Skip to content

AM3DB Architecture

The following describes how the database is designed and the attributes of reaction objects stored in it.

The AMReaction object stores the following arguments in the database:

  • label (str): The reaction label.
  • multiplicity (int): The spin multipicity of the reaction potential energy surface.
  • charge (int): The reaction potential energy surface net electric charge.
  • r_adjacency_lists (List[List[str]]): all representative resonance structures per reactant.
  • p_adjacency_lists (List[List[str]]): all representative resonance structures per product.
  • r_xyz (List[dict]): Entries represent cartesian coordinates per reactant.
  • p_xyz (List[dict]): Entries represent cartesian coordinates per products.
  • r_rmg_label Dict[str, int]: The reactant atom indices identified by the RMG family recipe.
  • r_rmg_label Dict[str, int]: The product atom indices identified by the RMG family recipe.
  • atom_maps (List[List[int]]): A comprehensive list of possible atom-maps.
  • clustering (List[List[int]]): Storing the indices of redundant atom-maps.
  • approved_by (List[str]): variable that represents name of person that approved reaction modeling.
  • rejected_by (List[str]): variable that represents name of person that rejected reaction modeling.
  • rejected_reasons (List[str]): variable that represents a comment explaining the reason for rejecting the reaction modeling.