scine_chemoton.gears.network_refinement.enabling¶

Classes

`AggregateEnabling`()	Base class for aggregate enabling.
`ApplyToAllStepsInReaction`(step_enabling_policy)	Apply the given step enabling policy to all steps in the reaction.
`ApplyToAllStructuresInAggregate`(...)	Apply a structure enabling policy to all structures of a given aggregate.
`DBObjectEnabling`()	These classes allow the enabling of previously disabled database objects like structures, calculation etc.
`EnableAllAggregates`()	Enable all aggregates.
`EnableAllReactions`()	Enable all reactions.
`EnableAllSteps`([reaction_enabling_policy])	Enables all elementary steps.
`EnableAllStructures`([aggregate_enabling_policy])	Enable all structures.
`EnableCalculationResults`([...])	Apply the given step enabling and structure enabling policies to all elementary steps and structures resulting from a given calculation.
`EnableJobSpecificCalculations`(model, job_order)	Apply the given step enabling and structure enabling policies to all elementary steps and structures resulting from a given calculation with given job order and electronic structure model.
`EnableStructureByModel`(model[, ...])	Enable a structure if its electronic structure model matches the given model, or it has an energy with this model.
`FilteredStepEnabling`(step_filter[, ...])	Enable elementary steps that parse the given elementary step filter.
`PlaceHolderAggregateEnabling`()	A place-holder for the aggregate enabling logic that can be used instead of a None default argument.
`PlaceHolderCalculationEnabling`([...])	A place-holder calculation enabling policy that can be used instead of None default arguments and replaced later.
`PlaceHolderReactionEnabling`()	A place-holder reaction enabling policy that can be used instead of None default arguments and replaced later.
`ReactionEnabling`()	Base class for reaction enabling.
`StepEnabling`()	Base class for elementary step enabling.
`StructureEnabling`()	Base class for structure enabling.

class scine_chemoton.gears.network_refinement.enabling.AggregateEnabling[source]¶

Base class for aggregate enabling.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

property name: str¶

process(_)[source]¶: Process an aggregate. By default, do nothing

class scine_chemoton.gears.network_refinement.enabling.ApplyToAllStepsInReaction(step_enabling_policy)[source]¶

Apply the given step enabling policy to all steps in the reaction.

Parameters:

step_enabling_policyStepEnabling: The step enabling policy.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

initialize_collections(manager)[source]¶

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(reaction)[source]¶

Process a reaction by enabling it and applying the elementary step policy.

Parameters:

reactiondb.Reaction: The reaction.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.ApplyToAllStructuresInAggregate(structure_enabling_policy)[source]¶

Apply a structure enabling policy to all structures of a given aggregate.

Parameters:

structure_enabling_policyStructureEnabling: The structure enabling policy.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

initialize_collections(manager)[source]¶

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(aggregate)[source]¶: Process an aggregate by applying the structure enabling policy and enabling the aggregate.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.DBObjectEnabling[source]¶

These classes allow the enabling of previously disabled database objects like structures, calculation etc. and are intended to be used in combination with the classes implemented in disabling.py. See disabling.py for more information.

static enable(db_object)[source]¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

property name: str¶

class scine_chemoton.gears.network_refinement.enabling.EnableAllAggregates[source]¶

Enable all aggregates.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

property name: str¶

process(aggregate)[source]¶

Process an aggregate by enabling it.

Parameters:

aggregateUnion[db.Compound, db.Flask]: The aggregate.

class scine_chemoton.gears.network_refinement.enabling.EnableAllReactions[source]¶

Enable all reactions.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

property name: str¶

process(reaction)[source]¶

Process a reaction. Enable all reactions.

Parameters:

reactiondb.Reaction: The reaction to enable.

class scine_chemoton.gears.network_refinement.enabling.EnableAllSteps(reaction_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.EnableAllReactions object>)[source]¶

Enables all elementary steps. By default, also the associated reactions are enabled.

Parameters:

reaction_enabling_policyReactionEnabling: The enabling policy to be applied to the elementary step’s reaction. By default, all reactions are enabled.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(step)[source]¶

Process an elementary step.

Parameters:

stepdb.ElementaryStep: The elementary step process.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.EnableAllStructures(aggregate_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.EnableAllAggregates object>)[source]¶

Enable all structures. By default, also their associated aggregates are enabled.

