Reaction rules

The reaction rules extraction protocol is flexible and can adjust the specificity of extracted reaction rules.

Download example configuration

• GitHub: configs/rules_extraction.yaml

Quickstart (CLI)

Extract rules using the repository configuration in configs/rules_extraction.yaml:

synplan rule_extracting \
  --config configs/rules_extraction.yaml \
  --input reaction_data_filtered.smi \
  --output reaction_rules.tsv

Configuration file

min_popularity: 3
environment_atom_count: 1
multicenter_rules: True
include_rings: False
include_func_groups: False
func_groups_list: []
keep_leaving_groups: False
keep_incoming_groups: False
keep_reagents: False
atom_info_retention:
  reaction_center:
    neighbors: True
    implicit_hydrogens: False
    ring_sizes: False
  environment:
    neighbors: False
    implicit_hydrogens: False
    ring_sizes: False

Configuration parameters

Parameter	Description
environment_atom_count	Determines the number of layers of atoms around the reaction center to be included in the reaction rule. A value of 0 includes only the reaction center, 1 includes the first surrounding layer, and so on.
min_popularity	Determines the minimum number of occurrences of a reaction rule in the reaction dataset.
multicenter_rules	Determines whether a single rule is extracted for all centers in multicenter reactions (True) or if separate rules are generated for each center (False).
include_rings	Includes ring structures in the reaction rules connected to the reaction center atoms if set to True.
include_func_groups	If True, specific functional groups are included in the reaction rule in addition to the reaction center and its environment.
func_groups_list	Specifies a list of functional groups to be included when include_func_groups is True.
keep_leaving_groups	Keeps the leaving groups in the extracted reaction rule when set to True.
keep_incoming_groups	Retains incoming groups in the extracted reaction rule if set to True.
keep_reagents	Includes reagents in the extracted reaction rule when True.
atom_info_retention	Dictates the level of detail retained about atoms in the reaction center and their environment.