"""
Classifies: CHEBI:26255 prenylquinone
"""
"""
Classifies: prenylquinone
A quinone substituted by a polyprenyl-derived side-chain.
"""
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdMolDescriptors

def is_prenylquinone(smiles: str):
    """
    Determines if a molecule is a prenylquinone based on its SMILES string.
    
    Args:
        smiles (str): SMILES string of the molecule
        
    Returns:
        bool: True if molecule is a prenylquinone, False otherwise
        str: Reason for classification
    """
    # Parse SMILES
    mol = Chem.MolFromSmiles(smiles)
    if mol is None:
        return False, "Invalid SMILES string"

    # Expanded quinone patterns to catch more variants
    quinone_patterns = [
        "C1(=O)C=CC(=O)C=C1",  # para-quinone
        "C1(=O)C(=O)C=CC=C1",   # ortho-quinone
        "O=C1C(=C)C(=O)C=CC1",  # alternative quinone
        "O=C1C=CC(=O)C(*)=C1",  # substituted quinone
        "O=C1C(*)=C(*)C(=O)C(*)=C1*",  # heavily substituted quinone
        "O=C1C(O)=C(*)C(=O)C(*)=C1*",  # hydroxyquinone
        "[#6]1(=O)[#6]=,:[#6][#6](=O)[#6]=,:[#6]1",  # generic quinone
        "O=C1C(=C)C(=O)C(*)C(*)=C1*"  # complex quinone
    ]
    
    has_quinone = False
    for pattern in quinone_patterns:
        if mol.HasSubstructMatch(Chem.MolFromSmarts(pattern)):
            has_quinone = True
            break
            
    if not has_quinone:
        return False, "No quinone core structure found"

    # Improved prenyl/polyprenyl patterns
    prenyl_patterns = [
        "CC(C)=CCC",  # basic prenyl
        "C/C=C(/C)CC",  # trans prenyl
        "CC(C)=CCCC(C)=C",  # diprenyl
        "[CH3][C]=[C][CH2][CH2]",  # isoprene unit
        "C/C=C(/C)CC/C=C(/C)",  # extended prenyl
        "[CH3][C](=[CH2])[CH2][CH2]",  # terminal prenyl
        "CC(C)=CCCC(=C)C",  # branched prenyl
    ]
    
    prenyl_count = 0
    for pattern in prenyl_patterns:
        matches = mol.GetSubstructMatches(Chem.MolFromSmarts(pattern))
        prenyl_count += len(matches)

    if prenyl_count == 0:
        return False, "No prenyl/polyprenyl chain found"

    # Calculate molecular descriptors
    mol_wt = rdMolDescriptors.CalcExactMolWt(mol)
    n_rotatable = rdMolDescriptors.CalcNumRotatableBonds(mol)
    
    # Count carbons and oxygens
    c_count = sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 6)
    o_count = sum(1 for atom in mol.GetAtoms() if atom.GetAtomicNum() == 8)

    # Specific subclass patterns
    menaquinone_pattern = Chem.MolFromSmarts("[#6]1=CC=CC2=C1C(=O)C=C(CC=C)C2=O")
    ubiquinone_pattern = Chem.MolFromSmarts("COC1=C(OC)C(=O)C=C(CC=C)C1=O")
    plastoquinone_pattern = Chem.MolFromSmarts("CC1=C(C)C(=O)C=C(CC=C)C1=O")

    features = []
    if mol.HasSubstructMatch(menaquinone_pattern):
        features.append("menaquinone-like")
    if mol.HasSubstructMatch(ubiquinone_pattern):
        features.append("ubiquinone-like")
    if mol.HasSubstructMatch(plastoquinone_pattern):
        features.append("plastoquinone-like")
    
    # Check for characteristic substitution
    if mol.HasSubstructMatch(Chem.MolFromSmarts("COC")):
        features.append("methoxy-substituted")
    if n_rotatable >= 7:
        features.append("long prenyl chain")

