Removes self-inspection of constructor arguments (#91)

* Removed self-inspection of arguments

* Added classes to __all__ to facilitate import

Author: Charlles Abreu

cvpack/__init__.py

@@ -27,3 +27,28 @@
 from .sheet_rmsd_content import SheetRMSDContent  # noqa: F401
 from .torsion import Torsion  # noqa: F401
 from .torsion_similarity import TorsionSimilarity  # noqa: F401
+
+__all__ = [
+    "Angle",
+    "AtomicFunction",
+    "AttractionStrength",
+    "CentroidFunction",
+    "CollectiveVariable",
+    "CompositeRMSD",
+    "Distance",
+    "HelixAngleContent",
+    "HelixHBondContent",
+    "HelixRMSDContent",
+    "HelixTorsionContent",
+    "MetaCollectiveVariable",
+    "NumberOfContacts",
+    "OpenMMForceWrapper",
+    "PathInCVSpace",
+    "RadiusOfGyration",
+    "RadiusOfGyrationSq",
+    "ResidueCoordination",
+    "RMSD",
+    "SheetRMSDContent",
+    "Torsion",
+    "TorsionSimilarity",
+]

cvpack/angle.py

@@ -72,7 +72,9 @@ def __init__(
         super().__init__("theta")
         self.addAngle(atom1, atom2, atom3, [])
         self.setUsesPeriodicBoundaryConditions(pbc)
-        self._registerCV(name, mmunit.radians, atom1, atom2, atom3, pbc)
+        self._registerCV(
+            name, mmunit.radians, atom1=atom1, atom2=atom2, atom3=atom3, pbc=pbc
+        )
         self._registerPeriodicBounds(-np.pi, np.pi)
 
 

cvpack/atomic_function.py

@@ -150,11 +150,11 @@ def __init__(
         self._registerCV(
             name,
             unit,
-            function,
-            unit,
-            groups,
-            periodicBounds,
-            pbc,
+            function=function,
+            unit=unit,
+            groups=groups,
+            periodicBounds=periodicBounds,
+            pbc=pbc,
             **overalls,
             **perbonds,
         )

cvpack/attraction_strength.py

@@ -230,13 +230,13 @@ def __init__(  # pylint: disable=too-many-locals
 
         self._registerCV(
             name,
-            None,
-            group1,
-            group2,
-            nonbondedForce,
-            contrastGroup,
-            reference,
-            contrastScaling,
+            mmunit.dimensionless,
+            group1=group1,
+            group2=group2,
+            nonbondedForce=nonbondedForce,
+            contrastGroup=contrastGroup,
+            reference=reference,
+            contrastScaling=contrastScaling,
         )
 
 

cvpack/centroid_function.py

@@ -193,13 +193,13 @@ def __init__(
         self._registerCV(
             name,
             unit,
-            function,
-            unit,
-            groups,
-            collections,
-            periodicBounds,
-            pbc,
-            weighByMass,
+            function=function,
+            unit=unit,
+            groups=groups,
+            collections=collections,
+            periodicBounds=periodicBounds,
+            pbc=pbc,
+            weighByMass=weighByMass,
             **overalls,
             **perbonds,
         )

cvpack/collective_variable.py

@@ -7,9 +7,7 @@
 
 """
 
-import inspect
 import typing as t
-from collections import OrderedDict
 
 import openmm
 import yaml
@@ -46,8 +44,7 @@ def __deepcopy__(self, _) -> "CollectiveVariable":
     def _registerCV(
         self,
         name: str,
-        unit: t.Optional[mmunit.Unit],
-        *args: t.Any,
+        cvUnit: Unit,
         **kwargs: t.Any,
     ) -> None:
         """
@@ -63,18 +60,13 @@ def _registerCV(
             The unit of measurement of this collective variable. It must be a unit
             in the MD unit system (mass in Da, distance in nm, time in ps,
             temperature in K, energy in kJ/mol, angle in rad).
-        args
-            The arguments needed to construct this collective variable
         kwargs
             The keyword arguments needed to construct this collective variable
         """
         self.setName(name)
-        self._unit = Unit("dimensionless") if unit is None else unit
+        self._unit = cvUnit
         self._mass_unit = Unit(mmunit.dalton * (mmunit.nanometers / self._unit) ** 2)
-        arguments, _ = self._getArguments()
-        arguments.pop("name")
-        self._args = dict(zip(arguments, args))
-        self._args["name"] = name
+        self._args = {"name": name}
         self._args.update(kwargs)
 
     def _registerPeriodicBounds(
@@ -99,40 +91,6 @@ def _registerPeriodicBounds(
             upper = upper.value_in_unit(self.getUnit())
         self._periodic_bounds = Quantity((lower, upper), self.getUnit())
 
