yjy616 / rxn4chemistry

Python wrapper for the IBM RXN for Chemistry API

Python wrapper for the IBM RXN for Chemistry API

A python wrapper to access the API of the IBM RXN for Chemistry website.

Install

From PYPI:

pip install rxn4chemistry

Or directly from the repo:

pip install git+https://github.com/rxn4chemistry/rxn4chemistry.git

Usage

By default, the wrapper connects to the https://rxn.res.ibm.com server. This can be overriden by setting an environment variable. To set a different url, simply do:

export RXN4CHEMISTRY_BASE_URL="https://some.other.rxn.server"

The base url can be directly set when instantiating the RXN4ChemistryWrapper (this will overwrite the environment variable):

api_key = 'API_KEY'
from rxn4chemistry import RXN4ChemistryWrapper

rxn4chemistry_wrapper = RXN4ChemistryWrapper(api_key=api_key, base_url='https://some.other.rxn.server')
# or set it afterwards
# rxn4chemistry_wrapper = RXN4ChemistryWrapper(api_key=api_key)
# rxn4chemistry_wrapper.set_base_url('https://some.other.rxn.server')

Create a project

Get your API key from here and build the wrapper:

api_key = 'API_KEY'
from rxn4chemistry import RXN4ChemistryWrapper

rxn4chemistry_wrapper = RXN4ChemistryWrapper(api_key=api_key)
# NOTE: you can create a project or set an esiting one using:
# rxn4chemistry_wrapper.set_project('PROJECT_ID')
rxn4chemistry_wrapper.create_project('test_wrapper')
print(rxn4chemistry_wrapper.project_id)

Reaction prediction

Running a reaction prediction is as simple as:

response = rxn4chemistry_wrapper.predict_reaction(
    'BrBr.c1ccc2cc3ccccc3cc2c1'
)
results = rxn4chemistry_wrapper.get_predict_reaction_results(
    response['prediction_id']
)
print(results['response']['payload']['attempts'][0]['smiles'])

Extracting actions from a paragraph describing a recipe

Extract the actions from a recipe:

results = rxn4chemistry_wrapper.paragraph_to_actions(
    'To a stirred solution of '
    '7-(difluoromethylsulfonyl)-4-fluoro-indan-1-one (110 mg, '
    '0.42 mmol) in methanol (4 mL) was added sodium borohydride '
    '(24 mg, 0.62 mmol). The reaction mixture was stirred at '
    'ambient temperature for 1 hour.'
)
print(results['actions'])

Retrosynthesis prediction

Predict a retrosynthetic pathway given a product:

response = rxn4chemistry_wrapper.predict_automatic_retrosynthesis(
    'Brc1c2ccccc2c(Br)c2ccccc12'
)
results = rxn4chemistry_wrapper.get_predict_automatic_retrosynthesis_results(
    response['prediction_id']
)
print(results['status'])
# NOTE: upon 'SUCCESS' you can inspect the predicted retrosynthetic paths.
print(results['retrosynthetic_paths'][0])

See here for a more comprehensive example.

Create a synthesis and start it on Robot (or Simulator)

Create a synthesis from a retrosynthesis sequence:

# Each retrosynthetic path predicted has a unique sequence_id that can
# be used to create a new synthesis
response = rxn4chemistry_wrapper.create_synthesis_from_sequence(
    sequence_id=results['retrosynthetic_paths'][0]['sequenceId']
)
print(response['synthesis_id'])

# get the entire list of actions for the entire synthesis, as well as a tree representation
synthesis_tree, ordered_tree_nodes, ordered_list_of_actions = rxn4chemistry_wrapper.get_synthesis_plan(
    synthesis_id=response['synthesis_id']
)
for action in ordered_list_of_actions:
    print(action)

synthesis_status_result = rxn4chemistry_wrapper.start_synthesis(
    synthesis_id=response['synthesis_id']
)
print(synthesis_status_result['status'])

synthesis_status_result = rxn4chemistry_wrapper.get_synthesis_status(
    synthesis_id=response['synthesis_id']
)
print(synthesis_status_result['status'])

# NOTE: upon 'SUCCESS' you can download any analysis reports that are available as pdf
# The pdf contents are returned as text
analysis_actions = rxn4chemistry_wrapper.get_synthesis_actions_with_spectrometer_pdf(
    synthesis_id=response['synthesis_id']
)
pdfs = []
for action in analysis_actions:
    pdfs.append(
        rxn4chemistry_wrapper.get_synthesis_analysis_report_pdf(
            **action
        )
    )
print(pdfs[0])

Forward prediction in batch

It is possible to run a batch of forward reaction predictions without linking them to a project:

response = rxn4chemistry_wrapper.predict_reaction_batch(precursors_list=['BrBr.c1ccc2cc3ccccc3cc2c1', 'Cl.c1ccc2cc3ccccc3cc2c1']*5)
# wait for the predictions to complete
time.sleep(2)
print(rxn4chemistry_wrapper.get_predict_reaction_batch_results(response["task_id"]))

NOTE: the results for batch prediction are not stored permanently in our databases, so we strongly recommend to save them since they will expire.

Examples

To learn more see the examples.

Documentation

The documentation is hosted here using GitHub pages.