    # Classification criteria
    is_prenylquinone = False
    reason = "Missing characteristic prenylquinone features"

    # Main classification logic
    if has_quinone and prenyl_count >= 1:
        if len(features) >= 1:
            is_prenylquinone = True
            reason = f"Prenylquinone with features: {', '.join(features)}"
        elif n_rotatable >= 5 and c_count >= 15 and o_count >= 2:
            # Check for minimum size and composition
            if mol_wt >= 200:  # Minimum weight for a basic prenylquinone
                is_prenylquinone = True
                reason = "Basic prenylquinone structure with prenyl chain"

    return is_prenylquinone, reason


__metadata__ = {   'chemical_class': {   'id': 'CHEBI:26255',
                          'name': 'prenylquinone',
                          'definition': 'A quinone substituted by a '
                                        'polyprenyl-derived side-chain. '
                                        'Prenylquinones occur in all living '
                                        'cells. Due to their amphiphilic '
                                        'character, they are mainly located in '
                                        'biological membranes where they '
                                        'function as electron and proton '
                                        'carriers in the photosynthetic and '
                                        'respiratory electron transport '
                                        'chains. Some prenylquinones also '
                                        'perform more specialised roles sucy '
                                        'as antioxidants and enzyme cofactors. '
                                        'Prenylquinones are classified '
                                        'according to ring structure: the main '
                                        'classes are menaquinones, '
                                        'phylloquinones, ubiquinones and '
                                        'plastoquinones.',
                          'parents': ['CHEBI:25830'],
                          'xrefs': [   'PMID:19928587',
                                       'PMID:21777468',
                                       'PMID:21844348',
                                       'PMID:22371323',
                                       'PMID:3985624'],
                          'all_positive_examples': []},
    'config': None,
    'message': '\n'
               'Attempt failed: F1 score of 0.38738738738738737 is too low.\n'
               'Outcomes:\n'
               '------\n'
               '\n'
               'True positives: SMILES: '
               'COC1=CC(=O)C(C)=C(C\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CCC=C(C)C)C1=O '
               'NAME: 3-methyl-6-methoxy-2-octaprenyl-1,4-benzoquinone REASON: '
               'CORRECT Prenylquinone with features: methoxy-substituted, long '
               'prenyl chain\n'
               ' * SMILES: '
               'COC1=C(OC)C(=O)C(C\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CCC=C(C)C)=C(C)C1=O '
               'NAME: ubiquinone-9 REASON: CORRECT Prenylquinone with '
               'features: ubiquinone-like, methoxy-substituted, long prenyl '
               'chain\n'
               ' * SMILES: O(C=1C(=O)C([C@@H](C2=CC=C(O)C=C2)C=C)=CC(=O)C1OC)C '
               "NAME: (R)-4'-Hydroxy-3,4-dimethoxydalbergione REASON: CORRECT "
               'Prenylquinone with features: methoxy-substituted\n'
               ' * SMILES: CC(C)=CCC1=CC(=O)C(C)=C(C)C1=O NAME: '
               'Plastoquinone-1 REASON: CORRECT Prenylquinone with features: '
               'plastoquinone-like\n'
               ' * SMILES: COC1=C(OC)C(=O)C(CC=C(C)C)=C(C)C1=O NAME: '
               'ubiquinone-1 REASON: CORRECT Prenylquinone with features: '
               'ubiquinone-like, methoxy-substituted\n'
               ' * SMILES: '
               'C1(=C(C(C(=C(C1=O)OC)[O-])=O)C)C/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CCC=C(C)C)\\C)\\C)\\C)\\C)\\C)\\C '
