Plugins

This folder contains some features for aizynthfinder that does not yet fit into the main codebase. It could be experimental features, or features that require the user to install some additional third-party dependencies.

For the expansion models, you generally need to add the plugins folder to the PYTHONPATH, e.g.

export PYTHONPATH=~/aizynthfinder/plugins/

where the aizynthfinder repository is in the home folder

Chemformer expansion model

An expansion model using a REST API for the Chemformer model is supplied in the expansion_strategies module.

To use it, you first need to install the chemformer package and launch the REST API service that comes with it.

To use the expansion model in aizynthfinder you can use a config-file containing these lines

expansion:
    chemformer:
        type: expansion_strategies.ChemformerBasedExpansionStrategy
        url: http://localhost:8000/chemformer-api/predict
search:
    algorithm_config:
        immediate_instantiation: [chemformer]
    time_limit: 300

The time_limit is a recommandation for allowing the more expensive expansion model to finish a sufficient number of retrosynthesis iterations.

You would have to change localhost:8000 to the name and port of the machine hosting the REST service.

You can then use the config-file with either aizynthcli or the Jupyter notebook interface.

ModelZoo expansion model

An expansion model using the ModelZoo feature is supplied in the expansion_strategies module. This is an adoption of the code from this repo: https://github.com/AlanHassen/modelsmatter that were used in the publications Models Matter: The Impact of Single-Step Models on Synthesis Prediction and Mind the Retrosynthesis Gap: Bridging the divide between Single-step and Multi-step Retrosynthesis Prediction.

To use it, you first need to install the modelsmatter_modelzoo package from https://github.com/PTorrenPeraire/modelsmatter_modelzoo and set up the ssbenchmark environment.

Ensure that the external_models sub-package contains the models required. If it does not, you will need to manually clone the required model repositories within external_models.

To use the expansion model in aizynthfinder, you can specify it in the config-file under expansion. Here is an example setting to use the expansion model with chemformer as the external model:

expansion:
    chemformer:
        type: expansion_strategies.ModelZooExpansionStrategy:
        module_path: /path_to_folder_containing_cloned_repository/modelsmatter_modelzoo/external_models/modelsmatter_chemformer_hpc/
        use_gpu: False
        params:
            module_path: /path_to_model_file/chemformer_backward.ckpt
            vocab_path: /path_to_vocab_file/bart_vocab_downstream.txt
search:
    algorithm_config:
        immediate_instantiation: [chemformer]
    time_limit: 300