Parameters:

aggregate_enabling_policyAggregateEnabling: The policy to apply to the associated aggregates.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

enable_structure(structure)¶

Enable a structure.

Parameters:

structuredb.Structure: The structure.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(structure)[source]¶

Process a structure by enabling it and applying the aggregate policy to its aggregate.

Parameters:

structuredb.Structure: The structure.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.EnableCalculationResults(step_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.StepEnabling object>, structure_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.StructureEnabling object>)[source]¶

Apply the given step enabling and structure enabling policies to all elementary steps and structures resulting from a given calculation.

Parameters:

step_enabling_policyStepEnabling: The step enabling policy.
structure_enabling_policyStructureEnabling: The structure enabling policy.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

initialize_collections(manager)[source]¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(calculation)[source]¶: Process a calculation by enabling it and applying the given step and structure enabling policies.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.EnableJobSpecificCalculations(model, job_order, step_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.StepEnabling object>, structure_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.StructureEnabling object>)[source]¶

Apply the given step enabling and structure enabling policies to all elementary steps and structures resulting from a given calculation with given job order and electronic structure model.

Parameters:

modeldb.Model: The electronic structure model.
job_orderstr: The job order.
step_enabling_policyStepEnabling: The step enabling policy.
structure_enabling_policyStructureEnabling: The structure enabling policy.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(calculation)[source]¶: Process the calculation.

process_calculations_of_structures(structure_ids)[source]¶

Process all calculations of a given list of structures.

Return type:

None

Parameters:

structure_idsList[db.ID]: The list of structure ids.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.EnableStructureByModel(model, check_only_energy=False)[source]¶

Enable a structure if its electronic structure model matches the given model, or it has an energy with this model.

Parameters:

modeldb.Mode: The electronic structure model to match.
check_only_energybool: Whether to check only if the structure has an electronic energy with the given model.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

enable_structure(structure)¶

Enable a structure.

Parameters:

structuredb.Structure: The structure.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(structure)[source]¶

Process a structure.

Parameters:

structuredb.Structure: The structure.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.FilteredStepEnabling(step_filter, reaction_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.ReactionEnabling object>)[source]¶

Enable elementary steps that parse the given elementary step filter.

Parameters:

step_filterElementaryStepFilter: The filter.
reaction_enabling_policyReactionEnabling: The reaction enabling policy to be applied to the step’s reaction.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

initialize_collections(manager)[source]¶

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(step)[source]¶

Process an elementary step.

Parameters:

stepdb.ElementaryStep: The elementary step process.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.PlaceHolderAggregateEnabling[source]¶

A place-holder for the aggregate enabling logic that can be used instead of a None default argument.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

property name: str¶

process(_)[source]¶: Process an aggregate. By default, do nothing

class scine_chemoton.gears.network_refinement.enabling.PlaceHolderCalculationEnabling(step_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.StepEnabling object>, structure_enabling_policy=<scine_chemoton.gears.network_refinement.enabling.StructureEnabling object>)[source]¶

A place-holder calculation enabling policy that can be used instead of None default arguments and replaced later.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(_)[source]¶: Process a calculation by enabling it and applying the given step and structure enabling policies.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.PlaceHolderReactionEnabling[source]¶

A place-holder reaction enabling policy that can be used instead of None default arguments and replaced later.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

property name: str¶

process(_)[source]¶: Process a reaction. By default, do nothing.

class scine_chemoton.gears.network_refinement.enabling.ReactionEnabling[source]¶

Base class for reaction enabling. By default, this class does nothing.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

property name: str¶

process(_)[source]¶: Process a reaction. By default, do nothing.

class scine_chemoton.gears.network_refinement.enabling.StepEnabling[source]¶

Base class for elementary step enabling.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(_)[source]¶: Process an elementary step. By default, do nothing.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.enabling.StructureEnabling[source]¶

Base class for structure enabling. This base class does nothing on its own.

static enable(db_object)¶

Enabling a database object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction, db.Calculation]: The database object to be enabled.

enable_structure(structure)[source]¶

Enable a structure.

Parameters:

structuredb.Structure: The structure.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(_)[source]¶

Process a structure. By default, do nothing.

Parameters:

_db.Structure: The structure.

unset_collections()¶

Return type:: None