               'NAME: 3-demethyl-ubiquinone-7(1-) REASON: CORRECT '
               'Prenylquinone with features: methoxy-substituted, long prenyl '
               'chain\n'
               ' * SMILES: '
               'O=C1C(OC)=C(OC)C(=O)C(=C1C/C=C(/CC/C=C(/C[C@H](O)C=C(C)C)\\C)\\C)C '
               'NAME: Antroquinonol N REASON: CORRECT Prenylquinone with '
               'features: ubiquinone-like, methoxy-substituted, long prenyl '
               'chain\n'
               ' * SMILES: '
               'COC1=CC(=O)C=C(C\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CCC=C(C)C)C1=O '
               'NAME: 2-hexaprenyl-6-methoxy-1,4-benzoquinone REASON: CORRECT '
               'Prenylquinone with features: methoxy-substituted, long prenyl '
               'chain\n'
               ' * SMILES: '
               'C1(C(=C(C(C(=C1OC)O)=O)C)C/C=C(\\C)/CC/C=C(\\C)/CC/C=C(\\C)/CC/C=C(\\C)/CC/C=C(\\C)/CC/C=C(\\C)/CC/C=C(\\C)/CC/C=C(\\C)/CC/C=C(\\C)/CCC=C(C)C)=O '
               'NAME: 3-demethylubiquinone-10 REASON: CORRECT Prenylquinone '
               'with features: methoxy-substituted, long prenyl chain\n'
               ' * SMILES: '
               'O=C1C(C\\C=C(\\CC\\C=C(\\CC\\C=C(\\CC\\C=C(\\CC\\C=C(\\CC/C=C(\\CC/C=C(/CCC=C(C)C)\\C)/C)/C)/C)/C)/C)/C)=CC(=O)C(=C1C)C '
               'NAME: Plastoquinone 8 REASON: CORRECT Prenylquinone with '
               'features: plastoquinone-like, long prenyl chain\n'
               ' * SMILES: O=C1C(OC)=C(O)C(=O)C(=C1CCOC(=O)C)C NAME: '
               'Fumiquinone A REASON: CORRECT Prenylquinone with features: '
               'methoxy-substituted\n'
               ' * SMILES: '
               'C1(=C(C(C(=C(C1=O)OC)[O-])=O)C)C/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CCC=C(C)C)\\C)\\C)\\C)\\C)\\C)\\C)\\C '
               'NAME: 3-demethylubiquinone-8(1-) REASON: CORRECT Prenylquinone '
               'with features: methoxy-substituted, long prenyl chain\n'
               ' * SMILES: O(C=1C(=O)C([C@@H](C2=CC=CC=C2)C=C)=CC(=O)C1OC)C '
               'NAME: (R)-3,4-Dimethoxydalbergione REASON: CORRECT '
               'Prenylquinone with features: methoxy-substituted\n'
               ' * SMILES: O=C1C(OC)=C(OC)C(=O)C(=C1CC=C(CCCC(=O)C)C)C NAME: '
               'Pseudoalteromone A REASON: CORRECT Prenylquinone with '
               'features: ubiquinone-like, methoxy-substituted, long prenyl '
               'chain\n'
               ' * SMILES: '
               'O(C=1C(=O)C(C\\C=C(\\CC\\C=C(\\CC\\C=C(\\CCC=C(C)C)/C)/C)/C)=C(C(=O)C1OC)C)C '
               'NAME: Coenzyme Q4 REASON: CORRECT Prenylquinone with features: '
               'ubiquinone-like, methoxy-substituted, long prenyl chain\n'
               ' * SMILES: O=C1C(OC)=C(OC)C(=O)C=C1[C@H](C(=O)C)C NAME: '
               '2,3-dimethoxy-5-(3-oxobutan-2-yl)cyclohexa-2,5-diene-1,4-dione '
               'REASON: CORRECT Prenylquinone with features: '
               'methoxy-substituted\n'
               ' * SMILES: O=C1C(OC)=CC(=O)C(=C1C)[C@]2(OC=C(C2=O)C)C NAME: '
               '(+/-)-sclerotiorumin A REASON: CORRECT Prenylquinone with '
               'features: methoxy-substituted\n'
               ' * SMILES: '
               'O(C=1C(=O)C(C\\C=C(\\CC\\C=C(\\CC\\C=C(\\CC\\C=C(\\CC\\C=C(\\CC\\C=C(\\CCC=C(C)C)/C)/C)/C)/C)/C)/C)=C(C(=O)C1)C)C '
               'NAME: '
               '2-methoxy-3-methyl-6-all-trans-heptaprenyl-1,4-benzoquinone '
               'REASON: CORRECT Prenylquinone with features: '
               'methoxy-substituted, long prenyl chain\n'
               ' * SMILES: '
               'COC1=C(OC)C(=O)C(C\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CCC=C(C)C)=C(C)C1=O '
               'NAME: ubiquinone-8 REASON: CORRECT Prenylquinone with '
               'features: ubiquinone-like, methoxy-substituted, long prenyl '
               'chain\n'
               ' * SMILES: '
               'COC1=C(OC)C(=O)C(C\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CCC=C(C)C)=C(C)C1=O '
