Improved documentation of default values (#96)

Author: Charlles Abreu

cvpack/attraction_strength.py

@@ -13,7 +13,7 @@
 from openmm import unit as mmunit
 
 from .collective_variable import CollectiveVariable
-from .units import ScalarQuantity
+from .units import Quantity, ScalarQuantity
 from .utils import evaluate_in_context
 
 ONE_4PI_EPS0 = 138.93545764438198
@@ -173,7 +173,7 @@ def __init__(  # pylint: disable=too-many-locals
         group2: t.Iterable[int],
         nonbondedForce: openmm.NonbondedForce,
         contrastGroup: t.Optional[t.Iterable[int]] = None,
-        reference: t.Union[ScalarQuantity, openmm.Context] = (
+        reference: t.Union[ScalarQuantity, openmm.Context] = Quantity(
             1.0 * mmunit.kilojoule_per_mole
         ),
         contrastScaling: float = 1.0,

cvpack/helix_angle_content.py

@@ -14,7 +14,7 @@
 from openmm import unit as mmunit
 
 from .collective_variable import CollectiveVariable
-from .units import ScalarQuantity
+from .units import Quantity, ScalarQuantity
 
 
 class HelixAngleContent(openmm.CustomAngleForce, CollectiveVariable):
@@ -95,8 +95,8 @@ def __init__(
         self,
         residues: t.Sequence[mmapp.topology.Residue],
         pbc: bool = False,
-        thetaReference: ScalarQuantity = 88 * mmunit.degrees,
-        tolerance: ScalarQuantity = 15 * mmunit.degrees,
+        thetaReference: ScalarQuantity = Quantity(88 * mmunit.degrees),
+        tolerance: ScalarQuantity = Quantity(15 * mmunit.degrees),
         halfExponent: int = 3,
         normalize: bool = False,
         name: str = "helix_angle_content",

cvpack/helix_hbond_content.py

@@ -15,7 +15,7 @@
 from openmm import unit as mmunit
 
 from .collective_variable import CollectiveVariable
-from .units import ScalarQuantity
+from .units import Quantity, ScalarQuantity
 
 
 class HelixHBondContent(openmm.CustomBondForce, CollectiveVariable):
@@ -83,7 +83,7 @@ def __init__(
         self,
         residues: t.Sequence[mmapp.topology.Residue],
         pbc: bool = False,
-        thresholdDistance: ScalarQuantity = 0.33 * mmunit.nanometers,
+        thresholdDistance: ScalarQuantity = Quantity(0.33 * mmunit.nanometers),
         halfExponent: int = 3,
         normalize: bool = False,
         name: str = "helix_hbond_content",

cvpack/helix_rmsd_content.py

@@ -13,7 +13,7 @@
 from openmm import unit as mmunit
 
 from .base_rmsd_content import BaseRMSDContent
-from .units import ScalarQuantity
+from .units import Quantity, ScalarQuantity
 
 # pylint: disable=protected-access
 ALPHA_POSITIONS = BaseRMSDContent._loadPositions("ideal_alpha_helix.csv")
@@ -131,7 +131,7 @@ def __init__(
         self,
         residues: t.Sequence[mmapp.topology.Residue],
         numAtoms: int,
-        thresholdRMSD: ScalarQuantity = 0.08 * mmunit.nanometers,
+        thresholdRMSD: ScalarQuantity = Quantity(0.08 * mmunit.nanometers),
         stepFunction: str = "(1+x^4)/(1+x^4+x^8)",
         normalize: bool = False,
         name: str = "helix_rmsd_content",

cvpack/helix_torsion_content.py

@@ -14,7 +14,7 @@
 from openmm import unit as mmunit
 
 from .collective_variable import CollectiveVariable
-from .units import ScalarQuantity
+from .units import Quantity, ScalarQuantity
 
 
 class HelixTorsionContent(openmm.CustomTorsionForce, CollectiveVariable):
@@ -105,9 +105,9 @@ def __init__(
         self,
         residues: t.Sequence[mmapp.topology.Residue],
         pbc: bool = False,
-        phiReference: ScalarQuantity = -63.8 * mmunit.degrees,
-        psiReference: ScalarQuantity = -41.1 * mmunit.degrees,
-        tolerance: ScalarQuantity = 25 * mmunit.degrees,
+        phiReference: ScalarQuantity = Quantity(-63.8 * mmunit.degrees),
+        psiReference: ScalarQuantity = Quantity(-41.1 * mmunit.degrees),
+        tolerance: ScalarQuantity = Quantity(25 * mmunit.degrees),
         halfExponent: int = 3,
         normalize: bool = False,
         name: str = "helix_torsion_content",

cvpack/number_of_contacts.py

@@ -14,7 +14,7 @@
 from openmm import unit as mmunit
 
 from .collective_variable import CollectiveVariable
-from .units import ScalarQuantity
+from .units import Quantity, ScalarQuantity
 from .utils import evaluate_in_context
 
 
@@ -130,7 +130,7 @@ def __init__(
         nonbondedForce: openmm.NonbondedForce,
         reference: t.Union[Real, openmm.Context] = 1.0,
         stepFunction: str = "1/(1+x^6)",
-        thresholdDistance: ScalarQuantity = 0.3 * mmunit.nanometers,
+        thresholdDistance: ScalarQuantity = Quantity(0.3 * mmunit.nanometers),
         cutoffFactor: float = 2.0,
         switchFactor: t.Optional[float] = 1.5,
         name: str = "number_of_contacts",

cvpack/residue_coordination.py

@@ -15,7 +15,7 @@
 from openmm.app.topology import Residue
 
 from .collective_variable import CollectiveVariable
-from .units import ScalarQuantity, value_in_md_units
+from .units import Quantity, ScalarQuantity, value_in_md_units
 
 
 class ResidueCoordination(openmm.CustomCentroidBondForce, CollectiveVariable):
@@ -111,7 +111,7 @@ def __init__(
         residueGroup2: t.Iterable[Residue],
         pbc: bool = True,
         stepFunction: str = "1/(1+x^6)",
-        thresholdDistance: ScalarQuantity = 1.0 * mmunit.nanometers,
+        thresholdDistance: ScalarQuantity = Quantity(1.0 * mmunit.nanometers),
         normalize: bool = False,
         weighByMass: bool = True,
         includeHydrogens: bool = True,

cvpack/sheet_rmsd_content.py

@@ -14,7 +14,7 @@
 from openmm import unit as mmunit
 
 from .base_rmsd_content import BaseRMSDContent
-from .units import ScalarQuantity
+from .units import Quantity, ScalarQuantity
 
 # pylint: disable=protected-access
 PARABETA_POSITIONS = BaseRMSDContent._loadPositions("ideal_parallel_beta_sheet.csv")
@@ -182,7 +182,7 @@ def __init__(
         numAtoms: int,
         parallel: bool = False,
         blockSizes: t.Optional[t.Sequence[int]] = None,
-        thresholdRMSD: ScalarQuantity = 0.08 * mmunit.nanometers,
+        thresholdRMSD: ScalarQuantity = Quantity(0.08 * mmunit.nanometers),
         stepFunction: str = "(1+x^4)/(1+x^4+x^8)",
         normalize: bool = False,
         name: str = "sheet_rmsd_content",