arc.rmgdb

A module for working with the RMG database.

arc.rmgdb.clean_rmg_database_object(db: RMGDatabase) → RMGDatabase[source]

clears the global RMG database object.

Parameters:

db (RMGDatabase) – the database object

Returns:

the database object

Return type:

RMGDatabase

arc.rmgdb.determine_family(reaction: ARCReaction, db: Optional[RMGDatabase] = None)[source]

Determine the RMG reaction family for an ARC reaction. A wrapper for ARCReaction.determine_family(). This wrapper is useful because it makes a new instance of the rmgdb if needed.

Parameters:

  • reaction ('ARCReaction') – An ARCReaction object instance.

  • db (RMGDatabase, optional) – The RMG database instance.

arc.rmgdb.determine_reaction_family(rmgdb: RMGDatabase, reaction: Reaction, save_order: bool = True) → Tuple[Optional[KineticsFamily], bool][source]

Determine the RMG kinetic family for a given ARCReaction object instance. Returns None if no family found or more than one family found.

Parameters:

  • rmgdb (RMGDatabase) – The RMG database instance.

  • reaction (Reaction) – The RMG Reaction object.

  • save_order (bool, optional) – Whether to retain atomic order of the RMG reaction object instance.

Returns: Tuple[Optional[KineticsFamily], bool]

  • The corresponding RMG reaction’s family. None if no family was found or more than one family were found.

  • Whether the family is its own reverse. True if it is.

arc.rmgdb.determine_rmg_kinetics(rmgdb: RMGDatabase, reaction: Reaction, dh_rxn298: float) → List[Reaction][source]

Determine kinetics for reaction (an RMG Reaction object) from RMG’s database, if possible. Assigns a list of all matching entries from both libraries and families.

Parameters:

  • rmgdb (RMGDatabase) – The RMG database instance.

  • reaction (Reaction) – The RMG Reaction object.

  • dh_rxn298 (float) – The heat of reaction at 298 K in J/mol.

Returns: List[Reaction]

All matching RMG reactions (both libraries and families) with a populated .kinetics attribute.

arc.rmgdb.get_family(rmgdb: RMGDatabase, label: Optional[str]) → Optional[KineticsFamily][source]

Get a KineticsFamily object instance corresponding to the input family label.

Parameters:

  • rmgdb (RMGDatabase) – The RMG database instance.

  • label (str) – The label of the desired family.

Returns:

The desired family object instance.

Return type:

Optional[‘KineticsFamily’]

arc.rmgdb.load_families_only(rmgdb: RMGDatabase, kinetics_families: Union[str, list] = 'all')[source]

A helper function for loading kinetic families from RMG’s database.

Parameters:

  • rmgdb (RMGDatabase) – The RMG database instance.

  • kinetics_families (Union[str, list], optional) – Specific kinetics families to load.

arc.rmgdb.load_rmg_database(rmgdb: RMGDatabase, thermo_libraries: Optional[list] = None, reaction_libraries: Optional[list] = None, kinetics_families: Union[str, list] = 'default', load_thermo_libs: bool = True, load_kinetic_libs: bool = True, include_nist: bool = False) → None[source]

A helper function for loading the RMG database.

Parameters:

  • rmgdb (RMGDatabase) – The RMG database instance.

  • thermo_libraries (list, optional) – Specific thermodynamic libraries to load (None will load all).

  • reaction_libraries (list, optional) – Specific kinetics libraries to load (None will load all).

  • kinetics_families (list, str, optional) – Specific kinetics families to load (either a list or ‘default’, ‘all’, ‘none’)

  • load_thermo_libs (bool, optional) – Whether to load thermodynamic libraries, True to load.

  • load_kinetic_libs (bool, optional) – Whether to load kinetics libraries, True to load.

  • include_nist (bool, optional) – Whether to include the NIST kinetics libraries, True to include, default is False

arc.rmgdb.loop_families(rmgdb: RMGDatabase, reaction: Reaction) → List[Tuple[KineticsFamily, list]][source]

Loop through kinetic families and return a list of tuples of (family, degenerate_reactions) corresponding to reaction.

Parameters:

  • rmgdb (RMGDatabase) – The RMG database instance.

  • reaction (Reaction) – The RMG Reaction object instance.

Returns: List[Tuple[‘KineticsFamily’, list]]

Entries are tuples of a corresponding RMG KineticsFamily instance and a list of degenerate reactions.

arc.rmgdb.make_rmg_database_object() → RMGDatabase[source]

Make a clean RMGDatabase object.

Returns: RMGDatabase

A clean RMG database object.