               'NAME: ubiquinone-5 REASON: CORRECT Prenylquinone with '
               'features: ubiquinone-like, methoxy-substituted, long prenyl '
               'chain\n'
               ' * SMILES: '
               'O=C1C(=CC(=O)C=C1C)C/C=C(/CC=2O[C@@]3(OC(C)(C)[C@@H](C3)OC)[C@]4(CCC[C@]4(C2)C)C)\\C '
               'NAME: (7S,11S,12S,14R)-14-methoxyamentol quinone REASON: '
               'CORRECT Prenylquinone with features: methoxy-substituted\n'
               ' * SMILES: '
               'COC1=C(O)C(=O)C(C)=C(C\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CC\\C=C(/C)CCC=C(C)C)C1=O '
               'NAME: 3-demethylubiquinone-8 REASON: CORRECT Prenylquinone '
               'with features: methoxy-substituted, long prenyl chain\n'
               ' * SMILES: '
               '[H][C@@]12CCCC(=C)[C@@]1(C)CC[C@H](C)[C@@]2(C)CC1=C(O)C(=O)C=C(NCC(O)=O)C1=O '
               'NAME: Smenospongines B REASON: CORRECT Basic prenylquinone '
               'structure with prenyl chain\n'
               ' * SMILES: S(C=1C(=O)C(OC)=C(OC)C(C1CC(=O)OC)=O)C NAME: '
               'Coptirhoquinone A REASON: CORRECT Prenylquinone with features: '
               'methoxy-substituted\n'
               ' * SMILES: '
               'C1=C(C(C(=CC1=O)OC)=O)C/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CCC=C(C)C)\\C)\\C)\\C)\\C)\\C)\\C '
               'NAME: 2-methoxy-6-all-trans-heptaprenyl-1,4-benzoquinone '
               'REASON: CORRECT Prenylquinone with features: '
               'methoxy-substituted, long prenyl chain\n'
               'False positives: SMILES: '
               'O=C1C(OC)=CC(=O)C(=C1C)C2=C(O)C=C(O)C=C2C NAME: Peniquinone B '
               'REASON: WRONGLY CLASSIFIED Prenylquinone with features: '
               'methoxy-substituted\n'
               ' * SMILES: '
               'O=C1C(=O)C(=C(C2=C(O)C(=C(O)C=C2C)C/C=C(/CC/C=C(/CCC=C(C)C)\\C)\\C)C(=C1C/C=C(/CC/C=C(/CCC=C(C)C)\\C)\\C)O)C '
               'NAME: (+)-(R)-grifolinone C REASON: WRONGLY CLASSIFIED '
               'Prenylquinone with features: long prenyl chain\n'
               ' * SMILES: '
               '[H][C@]12CC[C@](C)(O)[C@@H](CC3=CC(=O)C=C(OC)C3=O)[C@]1(C)CC[C@@]1([H])[C@]3(C)CCC[C@]21COC3=O '
               'NAME: strongylophorine-26 REASON: WRONGLY CLASSIFIED '
               'Prenylquinone with features: methoxy-substituted\n'
               ' * SMILES: '
               'COC1=C(C)C(=O)C2=C([C-](COC(N)=O)[C@@]3(OC)[C@H]4N[C@H]4CN23)C1=O '
               'NAME: mitomycin A(1-) REASON: WRONGLY CLASSIFIED Prenylquinone '
               'with features: methoxy-substituted\n'
               ' * SMILES: O=C1C(OC)=CC(=O)C=C1[C@H](C(=O)C)C NAME: '
               'Malbranicin REASON: WRONGLY CLASSIFIED Prenylquinone with '
               'features: methoxy-substituted\n'
               ' * SMILES: CC1=C(C)C(=O)C(CCCCC#CCCCC#CCO)=C(C)C1=O NAME: '
               'docebenone REASON: WRONGLY CLASSIFIED Basic prenylquinone '
               'structure with prenyl chain\n'
               ' * SMILES: '
               'C[C@H]1CC[C@@]2(C)[C@@H](CCCC2=C)[C@]1(C)CC1=C(O)C(=O)C=C(NCCC(O)=O)C1=O '
               'NAME: smenospongines C REASON: WRONGLY CLASSIFIED Basic '
               'prenylquinone structure with prenyl chain\n'
               ' * SMILES: '
               'O=C1C(OC)=C(C(=O)C2=C1C3N4C([C@@H]5C[C@@H]6C7N(C2C4C6N5C)CCO7)OC3)C '
               'NAME: Bioxalomycin beta2 REASON: WRONGLY CLASSIFIED '
               'Prenylquinone with features: methoxy-substituted\n'
               ' * SMILES: '
               'O(C1=C(C(=C(CC/C(=C/CC=2C(=O)C=CC(=O)C2)/C)C(=C1)C)C)C)C NAME: '
               'Panicein A REASON: WRONGLY CLASSIFIED Basic prenylquinone '
               'structure with prenyl chain\n'
               ' * SMILES: '
               'O=C1C(O)=C2C(=O)C=C1[C@@H](CCCCC[C@@H](C3=C(O)C=C([C@@H](CCCCC[C@@H]2CCCC)C)C=C3O)CCCC)C '
               'NAME: Merocyclophane B REASON: WRONGLY CLASSIFIED Basic '
               'prenylquinone structure with prenyl chain\n'
               ' * SMILES: '
               'O=C1NC=2C(=O)C(=C(OC)C(C2)=O)C[C@H](C[C@H](OC)[C@H](O)[C@H](C=C([C@@H]([C@H](C[C@@H](C=C1C)O)OC)OC(=O)N)C)C)C '
               'NAME: (4S)-4,5-dihydro-4-hydroxygeldanamycin REASON: WRONGLY '
               'CLASSIFIED Prenylquinone with features: methoxy-substituted\n'
               ' * SMILES: O=C1C(O)=CC(=O)C(=C1CCCCCCCCCCCCCCC)O NAME: '
               '2,5-Dihydroxy-3-pentadecyl-1,4-benzoquinone REASON: WRONGLY '
               'CLASSIFIED Prenylquinone with features: long prenyl chain\n'
               ' * SMILES: '
               'O=C1NC2=C(O)C(=C(OC)C(C2=O)=O)C[C@H](C[C@H](OC)[C@H](O)[C@H](C=C([C@@H]([C@H](C=CC=C1C)OC)OC(=O)N)C)C)C '
               'NAME: Geldanamycin B REASON: WRONGLY CLASSIFIED Prenylquinone '
               'with features: methoxy-substituted\n'
               ' * SMILES: O=C1C(OC)=CC(=O)C(=C1CCCCCCCCCCCC/C=C/C(=O)O)O '
               'NAME: Phlebiachrysoic acid B REASON: WRONGLY CLASSIFIED '
               'Prenylquinone with features: methoxy-substituted, long prenyl '
               'chain\n'
               ' * SMILES: CCCCCCCCCCC1=C(C)C(=O)C(OC)=C(OC)C1=O NAME: '
               '6-decylubiquinone REASON: WRONGLY CLASSIFIED Prenylquinone '
               'with features: ubiquinone-like, methoxy-substituted, long '
               'prenyl chain\n'
               ' * SMILES: '
               'O=C1C(OC)=C(C(=O)C2=C1C3=C(C=C(OC/C=C(/CO)\\C)C(=C3)OC)C[C@H]2C(=C)C)C4=CC=C(O)C=C4 '
               'NAME: Arenatin C REASON: WRONGLY CLASSIFIED Prenylquinone with '
               'features: methoxy-substituted, long prenyl chain\n'
               ' * SMILES: '
               'O=C1C=2O[C@]3([C@@H]([C@@]4([C@H](O[C@@H](C(O)(C)C)CC4)CC3)C)CC2C(=O)C=C1[C@@H](C(=O)/C(=C/C)/C)C)C '
               'NAME: Cochlioquinone D REASON: WRONGLY CLASSIFIED '
               'Prenylquinone with features: methoxy-substituted\n'
               ' * SMILES: '
               'O=C1C(N)=CC(=O)C2=C1C(N3C(C#N)C4CC5C6N(C2C3C5N4C)CCO6)CO NAME: '
               'Dnacin A1 REASON: WRONGLY CLASSIFIED Prenylquinone with '
               'features: methoxy-substituted\n'
               ' * SMILES: '
               'O=C1C(N)=CC(=O)C2=C1C(N3C(O)C4CC5C6N(C2C3C5N4C)CCO6)CO NAME: '
               'Dnacin B1 REASON: WRONGLY CLASSIFIED Prenylquinone with '
               'features: methoxy-substituted\n'
               ' * SMILES: '
               'O=C1C(O)=C(C(=O)C(=C1CC=2C3=C(C=CC=C3)N(C2)C(C=C)(C)C)O)CC=4C5=C(C=CC=C5)N(C4)C(C=C)(C)C '
               'NAME: '
               '2,5-dihydroxy-3,6-bis[[1-(2-methylbut-3-en-2-yl)indol-3-yl]methyl]cyclohexa-2,5-diene-1,4-dione '
               'REASON: WRONGLY CLASSIFIED Prenylquinone with features: long '
               'prenyl chain\n'
               ' * SMILES: '
               'O(C12N(CC3N(C31)C)C4=C(C2COC(=O)N)C(=O)C(N)=C(C4=O)C)C NAME: '
               'Porfiromycine REASON: WRONGLY CLASSIFIED Prenylquinone with '
               'features: methoxy-substituted\n'
               ' * SMILES: '
               'O=C1NC=2C(=O)C(=CC(C2)=O)C[C@H](C[C@H](OC)[C@H](O)[C@H](C=C([C@@H]([C@H](C=CC=C1C)OC)OC(=O)N)C)C)C '
               'NAME: Herbimycin B REASON: WRONGLY CLASSIFIED Prenylquinone '
               'with features: methoxy-substituted\n'
               ' * SMILES: O=C1C(OC)=CC(=O)C(=C1C)C2=C(O)C=C(OC)C(=C2C)OC '
               'NAME: Peniquinone A REASON: WRONGLY CLASSIFIED Prenylquinone '
               'with features: methoxy-substituted\n'
               ' * SMILES: '
               'N[C@@H](CCCCNC1=CC(=O)C(=O)C=C1C[C@H](N)C(O)=O)C(O)=O NAME: '
               "5'-(N(6)-L-lysine)-L-tyrosylquinone REASON: WRONGLY CLASSIFIED "
               'Prenylquinone with features: long prenyl chain\n'
               ' * SMILES: '
               'O1C2=C(CC(C3=C2C(O)=C(C(=O)C3=O)CC=C(C)C)C(C)=C)C(=O)C4=C1C=C(O)C(=C4O)CC=C(C)C '
               'NAME: Artonin O REASON: WRONGLY CLASSIFIED Basic prenylquinone '
               'structure with prenyl chain\n'
               'False negatives: SMILES: '
               'Cl[C@@]12C(=O)C3=C(O)C(=C(O)C=C3C([C@@]1(OC(C)(C)[C@@H](C2)Cl)C/C=C(/CCC=C(C)C)\\C)=O)C '
