Make utility functions partially visible.

src/somd2/_utils/_ghosts.py

@@ -19,6 +19,8 @@
 # along with SOMD2. If not, see <http://www.gnu.org/licenses/>.
 #####################################################################
 
+__all__ = ["boresch"]
+
 from sire.system import System as _System
 from sire.legacy.System import System as _LegacySystem
 
@@ -32,7 +34,7 @@
 from . import _lam_sym
 
 
-def _boresch(system, k_hard=100, k_soft=5, optimise_angles=True):
+def boresch(system, k_hard=100, k_soft=5, optimise_angles=True):
     """
     Apply Boresch modifications to ghost atom bonded terms to avoid non-physical
     coupling between the ghost atoms and the physical region.

src/somd2/_utils/_somd1.py

@@ -19,14 +19,16 @@
 # along with SOMD2. If not, see <http://www.gnu.org/licenses/>.
 #####################################################################
 
+__all__ = ["make_compatible", "apply_pert"]
+
 from sire.system import System as _System
 from sire.legacy.System import System as _LegacySystem
 
 import sire.legacy.MM as _SireMM
 import sire.legacy.Mol as _SireMol
 
 
-def _make_compatible(system):
+def make_compatible(system):
     """
     Makes a perturbation SOMD1 compatible.
 
@@ -547,7 +549,7 @@ def _make_compatible(system):
     return system
 
 
-def _apply_pert(system, pert_file):
+def apply_pert(system, pert_file):
     """
     Helper function to apply a perturbation to a reference system.
 

src/somd2/runner/_base.py

@@ -85,9 +85,9 @@ def __init__(self, system, config):
                 f"Applying perturbation to reference system: {self._config.pert_file}"
             )
             try:
-                from .._utils._somd1 import _apply_pert
+                from .._utils._somd1 import apply_pert
 
-                self._system = _apply_pert(self._system, self._config.pert_file)
+                self._system = apply_pert(self._system, self._config.pert_file)
             except Exception as e:
                 raise IOError(f"Unable to apply perturbation to reference system: {e}")
 
@@ -114,12 +114,12 @@ def __init__(self, system, config):
 
         # We're running in SOMD1 compatibility mode.
         if self._config.somd1_compatibility:
-            from .._utils._somd1 import _make_compatible
+            from .._utils._somd1 import make_compatible
 
             # First, try to make the perturbation SOMD1 compatible.
 
             _logger.info("Applying SOMD1 perturbation compatibility.")
-            self._system = _make_compatible(self._system)
+            self._system = make_compatible(self._system)
             self._system = _sr.morph.link_to_reference(self._system)
 
             # Next, swap the water topology so that it is in AMBER format.
@@ -163,9 +163,9 @@ def __init__(self, system, config):
         # Apply Boresch modifications to bonded terms involving ghost atoms to
         # avoid spurious couplings to the physical system at the end states.
         else:
-            from .._utils._ghosts import _boresch
+            from .._utils._ghosts import boresch
 
-            self._system = _boresch(self._system)
+            self._system = boresch(self._system)
 
         # Check for a periodic space.
         self._has_space = self._check_space()