--min-rmsd",
             "1.0",
             "-np",
             "1",