               'NAME: SF2415B3 REASON: MISSED No quinone core structure found\n'
               ' * SMILES: '
               'O=C1C(O)=C(C(=O)C(=C1C=2C3=C(C=CC=C3)NC2C(C=C)(C)C)O)C=4C5=C(C=CC=C5)NC4C(C=C)(C)C '
               'NAME: Hinnuliquinone REASON: MISSED No prenyl/polyprenyl chain '
               'found\n'
               ' * SMILES: '
               'O=C1C(O)=CC(=O)C(=C1C[C@H]2C(=C)CC[C@@H]3[C@@]2(CCCC3(C)C)C)O '
               'NAME: F12509A REASON: MISSED Missing characteristic '
               'prenylquinone features\n'
               ' * SMILES: '
               'O=C1C=C(C(=O)C[C@]1(O)C[C@H]2C(=C)CC[C@@H]3[C@@]2(CCC[C@]3(CO)C)C)CO '
               'NAME: Myrothecol H REASON: MISSED No quinone core structure '
               'found\n'
               ' * SMILES: '
               'Br[C@H]1C(O[C@]2(C(=O)C=3C=C(O)C(=C(C3C([C@]2(C1)Cl)=O)O)C)C/C=C(/CCC=C(C)C)\\C)(C)C '
               'NAME: Napyradiomycin CNQ525.538 REASON: MISSED No quinone core '
               'structure found\n'
               ' * SMILES: '
               'O=C1C(O)=C(C(=O)C=C1CO)C[C@H]2C(=C)CC[C@@H]3[C@@]2(CC[C@H](C3(C)C)O)C '
               'NAME: 3alpha-hydroxytauranin REASON: MISSED Missing '
               'characteristic prenylquinone features\n'
               ' * SMILES: '
               'C1(=C(C(C=2C(=CC=CC2C1=O)C)=O)C)C/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CC/C=C(/CCC=C(C)C)\\C)\\C)\\C)\\C)\\C '
               'NAME: 8-methylmenaquinone-6 REASON: MISSED No quinone core '
               'structure found\n'
               ' * SMILES: '
               'CC(C)=CCC\\C(C)=C\\CC\\C(C)=C\\CC\\C(C)=C\\CC1=C(C)C(=O)c2ccccc2C1=O '
               'NAME: menaquinone-4 REASON: MISSED No quinone core structure '
               'found\n'
               ' * SMILES: '
               'O=C1C(OC)=C(C(=O)C(=C1C=2C3=C(C=CC=C3)NC2C(C=C)(C)C)OC)C=4C5=C(C(=CC=C5)CC=C(C)C)NC4 '
               'NAME: Asterriquinone B1 REASON: MISSED No prenyl/polyprenyl '
               'chain found\n'
               ' * SMILES: '
               'O=C1C(OC)=C(C(=O)C(=C1C=2C3=C(C=CC=C3)NC2C(C=C)(C)C)O)C=4C5=C(C=CC=C5)NC4 '
               'NAME: Truncaquinone A REASON: MISSED No prenyl/polyprenyl '
               'chain found\n'
               '------\n'
               '\n'
               'In your reasoning step, analyze the previous program and the '
               'above outcomes, hypothesizing about what went wrong, and how '
               'to improve.\n',
    'sample_true_negatives': [   {   'smiles': 'Cc1cc(C)c2Cc3c(C)cc(C)c(Cc4c(C)cc(C)c(Cc5c(C)cc(C)c(Cc1c2C)c5C)c4C)c3C',
                                     'name': '4,6,10,12,16,18,22,24,25,26,27,28-dodecamethylcalix[4]arene',
                                     'reason': 'No quinone core structure '
                                               'found'},
                                 {   'smiles': 'O=C1C(=C2C=C3[C@]([C@@H](C(C)C)[C@@H]([C@H]3O)OC(=O)C)(C)CC[C@]2(C)CC1)COC(=O)C',
                                     'name': 'Dahliane E',
                                     'reason': 'No quinone core structure '
                                               'found'},
                                 {   'smiles': 'O[C@@H]([C@H](NC(=O)[C@@H](N)CCC(O)=O)C(=O)N[C@@H](CC(C)C)C(O)=O)C',
                                     'name': 'Glu-Thr-Leu',
                                     'reason': 'No quinone core structure '
                                               'found'},
                                 {   'smiles': 'CCOc1ccc(NC(=O)C(C)O)cc1',
                                     'name': 'p-Lactophenetide',
                                     'reason': 'No quinone core structure '
                                               'found'},
                                 {   'smiles': 'O=C1NCC=2C1=C3C(N([C@@H]4O[C@H]([C@@H](O)[C@H]([C@H]4OC)O)C)C5=C3C=CC=C5)=C6NC7=C(C26)C=CC=C7',
                                     'name': "3'-epi-5'-methoxy-K252d",
                                     'reason': 'No quinone core structure '
