Implemented generic collective variable

cvpack/__init__.py

@@ -10,6 +10,7 @@
 from .centroid_function import CentroidFunction  # noqa: F401
 from .composite_rmsd import CompositeRMSD  # noqa: F401
 from .distance import Distance  # noqa: F401
+from .generic import Generic  # noqa: F401
 from .helix_angle_content import HelixAngleContent  # noqa: F401
 from .helix_hbond_content import HelixHBondContent  # noqa: F401
 from .helix_rmsd_content import HelixRMSDContent  # noqa: F401
@@ -31,6 +32,7 @@
     CentroidFunction,
     CompositeRMSD,
     Distance,
+    Generic,
     HelixAngleContent,
     HelixHBondContent,
     HelixRMSDContent,

cvpack/generic.py

@@ -0,0 +1,77 @@
+"""
+.. class:: Generic
+   :platform: Linux, MacOS, Windows
+   :synopsis: Generic collective variable
+
+.. classauthor:: Charlles Abreu <[email protected]>
+
+"""
+
+import typing as t
+
+import openmm
+
+from cvpack import unit as mmunit
+
+from .cvpack import BaseCollectiveVariable
+
+
+class Generic(BaseCollectiveVariable):
+    r"""
+    A generic collective variable.
+
+    Parameters
+    ----------
+        atom1
+            The index of the first atom
+        atom2
+            The index of the second atom
+        atom3
+            The index of the third atom
+        pbc
+            Whether to use periodic boundary conditions
+
+    Example:
+        >>> import cvpack
+        >>> import numpy as np
+        >>> import openmm
+        >>> from openmm import unit
+        >>> from openmmtools import testsystems
+        >>> model = testsystems.AlanineDipeptideVacuum()
+        >>> cv1 = cvpack.Angle(0, 1, 2)
+        >>> model.system.addForce(cv1)
+        5
+        >>> angle = openmm.CustomAngleForce("theta")
+        >>> angle.addAngle(0, 1, 2)
+        0
+        >>> cv2 = cvpack.Generic(angle, unit.radian, period=2*np.pi)
+        >>> model.system.addForce(cv2)
+        6
+        >>> integrator = openmm.VerletIntegrator(0)
+        >>> platform = openmm.Platform.getPlatformByName('Reference')
+        >>> context = openmm.Context(model.system, integrator, platform)
+        >>> context.setPositions(model.positions)
+        >>> print(cv1.getValue(context))
+        1.911... rad
+        >>> print(cv2.getValue(context))
+        1.911... rad
+        >>> assert isinstance(cv2, openmm.CustomAngleForce)
+    """
+
+    yaml_tag = "!cvpack.Generic"
+
+    def __init__(  # pylint: disable=too-many-arguments, super-init-not-called
+        self,
+        openmmForce: t.Union[openmm.Force, str],
+        unit: mmunit.Unit,
+        period: t.Optional[mmunit.ScalarQuantity] = None,
+    ) -> None:
+        if isinstance(openmmForce, openmm.Force):
+            openmmForce = openmm.XmlSerializer.serialize(openmmForce)
+        unit = mmunit.SerializableUnit(unit)
+        force_copy = openmm.XmlSerializer.deserialize(openmmForce)
+        self.__dict__.update(force_copy.__dict__)
+        self.__class__.__bases__ += (force_copy.__class__,)
+        self._registerCV(unit, openmmForce, unit, period)
+        if period is not None:
+            self._registerPeriod(period)