-    @classmethod
-    def _getArguments(cls) -> t.Tuple[OrderedDict, OrderedDict]:
-        """
-        Inspect the arguments needed for constructing an instance of this collective
-        variable.
-
-        Returns
-        -------
-        OrderedDict
-            A dictionary with the type annotations of all arguments
-        OrderedDict
-            A dictionary with the default values of optional arguments
-
-        Example
-        -------
-        >>> import cvpack
-        >>> args, defaults = cvpack.RadiusOfGyration._getArguments()
-        >>> for name, annotation in args.items():
-        ...     print(f"{name}: {annotation}")
-        group: typing.Iterable[int]
-        pbc: <class 'bool'>
-        weighByMass: <class 'bool'>
-        name: <class 'str'>
-        >>> print(*defaults.items())
-        ('pbc', False) ('weighByMass', False) ('name', 'radius_of_gyration')
-        """
-        arguments = OrderedDict()
-        defaults = OrderedDict()
-        for name, parameter in inspect.signature(cls).parameters.items():
-            arguments[name] = parameter.annotation
-            if parameter.default is not inspect.Parameter.empty:
-                defaults[name] = parameter.default
-        return arguments, defaults
-
     def _setUnusedForceGroup(self, system: openmm.System) -> None:
         """
         Set the force group of this collective variable to the one at a given position

cvpack/composite_rmsd.py

@@ -135,7 +135,13 @@ def __init__(
         super().__init__(all_coords)
         for group in groups:
             self.addGroup(group)
-        self._registerCV(name, mmunit.nanometers, defined_coords, groups, num_atoms)
+        self._registerCV(
+            name,
+            mmunit.nanometers,
+            referencePositions=defined_coords,
+            groups=groups,
+            numAtoms=num_atoms,
+        )
 
 
 CompositeRMSD.registerTag("!cvpack.CompositeRMSD")

cvpack/distance.py

@@ -57,7 +57,7 @@ def __init__(
         super().__init__("r")
         self.addBond(atom1, atom2, [])
         self.setUsesPeriodicBoundaryConditions(pbc)
-        self._registerCV(name, mmunit.nanometers, atom1, atom2, pbc)
+        self._registerCV(name, mmunit.nanometers, atom1=atom1, atom2=atom2, pbc=pbc)
 
 
 Distance.registerTag("!cvpack.Distance")

cvpack/helix_angle_content.py

@@ -129,13 +129,13 @@ def find_alpha_carbon(residue: mmapp.topology.Residue) -> int:
         self.setUsesPeriodicBoundaryConditions(pbc)
         self._registerCV(
             name,
-            None,
-            residues,
-            pbc,
-            thetaReference,
-            tolerance,
-            halfExponent,
-            normalize,
+            mmunit.dimensionless,
+            residues=residues,
+            pbc=pbc,
+            thetaReference=thetaReference,
+            tolerance=tolerance,
+            halfExponent=halfExponent,
+            normalize=normalize,
         )
 
 

cvpack/helix_hbond_content.py

@@ -113,7 +113,13 @@ def find_atom(residue: mmapp.topology.Residue, pattern: t.Pattern) -> int:
             )
         self.setUsesPeriodicBoundaryConditions(pbc)
         self._registerCV(
-            name, None, residues, pbc, thresholdDistance, halfExponent, normalize
+            name,
+            mmunit.dimensionless,
+            residues=residues,
+            pbc=pbc,
+            thresholdDistance=thresholdDistance,
+            halfExponent=halfExponent,
+            normalize=normalize,
         )
 
 

cvpack/helix_rmsd_content.py

@@ -150,7 +150,13 @@ def __init__(
             normalize,
         )
         self._registerCV(
-            name, None, residues, numAtoms, thresholdRMSD, stepFunction, normalize
+            name,
+            mmunit.dimensionless,
+            residues=residues,
+            numAtoms=numAtoms,
+            thresholdRMSD=thresholdRMSD,
+            stepFunction=stepFunction,
+            normalize=normalize,
         )
 
