<filename>reinvent_scoring/scoring/diversity_filters/lib_invent/identical_murcko_scaffold.py
from copy import deepcopy
from typing import List

import numpy as np
from rdkit import Chem
from rdkit.Chem.Scaffolds import MurckoScaffold
# from reinvent_scoring.scoring.score_summary import FinalSummary

from reinvent_scoring.scoring.diversity_filters.lib_invent.base_diversity_filter import BaseDiversityFilter
from reinvent_scoring.scoring.diversity_filters.lib_invent.diversity_filter_parameters import DiversityFilterParameters


class IdenticalMurckoScaffold(BaseDiversityFilter):
    """Penalizes compounds based on exact Murcko Scaffolds previously generated."""

    def __init__(self, parameters: DiversityFilterParameters):
        super().__init__(parameters)

    def update_score(self, score_summary, sampled_sequences: List, step=0) -> np.array:
        score_summary = deepcopy(score_summary)
        scores = score_summary.total_score
        smiles = score_summary.scored_smiles

        for i in score_summary.valid_idxs:
            smile = self._chemistry.convert_to_rdkit_smiles(smiles[i])
            scaffold = self._calculate_scaffold(smile)
            scores[i] = 0 if self._smiles_exists(smile) else scores[i]

            if scores[i] >= self.parameters.minscore:
                self._add_to_memory(i, scores[i], smile, scaffold, score_summary.scaffold_log, step)
                scores[i] = self._penalize_score(scaffold, scores[i])

        return scores

    #TODO: move this to reinvent chemistry
    def _calculate_scaffold(self, smile):
        mol = Chem.MolFromSmiles(smile)
        if mol:
            try:
                scaffold = MurckoScaffold.GetScaffoldForMol(mol)
                scaffold_smiles = Chem.MolToSmiles(scaffold, isomericSmiles=False)
            except ValueError:
                scaffold_smiles = ''
        else:
            scaffold_smiles = ''
        return scaffold_smiles

<filename>reinvent_scoring/scoring/diversity_filters/lib_invent/identical_murcko_scaffold.py
from copy import deepcopy
from typing import List

import numpy as np
from rdkit import Chem
from rdkit.Chem.Scaffolds import MurckoScaffold
# from reinvent_scoring.scoring.score_summary import FinalSummary

from reinvent_scoring.scoring.diversity_filters.lib_invent.base_diversity_filter import BaseDiversityFilter
from reinvent_scoring.scoring.diversity_filters.lib_invent.diversity_filter_parameters import DiversityFilterParameters


class IdenticalMurckoScaffold(BaseDiversityFilter):
    """Penalizes compounds based on exact Murcko Scaffolds previously generated."""

    def __init__(self, parameters: DiversityFilterParameters):
        super().__init__(parameters)

    def update_score(self, score_summary, sampled_sequences: List, step=0) -> np.array:
        score_summary = deepcopy(score_summary)
        scores = score_summary.total_score
        smiles = score_summary.scored_smiles

        for i in score_summary.valid_idxs:
            smile = self._chemistry.convert_to_rdkit_smiles(smiles[i])
            scaffold = self._calculate_scaffold(smile)
            scores[i] = 0 if self._smiles_exists(smile) else scores[i]

            if scores[i] >= self.parameters.minscore:
                self._add_to_memory(i, scores[i], smile, scaffold, score_summary.scaffold_log, step)
                scores[i] = self._penalize_score(scaffold, scores[i])

        return scores

    #TODO: move this to reinvent chemistry
    def _calculate_scaffold(self, smile):
        mol = Chem.MolFromSmiles(smile)
        if mol:
            try:
                scaffold = MurckoScaffold.GetScaffoldForMol(mol)
                scaffold_smiles = Chem.MolToSmiles(scaffold, isomericSmiles=False)
            except ValueError:
                scaffold_smiles = ''
        else:
            scaffold_smiles = ''
        return scaffold_smiles

# from reinvent_scoring.scoring.score_summary import FinalSummary Penalizes compounds based on exact Murcko Scaffolds previously generated. #TODO: move this to reinvent chemistry