                                               'found'},
                                 {   'smiles': 'O=C(OC1C(O)C(OC(C1O)CO)OCC2OC(OCC(OC(=O)CCCCCCCCCCCCCCC)COC(=O)CCCCCCC/C=C\\C/C=C\\C/C=C\\CC)C(O)C(C2O)O)CCCCCCCCCCCCCCC',
                                     'name': '[(2S)-2-hexadecanoyloxy-3-[(2S,3R,4S,5S,6R)-6-[[(2S,3R,4S,5S,6R)-4-hexadecanoyloxy-3,5-dihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxymethyl]-3,4,5-trihydroxy-tetrahydropyran-2-yl]oxy-propyl] '
                                             '(9E,12E,15E)-octadeca-9,12,15-trienoate',
                                     'reason': 'No quinone core structure '
                                               'found'},
                                 {   'smiles': 'O=C1C2=C(O)C=C(OC)C=C2C(=O)C3=C1[C@@H]([C@@H](O)[C@]([C@@H]3O)(O)C)C',
                                     'name': 'Altersolanol G',
                                     'reason': 'Missing characteristic '
                                               'prenylquinone features'},
                                 {   'smiles': '[H][C@]1(O[C@](O)(C[C@H](O)[C@H]1NC(=O)CO)C([O-])=O)[C@H](O)[C@H](O)CO',
                                     'name': 'N-glycoloyl-alpha-neuraminate',
                                     'reason': 'No quinone core structure '
                                               'found'},
                                 {   'smiles': 'OC(C(O)C/C=C\\C/C=C\\C/C=C\\CC)C/C=C\\C/C=C\\CCC(O)=O',
                                     'name': '10,11-DiHDPE',
                                     'reason': 'No quinone core structure '
                                               'found'},
                                 {   'smiles': '[Na+].[H][C@]12SCC(C)=C(N1C(=O)[C@H]2NC(=O)[C@H](N)c1ccccc1)C([O-])=O',
                                     'name': 'cephalexin sodium',
                                     'reason': 'No quinone core structure '
                                               'found'}],
    'sample_false_negatives': [   {   'smiles': 'Cl[C@@]12C(=O)C3=C(O)C(=C(O)C=C3C([C@@]1(OC(C)(C)[C@@H](C2)Cl)C/C=C(/CCC=C(C)C)\\C)=O)C',
                                      'name': 'SF2415B3',
                                      'reason': 'No quinone core structure '
                                                'found'},
                                  {   'smiles': 'O=C1C(O)=C(C(=O)C(=C1C=2C3=C(C=CC=C3)NC2C(C=C)(C)C)O)C=4C5=C(C=CC=C5)NC4C(C=C)(C)C',
                                      'name': 'Hinnuliquinone',
                                      'reason': 'No prenyl/polyprenyl chain '
                                                'found'},
                                  {   'smiles': 'O=C1C(O)=CC(=O)C(=C1C[C@H]2C(=C)CC[C@@H]3[C@@]2(CCCC3(C)C)C)O',
                                      'name': 'F12509A',
                                      'reason': 'Missing characteristic '
                                                'prenylquinone features'},
                                  {   'smiles': 'O=C1C=C(C(=O)C[C@]1(O)C[C@H]2C(=C)CC[C@@H]3[C@@]2(CCC[C@]3(CO)C)C)CO',
                                      'name': 'Myrothecol H',
                                      'reason': 'No quinone core structure '
                                                'found'},
                                  {   'smiles': 'Br[C@H]1C(O[C@]2(C(=O)C=3C=C(O)C(=C(C3C([C@]2(C1)Cl)=O)O)C)C/C=C(/CCC=C(C)C)\\C)(C)C',
                                      'name': 'Napyradiomycin CNQ525.538',
                                      'reason': 'No quinone core structure '
                                                'found'},
                                  {   'smiles': 'O=C1C(O)=C(C(=O)C=C1CO)C[C@H]2C(=C)CC[C@@H]3[C@@]2(CC[C@H](C3(C)C)O)C',
                                      'name': '3alpha-hydroxytauranin',
                                      'reason': 'Missing characteristic '
                                                'prenylquinone features'},
                                  {   'smiles': 'O=C1C(OC)=C(C(=O)C(=C1C=2C3=C(C=CC=C3)NC2C(C=C)(C)C)OC)C=4C5=C(C(=CC=C5)CC=C(C)C)NC4',
