scine_chemoton.gears.reaction¶
Classes
This Gear updates all Elementary Steps stored in the database such that they are added to an existing Reaction or that a new Reaction is created if the Step does not fit an existing one. |
- class scine_chemoton.gears.reaction.BasicReactionHousekeeping[source]¶
This Gear updates all Elementary Steps stored in the database such that they are added to an existing Reaction or that a new Reaction is created if the Step does not fit an existing one.
Notes
Checks for all Elementary Steps without a ‘reaction’.
- Attributes:
- optionsBasicReactionHousekeeping.Options
The options for the BasicReactionHousekeeping Gear.
- class Options[source]¶
The options for the BasicReactionHousekeeping 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.
- energy_tolerance¶
- float
The energy tolerance for the transition state energy deduplication.
-
model:
Model¶ - db.Model
The model the Gear is working with.
- rmsd_tolerance¶
- float
The RMSD tolerance for the transition state RMSD deduplication.
- unset_collections()¶
Duplicate name to HoldCollections method to be triggered in pickling process, so infinite _parent loops are avoided.
- Return type:
- use_energy_deduplication¶
- bool
If true duplicated elementary steps are not sorted into reactions. The criterion is that the total electronic energy of the transition state (if available) has to be within the threshold limits of energy_tolerance. This criterion can be combined with other selection criteria. Steps are only eliminated if all selection criteria signal identical steps.
- use_rmsd_deduplication¶
- bool
If true duplicated elementary steps are not sorted into reactions. The criterion is that the RMSD of the transition state coordinates (if available) have to be within the threshold limits of rmsd_tolerance. This criterion can be combined with other selection criteria. Steps are only eliminated if all selection criteria signal identical steps. Note that this deduplication strategy may fail to eliminate elementary steps if the atom ordering the transition state differs.
- use_structure_deduplication¶
- bool
If true duplicated elementary steps are not sorted into reactions. The criterion is that all structures on the lhs of the elementary step have to be identical. This criterion can be combined with other selection criteria. Steps are only eliminated if all selection criteria signal identical steps.
-
cycle_time: