"""
Classifies: CHEBI:33856 aromatic amino acid
"""
"""
Classifies: CHEBI:33857 aromatic amino acid
"""
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors

def is_aromatic_amino_acid(smiles: str):
    """
    Determines if a molecule is an aromatic amino acid based on its SMILES string.
    An aromatic amino acid is defined as an amino acid whose structure includes an aromatic ring.

    Args:
        smiles (str): SMILES string of the molecule

    Returns:
        bool: True if molecule is an aromatic amino acid, False otherwise
        str: Reason for classification
    """
    
    # Parse SMILES
    mol = Chem.MolFromSmiles(smiles)
    if mol is None:
        return False, "Invalid SMILES string"

    # Check for amino acid pattern: at least one amino group (NH2, NH, or N) and one carboxyl group (COOH, COOR, or CONH)
    amino_pattern = Chem.MolFromSmarts("[NH2,NH,N]")
    carboxyl_pattern = Chem.MolFromSmarts("C(=O)[OH,OR,NH2,NH]")
    
    if not mol.HasSubstructMatch(amino_pattern):
        return False, "No amino group found"
    if not mol.HasSubstructMatch(carboxyl_pattern):
        return False, "No carboxyl group found"

    # Check for aromatic rings
    aromatic_rings = mol.GetSubstructMatches(Chem.MolFromSmarts("[a]"))
    if not aromatic_rings:
        return False, "No aromatic ring found"

    # Ensure the aromatic ring is part of the amino acid structure
    for ring in aromatic_rings:
        for atom_idx in ring:
            atom = mol.GetAtomWithIdx(atom_idx)
            # Check if the aromatic ring is connected to the amino acid backbone or side chain
            for neighbor in atom.GetNeighbors():
                if neighbor.GetSymbol() == "C":
                    # Check if the carbon is part of the amino acid structure
                    for neighbor_neighbor in neighbor.GetNeighbors():
                        if neighbor_neighbor.GetSymbol() in ["N", "O"]:
                            return True, "Contains amino acid functional groups and an aromatic ring integrated into the structure"

    return False, "Aromatic ring not integrated into amino acid structure"


__metadata__ = {
    'chemical_class': {
        'id': 'CHEBI:33857',
        'name': 'aromatic amino acid',
        'definition': 'An amino acid whose structure includes an aromatic ring.',
        'parents': ['CHEBI:33704', 'CHEBI:33857']
    },
    'config': {
        'llm_model_name': 'lbl/claude-sonnet',
        'f1_threshold': 0.8,
        'max_attempts': 5,
        'max_positive_instances': None,
        'max_positive_to_test': None,
        'max_negative_to_test': None,
        'max_positive_in_prompt': 50,
        'max_negative_in_prompt': 20,
        'max_instances_in_prompt': 100,
        'test_proportion': 0.1
    },
    'message': None,
    'attempt': 0,
    'success': True,
    'best': True,
    'error': '',
    'stdout': None,
    'num_true_positives': 150,
    'num_false_positives': 4,
    'num_true_negatives': 182407,
    'num_false_negatives': 23,
    'num_negatives': None,
    'precision': 0.974025974025974,
    'recall': 0.8670520231213873,
    'f1': 0.9174311926605504,
    'accuracy': 0.9998521228585199
}


__metadata__ = {   'chemical_class': {   'id': 'CHEBI:33856',
                          'name': 'aromatic amino acid',
                          'definition': 'An amino acid whose structure '
                                        'includes an aromatic ring.',
                          'parents': ['CHEBI:33659', 'CHEBI:33709'],
                          'xrefs': [   'KEGG:C01021',
                                       'Wikipedia:Aromatic_amino_acid'],
                          'all_positive_examples': []},
    'config': None,
    'message': '\n'
               'Attempt failed: F1 score of 0.5703422053231938 is too low.\n'
               'Outcomes:\n'
               '------\n'
               '\n'
               'True positives: SMILES: O=C(O)C1=C(NCCO)C=CC=C1 NAME: '
               '2-((2-hydroxyethyl)amino)benzoic acid REASON: CORRECT Contains '
               'amino acid functional groups and an aromatic ring integrated '
               'into the backbone\n'
               ' * SMILES: CN[C@H](CC1=CC=C(O)C(O)=C1)C(O)=O NAME: '
               'N-methyl-D-dopa REASON: CORRECT Contains amino acid functional '
               'groups and an aromatic ring integrated into the backbone\n'
               ' * SMILES: C1(C(O)=O)=CC=C(N)C=C1 NAME: 4-aminobenzoic acid '
               'REASON: CORRECT Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               ' * SMILES: CC(=O)Nc1c(I)cc(I)c(C(O)=O)c1I NAME: Acetrizoic '
               'acid REASON: CORRECT Contains amino acid functional groups and '
               'an aromatic ring integrated into the backbone\n'
               ' * SMILES: Nc1ccc(cn1)C(O)=O NAME: 6-aminonicotinic acid '
               'REASON: CORRECT Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               ' * SMILES: C1=CC=CC2=C1NC=3[C@@H](C=CCC3N2)C(=O)O NAME: '
               '(1R)-1,4,5,10-tetrahydrophenazine-1-carboxylic acid REASON: '
               'CORRECT Contains amino acid functional groups and an aromatic '
               'ring integrated into the backbone\n'
               ' * SMILES: O=C(O)C1=C(N[C@@H](C(=O)C)C)C=CC=C1 NAME: '
               '(R)-2-(1-methyl-2-oxopropylamino)-benzoic acid REASON: CORRECT '
               'Contains amino acid functional groups and an aromatic ring '
               'integrated into the backbone\n'
               ' * SMILES: N[C@H](CC1=CC=C(CC(O)=O)C=C1)C(O)=O NAME: '
               '4-(carboxymethyl)-D-phenylalanine REASON: CORRECT Contains '
               'amino acid functional groups and an aromatic ring integrated '
               'into the backbone\n'
               ' * SMILES: N[C@@H](Cc1cc(Cl)c(O)c(Cl)c1)C(O)=O NAME: '
               '3,5-dichloro-L-tyrosine REASON: CORRECT Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: C1=CC=CC2=C1N[C@]3(C(=CC=CC3=N2)C(=O)O)[H] NAME: '
               '(10aS)-10,10a-dihydrophenazine-1-carboxylic acid REASON: '
               'CORRECT Contains amino acid functional groups and an aromatic '
               'ring integrated into the backbone\n'
               ' * SMILES: Cc1c(Cl)cccc1Nc1ccccc1C(O)=O NAME: tolfenamic acid '
               'REASON: CORRECT Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               ' * SMILES: CCCCNc1ccc(cc1)C(O)=O NAME: 4-(butylamino)benzoic '
               'acid REASON: CORRECT Contains amino acid functional groups and '
               'an aromatic ring integrated into the backbone\n'
               ' * SMILES: '
               'O=C1C=2O[C@@H]3O[C@H](C)[C@@H]([C@@H]([C@@]3(C2C(=O)C=C4C1=C5C(=C(N(C6=C(C(=O)O)C=CC=C6)C(=C5)C)CCC)C4=O)O)O)O '
               'NAME: Rubrulone B REASON: CORRECT Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: Cc1ccc(Cl)c(Nc2ccccc2C(O)=O)c1Cl NAME: meclofenamic '
               'acid REASON: CORRECT Contains amino acid functional groups and '
               'an aromatic ring integrated into the backbone\n'
               ' * SMILES: COc1cccc(C(O)=O)c1N NAME: 3-methoxyanthranilic acid '
               'REASON: CORRECT Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               ' * SMILES: NC(CC1=CC=C(C=C1)N=[N+]=[N-])C(O)=O NAME: '
