Routes

rxnutils contains routines to analyse synthesis routes. There are a number of readers that can be used to read routes from a number of formats, and there are routines to score the different routes.

Reading

The simplest route format supported is a text file, where each reaction is written as a reaction SMILES in a line. Routes are separated by new-line

For instance:

CC(C)N.Clc1cccc(Nc2ccoc2)n1>>CC(C)Nc1cccc(Nc2ccoc2)n1
Brc1ccoc1.Nc1cccc(Cl)n1>>Clc1cccc(Nc2ccoc2)n1

Nc1cccc(NC(C)C)n1.Brc1ccoc1>>CC(C)Nc1cccc(Nc2ccoc2)n1
CC(C)N.Nc1cccc(Cl)n1>>Nc1cccc(NC(C)C)n1

If this is saved to routes.txt, these can be read into route objects with

from rxnutils.routes.readers import read_reaction_lists
routes = read_reaction_lists("reactions.txt")

If you have an environment with rxnmapper installed and the NextMove software namerxn in your PATH then you can add atom-mapping and reaction classes to these routes with

# This can be set on the command-line as well
import os
os.environ["RXNMAPPER_ENV_PATH"] = "/home/username/miniconda/envs/rxnmapper/"

for route in routes:
    route.assign_atom_mapping(only_rxnmapper=True)
routes[1].remap(routes[0])

The last line of code also make sure that the second route shares mapping with the first route.

Other readers are available

• read_aizynthcli_dataframe - for reading routes from aizynthcli output dataframe

• read_reactions_dataframe - for reading routes stored as reactions in a dataframe

For instance, to read routes from a dataframe with reactions. You can do something like what follows. The dataframe has column reaction_smiles that holds the reaction SMILES, and the individual routes are identified by a target_smiles and route_id column. The dataframe also has a column classification, holding the NextMove classification. The dataframe is called data.

from rxnutils.routes.readers import read_reactions_dataframe
routes = read_reactions_dataframe(
    data,
    "reaction_smiles",
    group_by=["target_smiles", "route_id"],
    metadata_columns=["classification"]
)