scine_chemoton.gears.kinetics¶
Classes
This Gear enables the exploration of aggregates if they were inserted by the user or created by a reaction that requires only explorable aggregates and has a forward reaction barrier below a given threshold. |
|
Base class for kinetics gears. |
|
This Gear enables the exploration of compounds if they were inserted by the user, created by a reaction that requires only compounds with a concentration flux larger than a given threshold, has a forward reaction barrier below a given maximum, and has reached a minimum concentration larger than a given threshold during kinetic modeling. |
|
This Gear enables the exploration of aggregates (Compounds and Flasks) if they were inserted by the user or created by a reaction that requires only explorable aggregates. |
|
This Gear enables the exploration of compounds if they were inserted by the user or have a compound cost lower than a given compound cost threshold. |
|
This class will activate all aggregates fulfilling the aggregate_filter (see KineticsBase) and accessible by a reaction that fulfills the reaction_filter. |
- class scine_chemoton.gears.kinetics.BasicBarrierHeightKinetics[source]¶
This Gear enables the exploration of aggregates if they were inserted by the user or created by a reaction that requires only explorable aggregates and has a forward reaction barrier below a given threshold.
Notes
Checks for all aggregates that are accessed via a ‘reaction’. Manually inserted Compounds/Flasks are always activated by this gear.
- Attributes:
- optionsBasicBarrierHeightKinetics.Options
The options for the BasicBarrierHeightKinetics Gear.
- aggregate_filterAggregateFilter
An optional filter to limit the activated aggregates, by default none are filtered
- class Options[source]¶
The options for the BasicBarrierHeightKinetics Gear.
-
cycle_time:
int¶ - int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
- enforce_free_energies¶
- bool
Whether the gear should only enable aggregates based on free energy barriers or can also enable based on electronic energies alone. Make sure to run a Thermo gear if you set this to
True.
- max_allowed_barrier¶
- float
The maximum barrier height of the reaction resulting in the aggregate in kJ/mol to allow the aggregate to be further explored.
-
max_allowed_energy:
Optional[float]¶ - Optional[float]
The maximum energy threshold for the reaction energies allowed in the aggregate in kJ/mol to allow the aggregate to be further explored.
-
model:
Model¶ - db.Model
The model the Gear is working with.
- restart¶
- bool
Option to restart the filtering of the network, by disabling all aggregates again. Set this to
Trueif you want to reevaluate a network with different settings.
- stop_if_no_new_aggregates_are_activated¶
- bool
Option to stop the gear if no new aggregates are activated during a loop. This is useful if you want to run a gear for a certain number of iterations, but want to stop early if there is no more progress.
-
cycle_time:
- class scine_chemoton.gears.kinetics.KineticsBase[source]¶
Base class for kinetics gears.
- Attributes:
- optionsKineticsBase.Options
The options for the Kinetics Gear.
- aggregate_filterAggregateFilter
An optional filter to limit the activated aggregates, by default none are filtered
- class Options[source]¶
The options for the KineticsBase Gear.
-
cycle_time:
int¶ - int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
-
model:
Model¶ - db.Model
The model the Gear is working with.
- restart¶
- bool
Option to restart the filtering of the network, by disabling all aggregates again. Set this to
Trueif you want to reevaluate a network with different settings.
- stop_if_no_new_aggregates_are_activated¶
- bool
Option to stop the gear if no new aggregates are activated during a loop. This is useful if you want to run a gear for a certain number of iterations, but want to stop early if there is no more progress.
-
cycle_time:
- class scine_chemoton.gears.kinetics.MaximumFluxKinetics[source]¶
This Gear enables the exploration of compounds if they were inserted by the user, created by a reaction that requires only compounds with a concentration flux larger than a given threshold, has a forward reaction barrier below a given maximum, and has reached a minimum concentration larger than a given threshold during kinetic modeling.
Notes
Checks for all compounds that are accessed via a ‘reaction’. Manually inserted Compounds are always activated by this gear.
- Attributes:
- optionsMaximumFluxKinetics.Options
The options for the MaximumFluxKinetics Gear.
- aggregate_filterAggregateFilter
An optional filter to limit the activated aggregates, by default none are filtered
- class Options[source]¶
The options for the MaximumPopulationKinetics Gear.
-
cycle_time:
int¶ - int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
- min_allowed_concentration¶
- float
The minimum allowed concentration property to be considered for further exploration.
-
model:
Model¶ - db.Model
The model the Gear is working with.
- property_label¶
- float
The minimum concentration flux that is required to consider the compound as accessible.
- restart¶
- bool
Option to restart the filtering of the network, by disabling all aggregates again. Set this to
Trueif you want to reevaluate a network with different settings.
