scine_chemoton.gears.network_refinement.disabling¶

Classes

`AggregateDisabling`()	Base class for handling the disabling of aggregates + their structures.
`DBObjectDisabling`()	The idea of these disabling functions is to make the gears ignore structures, elementary steps etc.
`DisableAllAggregates`()	Disable all aggregates and their structures.
`DisableAllReactions`([step_disabling])	Disable all reactions and their steps.
`DisableAllSteps`([ignore_barrierless])	Disable all elementary steps.
`DisableAllStepsByModel`(model[, ...])	Disable all steps that match the given model.
`DisableReactionByJob`(black_list)	Disable all reactions associated to a job order within a given black-list, i.e, an elementary step assigned to this reaction was produced by a job with the given order.
`DisableStepByJob`(black_list)	Disable all elementary step associated to a job order within a given black-list, i.e., the elementary step was produced by a job with this order.
`ReactionDisabling`([step_disabling])	Base class for handling the disabling of reactions + their elementary steps after, e.g., step-refinement.
`StepDisabling`()	Base class for handling the disabling of elementary steps after, e.g., step-refinement.

class scine_chemoton.gears.network_refinement.disabling.AggregateDisabling[source]¶

Base class for handling the disabling of aggregates + their structures.

The process function should decide on the fate of the given elementary step. As an additional argument a job order can be given.

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

disable_aggregate(aggregate)[source]¶

Disable an aggregate and all its structures.

Parameters:

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

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

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

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.disabling.DBObjectDisabling[source]¶

The idea of these disabling functions is to make the gears ignore structures, elementary steps etc. if desired. For instance, one could start refinement calculations for elementary steps of a reaction and disables the old steps and only rely on the refined steps. A second application is to disable all steps/structures etc. in the database and enable these objects in a step-wise manner again through the gears if the gears intend to set up the calculation that produced these results. In this way an exploration can be simulated without executing any new exploration calculations and new logic for enabling compounds for exploration can be tested.

static disable(db_object)[source]¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

property name: str¶

class scine_chemoton.gears.network_refinement.disabling.DisableAllAggregates[source]¶

Disable all aggregates and their structures.

Parameters:

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

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

disable_aggregate(aggregate)¶

Disable an aggregate and all its structures.

Parameters:

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

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

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

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.disabling.DisableAllReactions(step_disabling=<scine_chemoton.gears.network_refinement.disabling.DisableAllSteps object>)[source]¶

Disable all reactions and their steps.

Parameters:

step_disablingStepDisabling: The step disabling policy. By default, all steps are disabled.

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

disable_reaction(reaction)¶

Apply the step disabling policy. If all steps where disabled, the reaction is also disabled.

Parameters:

reactiondb.Reaction: The reaction.

initialize_collections(manager)¶

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(reaction, __='')[source]¶

Disable all reactions and steps.

Parameters:

reactiondb.Reaction: The reaction.
__str: Optional job order. Not used here.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.disabling.DisableAllSteps(ignore_barrierless=False)[source]¶

Disable all elementary steps.

Parameters:

ignore_barrierlessbool: Whether to ignore barrier-less steps. False by default.

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

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 step to process.
__str: Optional string which may be used by other classes to decide whether disable.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.disabling.DisableAllStepsByModel(model, ignore_barrierless=False)[source]¶

Disable all steps that match the given model.

Parameters:

modeldb.Model: The model.
ignore_barrierlessbool: Whether to ignore barrier-less steps. False by default.

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

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 step to process.
__str: Optional string which may be used by other classes to decide whether disable.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.disabling.DisableReactionByJob(black_list)[source]¶

Disable all reactions associated to a job order within a given black-list, i.e, an elementary step assigned to this reaction was produced by a job with the given order.

Parameters:

black_listList[str]: The list of job orders.

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

disable_reaction(reaction)¶

Apply the step disabling policy. If all steps where disabled, the reaction is also disabled.

Parameters:

reactiondb.Reaction: The reaction.

initialize_collections(manager)¶

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(reaction, job_order='')[source]¶

Disable all reactions and steps.

Parameters:

reactiondb.Reaction: The reaction.
job_orderstr: The job order.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.disabling.DisableStepByJob(black_list)[source]¶

Disable all elementary step associated to a job order within a given black-list, i.e., the elementary step was produced by a job with this order.

Parameters:

black_listList[str]: List of job orders for which steps are disabled.

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(step, job_order='')[source]¶

Process an elementary step

Parameters:

stepdb.ElementaryStep: The step to process.
job_orderstr: The job order. By default, empty.

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.disabling.ReactionDisabling(step_disabling=<scine_chemoton.gears.network_refinement.disabling.DisableAllSteps object>)[source]¶

Base class for handling the disabling of reactions + their elementary steps after, e.g., step-refinement.

The process function should decide on the fate of the given elementary step. As an additional argument a job order can be given. Apply a disabling policy to all elementary steps of a reaction.

Parameters:

step_disablingStepDisabling: The step disabling policy.

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

disable_reaction(reaction)[source]¶

Apply the step disabling policy. If all steps where disabled, the reaction is also disabled.

Parameters:

reactiondb.Reaction: The reaction.

initialize_collections(manager)[source]¶

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(_, __='')[source]¶: Do nothing

unset_collections()¶

Return type:: None

class scine_chemoton.gears.network_refinement.disabling.StepDisabling[source]¶

Base class for handling the disabling of elementary steps after, e.g., step-refinement. Does nothing by default.

The process function should decide on the fate of the given elementary step. As an additional argument a job order can be given.

static disable(db_object)¶

Disable the given DB object.

Parameters:

db_objectUnion[db.Structure, db.Compound, db.Flask, db.ElementaryStep, db.Reaction]: The DB object to disable.

initialize_collections(manager)¶

Return type:: None

property name: str¶

static possible_attributes()¶

Return type:: List[str]

process(_, __='')[source]¶: Do nothing.

unset_collections()¶

Return type:: None