Add modification scoring and adjust stiffening of ring bridges.

* Angles through transmuting physical neighbours are skipped when
  a better scoring neighbour exists.
* The planar triple junction handler not picks the worst-scoring
  physical atom rather than the first.
* Angles involving ring bridge atoms now are now stiffened with
  a reduced k_kard_ring=75 to avoid strain on the ring geometry.

Author: lohedges

src/ghostly/_cli.py

@@ -99,6 +99,19 @@ def run():
         required=False,
     )
 
+    parser.add_argument(
+        "--k-hard-ring",
+        type=str,
+        help="""
+             The force constant to use when setting angle terms involving ghost
+             atoms to 90 degrees for bridge atoms that are in a ring. A lower
+             value reduces strain where the 90 degree target fights the natural
+             ring geometry.
+             """,
+        default="75 kcal/mol/rad**2",
+        required=False,
+    )
+
     parser.add_argument(
         "--k-soft",
         type=str,
@@ -279,6 +292,12 @@ def run():
         logger.error(f"An error occurred while parsing the k-hard value: {e}")
         sys.exit(1)
 
+    try:
+        k_hard_ring = sr.u(args.k_hard_ring)
+    except Exception as e:
+        logger.error(f"An error occurred while parsing the k-hard-ring value: {e}")
+        sys.exit(1)
+
     try:
         k_soft = sr.u(args.k_soft)
     except Exception as e:
@@ -289,6 +308,9 @@ def run():
     if not k_hard.has_same_units(u):
         logger.error("k-hard must have units of kcal/mol/rad**2")
         sys.exit(1)
+    if not k_hard_ring.has_same_units(u):
+        logger.error("k-hard-ring must have units of kcal/mol/rad**2")
+        sys.exit(1)
     if not k_soft.has_same_units(u):
         logger.error("k-soft must have units of kcal/mol/rad**2")
         sys.exit(1)
@@ -330,9 +352,10 @@ def run():
         system, modifications = modify(
             system,
             k_hard.value(),
-            k_soft.value(),
-            args.optimise_angles,
-            args.num_optimise,
+            k_hard_ring=k_hard_ring.value(),
+            k_soft=k_soft.value(),
+            optimise_angles=args.optimise_angles,
+            num_optimise=args.num_optimise,
             soften_anchors=args.soften_anchors,
             stiffen_rotamers=args.stiffen_rotamers,
             k_rotamer=k_rotamer.value(),