SMPrecursorPredictor

A ML pipeline for the prediction of specialised metabolites starting substances.

Installation

Manually

1. Clone the repository and move into the directory:

git clone
cd SMPrecursorPredictor

2. Create a conda environment and activate it:

conda create -n sm_precursor_predictor python=3.10
conda activate sm_precursor_predictor

3. Install the dependencies:

pip install -r requirements.txt

4. Install the package:

pip install .

Pypi

1. Create a conda environment and activate it:

conda create -n sm_precursor_predictor python=3.10
conda activate sm_precursor_predictor
pip install SMPrecursorPrediction

Making predictions

Models available:

• Layered FP + Low Variance FS + Ridge Classifier
• Morgan FP + Ridge Classifier

from sm_precursor_predictor import predict_precursors
precursors = predict_precursors(
            ["[H][C@]89CN(CCc1c([nH]c2ccccc12)[C@@](C(=O)OC)(c3cc4c(cc3OC)N(C)[C@@]5([H])[C@@]"
             "(O)(C(=O)OC)[C@H](OC(C)=O)[C@]7(CC)C=CCN6CC[C@]45[C@@]67[H])C8)C[C@](O)(CC)C9",
             "COC1=C(C=CC(=C1)C2=C(C(=O)C3=C(C=C(C=C3O2)O)O)O[C@H]4[C@@H]([C@H]([C@H]([C@H](O4)CO)O)O)O)O"],
             model="Layered FP + Low Variance FS + Ridge Classifier")
print(precursors)

or

read a csv file with a column of SMILES and a column of IDs and save the predictions in a csv file:

from sm_precursor_predictor import predict_from_csv
predictions = predict_from_csv("path_to_csv", 
                               smiles_field="SMILES", 
                               ids_field="ID",
                               model="Layered FP + Low Variance FS + Ridge Classifier")
predictions.to_csv("path_to_save_predictions.csv")

Making and explaining predictions

This is only possible with one model: Morgan FP + Ridge Classifier.

Example with linalool:

from sm_precursor_predictor import get_prediction_and_explanation

prediction, images, plots = get_prediction_and_explanation(smiles="CC(=CCCC(C)(C=C)O)C", threshold=0.20)

prediction

['Geranyl diphosphate']

images[0]