- stop_if_no_new_aggregates_are_activated¶
- bool
Option to stop the gear if no new aggregates are activated during a loop. This is useful if you want to run a gear for a certain number of iterations, but want to stop early if there is no more progress.
- unset_collections()¶
Duplicate name to HoldCollections method to be triggered in pickling process, so infinite _parent loops are avoided.
- Return type:
-
cycle_time:
- class scine_chemoton.gears.kinetics.MinimalConnectivityKinetics[source]¶
This Gear enables the exploration of aggregates (Compounds and Flasks) if they were inserted by the user or created by a reaction that requires only explorable aggregates. This should be the case for any aggregates after a sufficient number of iterations and simply drive the exploration.
- Attributes:
- optionsMinimalConnectivityKinetics.Options
The options for the MinimalConnectivityKinetics Gear.
- aggregate_filterAggregateFilter
An optional filter to limit the activated aggregates, by default none are filtered
- class Options[source]¶
The options for the MinimalConnectivityKinetics Gear.
-
cycle_time:
int¶ - int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
-
model:
Model¶ - db.Model
The model the Gear is working with.
- restart¶
- bool
Option to restart the filtering of the network, by disabling all aggregates again. Set this to
Trueif you want to reevaluate a network with different settings.
- stop_if_no_new_aggregates_are_activated¶
- bool
Option to stop the gear if no new aggregates are activated during a loop. This is useful if you want to run a gear for a certain number of iterations, but want to stop early if there is no more progress.
- unset_collections()¶
Duplicate name to HoldCollections method to be triggered in pickling process, so infinite _parent loops are avoided.
- Return type:
- user_input_only¶
- bool
Option to only ever allow compounds that contain structures added to the database by a user. If enabled, no other compounds will ever be enabled irrespective of any connectivity.
-
cycle_time:
- class scine_chemoton.gears.kinetics.PathfinderKinetics[source]¶
This Gear enables the exploration of compounds if they were inserted by the user or have a compound cost lower than a given compound cost threshold. The compound costs are determined by running Pathfinder with the set options and the given starting conditions. The graph is built and the compound costs determined if the ratio of structures over compounds considered for building the last graph have changed by more than a given excess ratio, by default 10%.
- Attributes:
- optionsPathfinderKinetics.Options
The options for the PathfinderKinetics Gear.
- class Options[source]¶
The options for the PathfinderKinetics Gear.
- allow_unsolved_compound_costs¶
- bool
Bool to indicate if unsolved compound costs (compounds still having a +inf cost) are allowed.
- barrierless_weight¶
- float
Weight for barrierless reactions, by default 1e12.
-
cycle_time:
int¶ - int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
- filter_negative_barriers¶
- bool
Bool to indicate if negative barriers should be considered.
- max_compound_cost¶
- float
The maximal compound cost allowed for a compound to be enabled for exploration.
-
model:
Model¶ - db.Model
The model the Gear is working with.
- restart¶
- bool
Option to restart the filtering of the network, by disabling all aggregates again. Set this to
Trueif you want to reevaluate a network with different settings.
- restart_excess_ratio¶
- float
Percentage of ratio (structure / compounds in graph) change to trigger pathfinder analysis.
-
start_conditions:
Dict[str,float]¶ - Dict[str, float]
Starting conditions for pathfinder with the compound IDs as string and the cost as float.
- stop_if_no_new_aggregates_are_activated¶
- bool
Option to stop the gear if no new aggregates are activated during a loop. This is useful if you want to run a gear for a certain number of iterations, but want to stop early if there is no more progress.
- store_pathfinder_output¶
- bool
Bool to indicate if graph and compound costs of run should be exported to files.
-
structure_model:
Optional[Model]¶ - Optional[db.Model]
Structure model for the structures to be considered.
- temperature¶
- float
Temperature to calculate the rate constants from the barriers.
- class scine_chemoton.gears.kinetics.ReactionFilterBasedKinetics[source]¶
This class will activate all aggregates fulfilling the aggregate_filter (see KineticsBase) and accessible by a reaction that fulfills the reaction_filter.
- Attributes:
- reaction_filterReactionFilter
The reaction filter.
- class Options¶
The options for the KineticsBase Gear.
-
cycle_time:
int¶ - int
The minimum number of seconds between two cycles of the Gear. Cycles are finished independently of this option, hence if a cycle takes longer than the cycle_time will effectively lead to longer cycle times and not cause multiple cycles of the same Gear.
-
model:
Model¶ - db.Model
The model the Gear is working with.
- restart¶
- bool
Option to restart the filtering of the network, by disabling all aggregates again. Set this to
Trueif you want to reevaluate a network with different settings.
- stop_if_no_new_aggregates_are_activated¶
- bool
Option to stop the gear if no new aggregates are activated during a loop. This is useful if you want to run a gear for a certain number of iterations, but want to stop early if there is no more progress.
-
cycle_time: