Source code for simba.core.data.ground_truth

import numpy as np
from myopic_mces.myopic_mces import MCES as MCES2

from simba.core.chemistry.edit_distance import edit_distance
from simba.core.chemistry.tanimoto import Tanimoto




class GroundTruth:


    def compute_edit_distance(spectra0, spectra1, max_value=5):
        ground_truth_ed = np.zeros((len(spectra0), len(spectra1)))
        smiles0 = [s.params["smiles"] for s in spectra0]
        smiles1 = [s.params["smiles"] for s in spectra1]

        for i, s0 in enumerate(smiles0):
            for j, s1 in enumerate(smiles1):
                ground_truth_ed[i, j] = edit_distance.get_edit_distance_from_smiles(
                    s0, s1, return_nans=True
                )

        ground_truth_ed[np.isnan(ground_truth_ed)] = max_value
        ground_truth_ed[ground_truth_ed >= max_value] = max_value
        return ground_truth_ed




    def compute_mces(spectra0, spectra1, threshold=20):
        ground_truth_mces = np.zeros((len(spectra0), len(spectra1)))
        smiles0 = [s.params["smiles"] for s in spectra0]
        smiles1 = [s.params["smiles"] for s in spectra1]

        for j, s1 in enumerate(smiles1):
            for i, s0 in enumerate(smiles0):
                # df_results = MCES.compute_mces_list_smiles([s0] * len(smiles1), smiles1)
                # mces_result = df_results["mces"]

                result = MCES2(
                    s0,
                    s1,
                    threshold=threshold,
                    i=0,
                    # solver='CPLEX_CMD',       # or another fast solver you have installed
                    solver="PULP_CBC_CMD",
                    solver_options={
                        "threads": 1,
                        "msg": False,
                        "timeLimit": 10,  # Stop CBC after 1 seconds
                    },
                    no_ilp_threshold=False,  # allow the ILP to stop early once the threshold is exceeded
                    always_stronger_bound=False,  # use dynamic bounding for speed
                    catch_errors=False,  # typically raise exceptions if something goes wrong
                )
                distance = result[1]
                time_taken = result[2]
                exact_answer = result[3]
                mces_result = distance

                ground_truth_mces[i, j] = mces_result

        return ground_truth_mces




    def compute_tanimoto(spectra0, spectra1):
        ground_tanimoto = np.zeros((len(spectra0), len(spectra1)))
        smiles0 = [s.params["smiles"] for s in spectra0]
        smiles1 = [s.params["smiles"] for s in spectra1]

        for i, s0 in enumerate(smiles0):
            for j, s1 in enumerate(smiles1):
                ground_tanimoto[i, j] = Tanimoto.compute_tanimoto_from_smiles(
                    s0,
                    s1,
                )

        return ground_tanimoto