                                      'name': 'Asterriquinone B1',
                                      'reason': 'No prenyl/polyprenyl chain '
                                                'found'},
                                  {   'smiles': 'O=C1C(OC)=C(C(=O)C(=C1C=2C3=C(C=CC=C3)NC2C(C=C)(C)C)O)C=4C5=C(C=CC=C5)NC4',
                                      'name': 'Truncaquinone A',
                                      'reason': 'No prenyl/polyprenyl chain '
                                                'found'},
                                  {   'smiles': 'CC(C)=CCC1=CC(=O)C(=CC1=O)C(C)(C)C=C',
                                      'name': '2-(3-methylbut-2-enyl)-5-(2-methylbut-3-en-2-yl)cyclohexa-2,5-diene-1,4-dione',
                                      'reason': 'Missing characteristic '
                                                'prenylquinone features'},
                                  {   'smiles': 'Cl[C@@]12C(=O)C3=C(O)C=C(O)C=C3C([C@@]1(OC(C)(C)[C@@H](C2)Cl)CC=C(CCC=C(C=O)C)C)=O',
                                      'name': '18-oxonapyradiomycin A1',
                                      'reason': 'No quinone core structure '
                                                'found'}],
    'attempt': 2,
    'reasoning': 'Let me analyze the issues and propose improvements:\n'
                 '\n'
                 '1. False Negatives Analysis:\n'
                 '- Several compounds (SF2415B3, Napyradiomycin CNQ525.538) '
                 'were missed due to overly strict quinone pattern matching\n'
                 '- Complex structures like Hinnuliquinone were missed due to '
                 'insufficient prenyl chain detection\n'
                 "- Menaquinone-4 wasn't detected despite being a clear "
                 'prenylquinone\n'
                 '\n'
                 '2. False Positives Analysis:\n'
                 '- Many compounds with methoxy groups were wrongly '
                 'classified\n'
                 '- Simple quinones with long alkyl chains were mistaken for '
                 'prenylquinones\n'
                 '- Some complex ring systems with quinone-like patterns were '
                 'misclassified\n'
                 '\n'
                 'Key improvements needed:\n'
                 '\n'
                 '1. Quinone Pattern Recognition:\n'
                 '- Need more flexible quinone patterns that can detect '
                 'substituted and complex quinone systems\n'
                 '- Should include patterns for benzoquinones with various '
                 'substitution patterns\n'
                 '- Need to handle cases where the quinone is part of a larger '
                 'ring system\n'
                 '\n'
                 '2. Prenyl Chain Detection:\n'
                 '- Current prenyl patterns are too simple and miss complex '
                 'cases\n'
                 '- Need better distinction between simple alkyl chains and '
                 'true prenyl/polyprenyl chains\n'
                 '- Should look for characteristic isoprene units (C5H8) in '
                 'chains\n'
                 '\n'
                 '3. Additional Structural Features:\n'
                 '- Add more specific checks for characteristic substitution '
                 'patterns\n'
                 '- Implement better distinction between different '
                 'prenylquinone subclasses\n'
                 '- Add molecular weight and composition checks\n'
                 '\n'
                 "Here's my improved version:",
    'success': True,
    'best': True,
    'error': '',
    'stdout': None,
    'num_true_positives': 54,
    'num_false_positives': 100,
    'num_true_negatives': 34425,
    'num_false_negatives': 25,
    'num_negatives': None,
    'precision': 0.35064935064935066,
    'recall': 0.6835443037974683,
    'f1': 0.46351931330472096,
    'accuracy': 0.9963877008438331,
    'negative_predictive_value': 0.9992743105950653}