Reaction standardization#

SynPlanner includes a variety of reaction standardizers. The list and order of application of standardizers can be specified in the configuration file.

Download example configuration#

GitHub: configs/reactions_standardization.yaml

Quickstart (CLI)#

Run reaction standardization using the repository configuration in configs/reactions_standardization.yaml:

synplan reaction_standardizing \
  --config configs/reactions_standardization.yaml \
  --input reaction_data_original.smi \
  --output reaction_data_standardized.smi

Configuration file

functional_groups_config:
kekule_form_config:
check_valence_config:
implicify_hydrogens_config:
check_isotopes_config:
aromatic_form_config:
mapping_fix_config:
unchanged_parts_config:
deduplicate: true

Configuration parameters

Reaction standardizer	Description
functional_groups_config	Standardization of functional groups
kekule_form_config	Transform molecules to Kekule form when possible
check_valence_config	Check atom valences
implicify_hydrogens_config	Remove hydrogen atoms
check_isotopes_config	Check and clean isotope atoms when possible
split_ions_config	Split ions in reaction when possible
aromatic_form_config	Transform molecules to aromatic form when possible
mapping_fix_config	Fix atom-to-atom mapping in reaction when needed and possible
unchanged_parts_config	Remove unchanged parts in reaction
small_molecules_config	Remove small molecule from reaction
remove_reagents_config	Remove reagents from reaction
rebalance_reaction_config	Rebalance reaction
deduplicate	Deduplicate reactions by CGR hash (default: true)

Note

If the reaction standardizer name is listed in the configuration file (see above), it means that this standardizer will be applied.
The order of standardizers listed in the configuration file defines the order of their application to the input reactions.