Reaction filtration#

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

Download example configuration#

Quickstart (CLI)#

Run reaction filtration using the repository configuration in configs/reactions_filtration.yaml:

synplan reaction_filtering \
  --config configs/reactions_filtration.yaml \
  --input reaction_data_standardized.smi \
  --output reaction_data_filtered.smi

Configuration file

multi_center_config:
no_reaction_config:
dynamic_bonds_config:
  min_bonds_number: 1
  max_bonds_number: 6
small_molecules_config:
  mol_max_size: 6

Configuration parameters

Reaction filter

Description

compete_products_config

Checks if there are compete reactions

dynamic_bonds_config

Checks if there is an unacceptable number of dynamic bonds in CGR

small_molecules_config

Checks if there are only small molecules in the reaction

cgr_connected_components_config

Checks if CGR contains unrelated components (without reagents)

rings_change_config

Checks if there is changing rings number in the reaction

strange_carbons_config

Checks if there are ‘strange’ carbons in the reaction

no_reaction_config

Checks if there is no reaction in the provided reaction container

multi_center_config

Checks if there is a multicenter reaction

wrong_ch_breaking_config

Checks for incorrect C-C bond formation from breaking a C-H bond

cc_sp3_breaking_config

Checks if there is C(sp3)-C bond breaking

cc_ring_breaking_config

Checks if a reaction involves ring C-C bond breaking

Note

  1. If the reaction filter name is listed in the configuration file, it means that this filter will be activated.

  2. The order of filters listed in the configuration file defines the order of their application to the input reactions.

  3. Some filters require additional parameters (e.g. small_molecules_config).

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