HostGuestBindingAffinity
- class openff.evaluator.properties.HostGuestBindingAffinity(thermodynamic_state=None, phase=PropertyPhase.Undefined, substance=None, value=None, uncertainty=None, source=None)[source]
A class representation of a host-guest binding affinity property
- __init__(thermodynamic_state=None, phase=PropertyPhase.Undefined, substance=None, value=None, uncertainty=None, source=None)
Constructs a new PhysicalProperty object.
- Parameters
thermodynamic_state (ThermodynamicState) – The thermodynamic state that the property was measured in.
phase (PropertyPhase) – The phase that the property was measured in.
substance (Substance) – The composition of the substance that was measured.
value (openff.evaluator.unit.Quantity) – The value of the measured physical property.
uncertainty (openff.evaluator.unit.Quantity) – The uncertainty in the measured value.
source (Source) – The source of this property.
Methods
__init__
([thermodynamic_state, phase, ...])Constructs a new PhysicalProperty object.
default_paprika_schema
([existing_schema, ...])Returns the default calculation schema to use when estimating a host-guest binding affinity measurement with an APR calculation using the
paprika
package.openff.evaluator.unit.Unit: The default unit (e.g.
default_yank_schema
([existing_schema])Returns the default calculation schema to use when estimating this class of property from direct simulations.
from_json
(file_path)Create this object from a JSON file.
get_attributes
([attribute_type])Returns all attributes of a specific attribute_type.
json
([file_path, format])Creates a JSON representation of this class.
parse_json
(string_contents)Parses a typed json string into the corresponding class structure.
validate
([attribute_type])Validate the values of the attributes.
Attributes
The gradients of this property with respect to different force field parameters.
A unique identifier string assigned to this property
Additional metadata associated with this property.
The phase / phases that this property was measured in.
The original source of this physical property.
The substance that this property was measured estimated for.
The thermodynamic state that this propertywas measured / estimated at.
The uncertainty in measured / estimated value of this property.
The measured / estimated value of this property.
- classmethod default_unit()[source]
openff.evaluator.unit.Unit: The default unit (e.g. g / mol) associated with this class of property.
- static default_yank_schema(existing_schema=None)[source]
Returns the default calculation schema to use when estimating this class of property from direct simulations.
- Parameters
existing_schema (SimulationSchema, optional) – An existing schema whose settings to use. If set, the schema’s workflow_schema will be overwritten by this method.
- Returns
The schema to follow when estimating this property.
- Return type
- classmethod default_paprika_schema(existing_schema: ~typing.Optional[~openff.evaluator.layers.simulation.SimulationSchema] = None, n_solvent_molecules: int = 2500, n_thermalization_steps: int = 50000, n_equilibration_steps: int = 200000, n_production_steps: int = 2500000, dt_thermalization: ~pint.util.Quantity = <Quantity(1.0, 'femtosecond')>, dt_equilibration: ~pint.util.Quantity = <Quantity(2.0, 'femtosecond')>, dt_production: ~pint.util.Quantity = <Quantity(2.0, 'femtosecond')>, debug: bool = False)[source]
Returns the default calculation schema to use when estimating a host-guest binding affinity measurement with an APR calculation using the
paprika
package.Notes
This schema requires additional metadata to be able to estimate each metadata. This metadata is automatically generated for properties loaded from the
taproom
package using theTaproomDataSet
object.
- Parameters
existing_schema (SimulationSchema, optional) – An existing schema whose settings to use. If set, the schema’s workflow_schema will be overwritten by this method.
n_solvent_molecules – The number of solvent molecules to add to the box.
n_thermalization_steps – The number of thermalization simulations steps to perform. Sample generated during this step will be discarded.
n_equilibration_steps – The number of equilibration simulations steps to perform. Sample generated during this step will be discarded.
n_production_steps – The number of production simulations steps to perform. Sample generated during this step will be used in the final free energy calculation.
dt_thermalization – The integration timestep during thermalization
dt_equilibration – The integration timestep during equilibration
dt_production – The integration timestep during production
debug – Whether to return a debug schema. This is nearly identical to the default schema, albeit with significantly less solvent molecules (10), all simulations run in NVT and much shorter simulation runs (500 steps). If True, the other input arguments will be ignored.
- Returns
The schema to follow when estimating this property.
- Return type
- classmethod from_json(file_path)
Create this object from a JSON file.
- Parameters
file_path (str) – The path to load the JSON from.
- Returns
The parsed class.
- Return type
cls
- classmethod get_attributes(attribute_type=None)
Returns all attributes of a specific attribute_type.
- Parameters
attribute_type (type of Attribute, optional) – The type of attribute to search for.
- Returns
The names of the attributes of the specified type.
- Return type
list of str
- gradients
The gradients of this property with respect to different force field parameters. The default value of this attribute is not set. This attribute is optional.
- Type
- metadata
Additional metadata associated with this property. All property metadata will be made accessible to estimation workflows. The default value of this attribute is not set. This attribute is optional.
- Type
- classmethod parse_json(string_contents)
Parses a typed json string into the corresponding class structure.
- phase
The phase / phases that this property was measured in. The default value of this attribute is not set and must be set by the user..
- Type
- source
The original source of this physical property. The default value of this attribute is not set. This attribute is optional.
- Type
- substance
The substance that this property was measured estimated for. The default value of this attribute is not set and must be set by the user..
- Type
- thermodynamic_state
The thermodynamic state that this propertywas measured / estimated at. The default value of this attribute is not set and must be set by the user..
- Type
- uncertainty
The uncertainty in measured / estimated value of this property. The default value of this attribute is not set. This attribute is optional.
- Type
Quantity
- validate(attribute_type=None)
Validate the values of the attributes. If attribute_type is set, only attributes of that type will be validated.
- Parameters
attribute_type (type of Attribute, optional) – The type of attribute to validate.
- Raises
ValueError or AssertionError –