 

cvpack/helix_torsion_content.py

@@ -146,13 +146,13 @@ def find_atom(residue: mmapp.topology.Residue, name: str) -> int:
         self.setUsesPeriodicBoundaryConditions(pbc)
         self._registerCV(
             name,
-            None,
-            residues,
-            pbc,
-            phiReference,
-            psiReference,
-            tolerance,
-            halfExponent,
+            mmunit.dimensionless,
+            residues=residues,
+            pbc=pbc,
+            phiReference=phiReference,
+            psiReference=psiReference,
+            tolerance=tolerance,
+            halfExponent=halfExponent,
         )
 
 

cvpack/meta_collective_variable.py

@@ -131,10 +131,10 @@ def __init__(
         self._registerCV(
             name,
             unit,
-            function,
-            variables,
-            unit,
-            periodicBounds,
+            function=function,
+            variables=variables,
+            unit=unit,
+            periodicBounds=periodicBounds,
             **self._parameters,
         )
         if periodicBounds is not None:

cvpack/number_of_contacts.py

@@ -162,15 +162,15 @@ def __init__(
         self.setEnergyFunction(expression.replace("/1;", f"/{reference};"))
         self._registerCV(
             name,
-            None,
-            group1,
-            group2,
-            nonbondedForce,
-            reference,
-            stepFunction,
-            thresholdDistance,
-            cutoffFactor,
-            switchFactor,
+            mmunit.dimensionless,
+            group1=group1,
+            group2=group2,
+            nonbondedForce=nonbondedForce,
+            reference=reference,
+            stepFunction=stepFunction,
+            thresholdDistance=thresholdDistance,
+            cutoffFactor=cutoffFactor,
+            switchFactor=switchFactor,
         )
 
 

cvpack/openmm_force_wrapper.py

@@ -77,7 +77,13 @@ def __init__(  # pylint: disable=super-init-not-called
         unit = Unit(unit)
         self._wrapped_force = openmm.XmlSerializer.deserialize(openmmForce)
         self.this = self._wrapped_force.this
-        self._registerCV(name, unit, openmmForce, unit, periodicBounds)
+        self._registerCV(
+            name,
+            unit,
+            openmmForce=openmmForce,
+            unit=unit,
+            periodicBounds=periodicBounds,
+        )
         if periodicBounds is not None:
             self._registerPeriodicBounds(*periodicBounds)
 

cvpack/path_in_cv_space.py

@@ -12,6 +12,7 @@
 from copy import deepcopy
 
 import openmm
+from openmm import unit as mmunit
 
 from .collective_variable import CollectiveVariable
 from .path import Metric, deviation, progress
@@ -173,12 +174,12 @@ def __init__(  # pylint: disable=too-many-branches
             self.addCollectiveVariable(f"cv{i}", deepcopy(variable))
         self._registerCV(
             name,
-            None,
-            metric,
-            variables,
-            milestones.tolist(),
-            sigma,
-            scales,
+            mmunit.dimensionless,
+            metric=metric,
+            variables=variables,
+            milestones=milestones.tolist(),
+            sigma=sigma,
+            scales=scales,
         )
 
 

cvpack/radius_of_gyration.py

@@ -90,7 +90,9 @@ def __init__(
             num_groups, f"sqrt(({sum_dist_sq})/{num_atoms})", group, pbc, weighByMass
         )
         self.addBond(list(range(num_groups)))
-        self._registerCV(name, mmunit.nanometers, group, pbc, weighByMass)
+        self._registerCV(
+            name, mmunit.nanometers, group=group, pbc=pbc, weighByMass=weighByMass
+        )
 
 
 RadiusOfGyration.registerTag("!cvpack.RadiusOfGyration")

cvpack/radius_of_gyration_sq.py

@@ -87,7 +87,9 @@ def __init__(
         super().__init__(2, f"distance(g1, g2)^2/{num_atoms}", group, pbc, weighByMass)
         for atom in group:
             self.addBond([atom, num_atoms])
-        self._registerCV(name, mmunit.nanometers**2, group, pbc, weighByMass)
+        self._registerCV(
+            name, mmunit.nanometers**2, group=group, pbc=pbc, weighByMass=weighByMass
+        )
 
 
 RadiusOfGyrationSq.registerTag("!cvpack.RadiusOfGyrationSq")