Merge pull request #55 from OpenBioSim/feature_ghost_handling

Add support for Boresch modifications to ghost atom bonded terms

.github/workflows/main.yaml

@@ -28,9 +28,9 @@ jobs:
       max-parallel: 9
       fail-fast: false
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.11"]
         platform:
-          - { name: "windows", os: "windows-latest", shell: "pwsh" }
+          #- { name: "windows", os: "windows-latest", shell: "pwsh" }
           - { name: "linux", os: "ubuntu-latest", shell: "bash -l {0}" }
           - { name: "macos", os: "macos-latest", shell: "bash -l {0}" }
     defaults:
@@ -48,7 +48,7 @@ jobs:
           ref: ${{ github.event.pull_request.head.sha }}
         if: github.event_name == 'pull_request'
 #
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}

src/somd2/_utils/__init__.py

@@ -0,0 +1,138 @@
+######################################################################
+# SOMD2: GPU accelerated alchemical free-energy engine.
+#
+# Copyright: 2023-2024
+#
+# Authors: The OpenBioSim Team <[email protected]>
+#
+# SOMD2 is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# SOMD2 is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with SOMD2. If not, see <http://www.gnu.org/licenses/>.
+#####################################################################
+
+import platform as _platform
+
+if _platform.system() == "Windows":
+    _lam_sym = "lambda"
+else:
+    _lam_sym = "λ"
+
+del _platform
+
+
+def _has_ghost(mol, idxs, is_lambda1=False):
+    """
+    Internal function to check whether any atom is a ghost.
+
+    Parameters
+    ----------
+
+    mol : sire.legacy.Mol.Molecule
+        The molecule.
+
+    idxs : [sire.legacy.Mol.AtomIdx]
+        A list of atom indices.
+
+    is_lambda1 : bool
+        Whether to check the lambda = 1 state.
+
+    Returns
+    -------
+
+    has_ghost : bool
+        Whether a ghost atom is present.
+    """
+
+    import sire.legacy.Mol as _SireMol
+
+    # We need to check by ambertype too since this molecule may have been
+    # created via sire.morph.create_from_pertfile, in which case the element
+    # property will have been set to the end state with the largest mass, i.e.
+    # may no longer by a ghost.
+    if is_lambda1:
+        element_prop = "element1"
+        ambertype_prop = "ambertype1"
+    else:
+        element_prop = "element0"
+        ambertype_prop = "ambertype0"
+
+    element_ghost = _SireMol.Element(0)
+    ambertype_ghost = "du"
+
+    # Check whether an of the atoms is a ghost.
+    for idx in idxs:
+        if (
+            mol.atom(idx).property(element_prop) == element_ghost
+            or mol.atom(idx).property(ambertype_prop) == ambertype_ghost
+        ):
+            return True
+
+    return False
+
+
+def _is_ghost(mol, idxs, is_lambda1=False):
+    """
+    Internal function to return whether each atom is a ghost.
+
+    Parameters
+    ----------
+
+    mol : sire.legacy.Mol.Molecule
+        The molecule.
+
+    idxs : [sire.legacy.Mol.AtomIdx]
+        A list of atom indices.
+
+    is_lambda1 : bool
+        Whether to check the lambda = 1 state.
+
+    Returns
+    -------
+
+    is_ghost : [bool]
+        Whether each atom is a ghost.
+    """
+
+    import sire.legacy.Mol as _SireMol
+
+    # We need to check by ambertype too since this molecule may have been
+    # created via sire.morph.create_from_pertfile, in which case the element
+    # property will have been set to the end state with the largest mass, i.e.
+    # may no longer by a ghost.
+    if is_lambda1:
+        element_prop = "element1"
+        ambertype_prop = "ambertype1"
+    else:
+        element_prop = "element0"
+        ambertype_prop = "ambertype0"
+
+    if is_lambda1:
+        element_prop = "element1"
+        ambertype_prop = "ambertype1"
+    else:
+        element_prop = "element0"
+        ambertype_prop = "ambertype0"
+
+    element_ghost = _SireMol.Element(0)
+    ambertype_ghost = "du"
+
+    # Initialise a list to store the state of each atom.
+    is_ghost = []
+
+    # Check whether each of the atoms is a ghost.
+    for idx in idxs:
+        is_ghost.append(
+            mol.atom(idx).property(element_prop) == element_ghost
+            or mol.atom(idx).property(ambertype_prop) == ambertype_ghost
+        )
+
+    return is_ghost