Issue 335 float quantity in settings (#657)

* use FloatQuantity type annotation in Settings

this is different to `unit.Quantity` as it then allows the coercion of strings to correct values through a pydantic validator

will eventually aid in ingesting CLI inputs to Settings as strings can be passed directly onto Settings

* tests for setting fields in Settings via strings

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

openfe/protocols/openmm_rfe/equil_rfe_settings.py

@@ -10,6 +10,7 @@
 
 from typing import Optional
 from openff.units import unit
+from openff.models.types import FloatQuantity
 import os
 
 from gufe.settings import (
@@ -91,7 +92,7 @@ class Config:
 
     Default False.
     """
-    explicit_charge_correction_cutoff = 0.8 * unit.nanometer
+    explicit_charge_correction_cutoff: FloatQuantity['nanometer'] = 0.8 * unit.nanometer
     """
     The minimum distance from the system solutes from which an
     alchemical water can be chosen. Default 0.8 * unit.nanometer.

openfe/protocols/openmm_utils/omm_settings.py

@@ -11,6 +11,7 @@
 
 from typing import Optional
 from openff.units import unit
+from openff.models.types import FloatQuantity
 import os
 
 from gufe.settings import (
@@ -38,7 +39,7 @@ class Config:
     Method for treating nonbonded interactions, currently only PME and
     NoCutoff are allowed. Default PME.
     """
-    nonbonded_cutoff = 1.0 * unit.nanometer
+    nonbonded_cutoff: FloatQuantity['nanometer'] = 1.0 * unit.nanometer
     """
     Cutoff value for short range nonbonded interactions.
     Default 1.0 * unit.nanometer.
@@ -80,7 +81,7 @@ class Config:
     Allowed values are; `tip3p`, `spce`, `tip4pew`, and `tip5p`.
     """
 
-    solvent_padding = 1.2 * unit.nanometer
+    solvent_padding: FloatQuantity['nanometer'] = 1.2 * unit.nanometer
     """Minimum distance from any solute atoms to the solvent box edge."""
 
     @validator('solvent_model')
@@ -152,7 +153,7 @@ class Config:
 
     Default `250`.
     """
-    online_analysis_target_error = 0.0 * unit.boltzmann_constant * unit.kelvin
+    online_analysis_target_error: FloatQuantity = 0.0 * unit.boltzmann_constant * unit.kelvin
     """
     Target error for the online analysis measured in kT. Once the free energy
     is at or below this value, the simulation will be considered complete. A
@@ -242,11 +243,11 @@ class IntegratorSettings(SettingsBaseModel):
     class Config:
         arbitrary_types_allowed = True
 
-    timestep = 4 * unit.femtosecond
+    timestep: FloatQuantity['femtosecond'] = 4 * unit.femtosecond
     """Size of the simulation timestep. Default 4 * unit.femtosecond."""
-    collision_rate = 1.0 / unit.picosecond
+    collision_rate: FloatQuantity['1/picosecond'] = 1.0 / unit.picosecond
     """Collision frequency. Default 1.0 / unit.pisecond."""
-    n_steps = 250 * unit.timestep
+    n_steps = 250 * unit.timestep  # todo: IntQuantity
     """
     Number of integration timesteps between each time the MCMC move
     is applied. Default 250 * unit.timestep.
@@ -263,7 +264,7 @@ class Config:
     """
     constraint_tolerance = 1e-06
     """Tolerance for the constraint solver. Default 1e-6."""
-    barostat_frequency = 25 * unit.timestep
+    barostat_frequency = 25 * unit.timestep  # todo: IntQuantity
     """
     Frequency at which volume scaling changes should be attempted.
     Default 25 * unit.timestep.
@@ -311,15 +312,15 @@ class Config:
 
     minimization_steps = 5000
     """Number of minimization steps to perform. Default 5000."""
-    equilibration_length: unit.Quantity
+    equilibration_length: FloatQuantity['nanosecond']
     """
     Length of the equilibration phase in units of time. The total number of
     steps from this equilibration length
     (i.e. ``equilibration_length`` / :class:`IntegratorSettings.timestep`)
     must be a multiple of the value defined for
     :class:`IntegratorSettings.n_steps`.
     """
-    production_length: unit.Quantity
+    production_length: FloatQuantity['nanosecond']
     """
     Length of the production phase in units of time. The total number of
     steps from this production length (i.e.
@@ -341,7 +342,7 @@ class Config:
     Selection string for which part of the system to write coordinates for.
     Default 'not water'.
     """
-    checkpoint_interval = 250 * unit.timestep
+    checkpoint_interval = 250 * unit.timestep  # todo: Needs IntQuantity
     """
     Frequency to write the checkpoint file. Default 250 * unit.timestep.
     """

openfe/tests/protocols/test_openmm_settings.py

@@ -0,0 +1,68 @@
+# This code is part of OpenFE and is licensed under the MIT license.
+# For details, see https://github.com/OpenFreeEnergy/openfe
+
+import pytest
+from openff.units import unit
+
+from openfe.protocols.openmm_rfe import equil_rfe_settings
+# afe settings currently have no FloatQuantity values
+from openfe.protocols.openmm_utils import omm_settings
+
+
+class TestOMMSettingsFromStrings:
+    # checks that we can set Settings fields via strings
+    def test_system_settings(self):
+        s = omm_settings.SystemSettings()
+
+        s.nonbonded_cutoff = '1.1 nm'
+
+        assert s.nonbonded_cutoff == 1.1 * unit.nanometer
+
+    def test_solvation_settings(self):
+        s = omm_settings.SolvationSettings()
+
+        s.solvent_padding = '1.1 nm'
+
+        assert s.solvent_padding == 1.1 * unit.nanometer
+
+    def test_alchemical_sampler_settings(self):
+        # todo: online_analysis_target_error is in kT, how to pass this as string?
+        pass
+
+    def test_integator_settings(self):
+        s = omm_settings.IntegratorSettings()
+
+        s.timestep = '3 fs'
+
+        assert s.timestep == 3.0 * unit.femtosecond
+
+        s.collision_rate = '1.1 / ps'
+
+        assert s.collision_rate == 1.1 / unit.picosecond
+
+        # todo: nsteps, barostat frequency require IntQuantity
+
+    def test_simulation_settings(self):
+        s = omm_settings.SimulationSettings(
+            equilibration_length=2.0 * unit.nanosecond,
+            production_length=5.0 * unit.nanosecond,
+        )
+
+        s.equilibration_length = '2.5 ns'
+        s.production_length = '10 ns'
+
+        assert s.equilibration_length == 2.5 * unit.nanosecond
+        assert s.production_length == 10.0 * unit.nanosecond
+
+        # todo: checkpoint_interval IntQuantity
+
+
+class TestEquilRFESettingsFromString:
+    def test_alchemical_settings(self):
+        s = equil_rfe_settings.AlchemicalSettings()
+
+        s.explicit_charge_correction_cutoff = '0.85 nm'
+
+        assert s.explicit_charge_correction_cutoff == 0.85 * unit.nanometer
+
+