               '4-azidophenylalanine REASON: CORRECT Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: Cc1cccc(Nc2ccccc2C(O)=O)c1C NAME: mefenamic acid '
               'REASON: CORRECT Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               ' * SMILES: N[C@H](Cc1c[nH]cn1)C(O)=O NAME: D-histidine REASON: '
               'CORRECT Contains amino acid functional groups and an aromatic '
               'ring integrated into the backbone\n'
               ' * SMILES: Nc1ccccc1C(O)=O NAME: anthranilic acid REASON: '
               'CORRECT Contains amino acid functional groups and an aromatic '
               'ring integrated into the backbone\n'
               ' * SMILES: N(C1=C(C(O)=O)C=CC(=C1)Cl)C2=C(C(O)=O)C=CC=C2 NAME: '
               'lobenzarit REASON: CORRECT Contains amino acid functional '
               'groups and an aromatic ring integrated into the backbone\n'
               ' * SMILES: Nc1ccc(C(O)=O)c(Cl)c1 NAME: 4-amino-2-chlorobenzoic '
               'acid REASON: CORRECT Contains amino acid functional groups and '
               'an aromatic ring integrated into the backbone\n'
               ' * SMILES: CNc1ccccc1C(O)=O NAME: N-methylanthranilic acid '
               'REASON: CORRECT Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               ' * SMILES: NC(Cc1ccc(O)c(O)c1)C(O)=O NAME: dopa REASON: '
               'CORRECT Contains amino acid functional groups and an aromatic '
               'ring integrated into the backbone\n'
               ' * SMILES: '
               'CNc1ccc2oc(C[C@@H]3OC4(CC[C@@H]3C)O[C@H](C(C)C(=O)c3ccc[nH]3)[C@H](C)C[C@H]4C)nc2c1C(O)=O '
               'NAME: Calcimycin REASON: CORRECT Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: N[C@@H](Cc1c[nH]cn1)C(O)=O NAME: L-histidine '
               'REASON: CORRECT Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               'False positives: SMILES: '
               'O=C(O)CC=1N=C2[C@H](NC(=O)C)[C@H](O)[C@@H]([C@H](N2C1)CO)O '
               'NAME: Nagstatin REASON: WRONGLY CLASSIFIED Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: '
               'ClC1=C(OC)C=CC(=C1)C[C@H](NC(=O)/C=C/C[C@H](O)[C@@H]([C@@H](O)[C@@H](O)C2=CC=CC=C2)C)C(=O)O '
               'NAME: Cryptophycin G REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: '
               'O=C1O[C@H]([C@H](CCCC)C)CC(=O)N[C@@H](CC2=CC=CC=C2)C(N[C@H](C(N[C@@H]1[C@@H](CC)C)=O)C)=O '
               'NAME: Beauveriolide III REASON: WRONGLY CLASSIFIED Contains '
               'amino acid functional groups and an aromatic ring integrated '
               'into the backbone\n'
               ' * SMILES: C1CCC(C(C1)C(=O)NC2=CC3=C(C=C2)OCCO3)C(=O)O NAME: '
               '2-[(2,3-dihydro-1,4-benzodioxin-6-ylamino)-oxomethyl]-1-cyclohexanecarboxylic '
               'acid REASON: WRONGLY CLASSIFIED Contains amino acid functional '
               'groups and an aromatic ring integrated into the backbone\n'
               ' * SMILES: '
               'O1C(C(CCCCC(O)C)C)CC(O)C(C(=O)N[C@@H](C(=O)N2[C@@](CCC2)(C1=O)[H])CC3=CC=CC=C3)C '
               'NAME: Acremolide A REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: '
               'OC(=O)\\C=C/C(O)=O.[H][C@@]12CN(C)C[C@@]1([H])c1cc(Cl)ccc1Oc1ccccc21 '
               'NAME: (R,R)-asenapine maleate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid functional groups and an aromatic ring '
               'integrated into the backbone\n'
               ' * SMILES: '
               'O=C1N(C=CC(N1)=O)[C@@H]2O[C@H]([C@@H](O[C@@H]3O[C@H](CN)[C@H]([C@H]3OC)O)[C@H](NCCCNC(=O)[C@@H](NC(=O)[C@@H](NC(=O)N[C@H](C(=O)O)C(C)C)[C@H]4NC(=NCC4)N)[C@@H](OC(=O)CCCCCC(C)C)C(C)C)C(=O)O)[C@H]([C@H]2O)O '
               'NAME: Muraymycin B4 REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: '
               'BrC1=C(O)C=CC(=C1)C[C@H]2N(C(=O)[C@@H](NC(=O)C[C@H](O)CC=C(CC[C@@H](OC(\\C(\\NC2=O)=C(/OC)\\C3=CC=CC=C3)=O)C)C)C)C '
               'NAME: Miuraenamide F REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: '
               'OC[C@H]1O[C@@H](Oc2cc3C[C@H](Nc3cc2O)C(O)=O)[C@H](O[C@@H]2O[C@@H]([C@@H](O)[C@H](O)[C@H]2O)C(O)=O)[C@@H](O)[C@@H]1O '
               'NAME: cyclo-Dopa-glucuronylglucoside REASON: WRONGLY '
               'CLASSIFIED Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               ' * SMILES: '
               'COc1cc2C(=O)O[C@@H]3[C@@H](O)C=C4CCN(C)[C@H]4[C@@H]3c2cc1O '
               'NAME: 9-O-Demethyl-2alpha-hydroxyhomolycorine REASON: WRONGLY '
               'CLASSIFIED Contains amino acid functional groups and an '
               'aromatic ring integrated into the backbone\n'
               ' * SMILES: '
               'O=C(N[C@@H](CC(=O)N)C(O)=O)[C@@H](NC(=O)CN)CC=1C=2C(NC1)=CC=CC2 '
               'NAME: Gly-Trp-Asn REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: CC(C(=O)O)OC1=CC=C(C=C1)C(=O)NC2=CC(=C(C=C2)OC)Cl '
               'NAME: '
               '2-[4-[(3-chloro-4-methoxyanilino)-oxomethyl]phenoxy]propanoic '
               'acid REASON: WRONGLY CLASSIFIED Contains amino acid functional '
               'groups and an aromatic ring integrated into the backbone\n'
               ' * SMILES: '
               'S(CC[C@H](N)C(=O)NCC(=O)N[C@@H](CC1=CC=C(O)C=C1)C(O)=O)C NAME: '
               'Met-Gly-Tyr REASON: WRONGLY CLASSIFIED Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: '
               'O=C1NC(=NC=2NCC(N(C21)C=O)CNC3=CC=C(C=C3)C(=O)N[C@H](CCC(O)=O)C(O)=O)N '
               'NAME: Pteroyl-D-glutamic acid REASON: WRONGLY CLASSIFIED '
               'Contains amino acid functional groups and an aromatic ring '
               'integrated into the backbone\n'
               ' * SMILES: '
               'O=C1O[C@H]([C@@H](NC(=O)[C@H](NC(=O)[C@@H](NC(=O)[C@H]2N(C(=O)[C@@H](NC(=O)C=3NC=CC3)[C@H](O)C)CCC2)C(C)C)C(C)C)C(=O)N[C@H]([C@@H](O)C)C(N[C@H](C(N[C@H]1CC4=CC=C(O)C=C4)=O)CC5=CC=C(O)C=C5)=O)C '
               'NAME: Endopyrrole C REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: O1C(N2C=3N=C(N=C(OCC(O)=O)C3N=C2)N)CC(O)C1CO NAME: '
               'O6-CM-dG REASON: WRONGLY CLASSIFIED Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: '
               'O=C(N[C@@H](CCC(=O)N)C(O)=O)[C@@H](NC(=O)[C@@H](N)C)CC=1C=2C(NC1)=CC=CC2 '
               'NAME: Ala-Trp-Gln REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: '
               'O=C(N1[C@@H](CCC1)C(=O)N[C@@H](CC(O)=O)C(O)=O)[C@@H](N)CC2=CC=C(O)C=C2 '
               'NAME: Tyr-Pro-Asp REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: '
               'O=C(NCC(=O)N[C@@H](CCC(O)=O)C(O)=O)[C@@H](N)CC1=CC=CC=C1 NAME: '
               'Phe-Gly-Glu REASON: WRONGLY CLASSIFIED Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: C1(=CNC2=C1C=C(C=C2)Cl)C[C@@H](C(=O)O)N NAME: '
               '5-chloro-L-tryptophan REASON: WRONGLY CLASSIFIED Contains '
               'amino acid functional groups and an aromatic ring integrated '
               'into the backbone\n'
               ' * SMILES: '
               'O=C1OC(CC(=O)OC(C=CC(C(=CCC=2C1=C(O)C=CC2)C)O)C)C/C=C/NC(=O)/C=C\\C=N/OC '
               'NAME: YM-75518 REASON: WRONGLY CLASSIFIED Contains amino acid '
               'functional groups and an aromatic ring integrated into the '
               'backbone\n'
               ' * SMILES: '
               '[H][C@]12SCC(C[N+]3(C)CCCC3)=C(N1C(=O)[C@H]2NC(=O)C(=N/OC)\\c1csc(N)n1)C(O)=O '
               'NAME: cefepime(1+) REASON: WRONGLY CLASSIFIED Contains amino '
               'acid functional groups and an aromatic ring integrated into '
               'the backbone\n'
               ' * SMILES: '
               'OC(=O)C(F)(F)F.[H][C@@]12CC[C@H](O)[C@H](O)[C@]11CCN2Cc2cc3OCOc3cc12 '
               'NAME: 4a-dehydroxycrinamabine Trifluoroacetic acid REASON: '
               'WRONGLY CLASSIFIED Contains amino acid functional groups and '
               'an aromatic ring integrated into the backbone\n'
               ' * SMILES: '
               'O=C1N(C(C(=O)NC(C(=O)NCCCCC(C(NC(C(NC1CCC2=CC=CC=C2)=O)C(CC)C)=O)NC(=O)NC(C(=O)O)CCCCN)CC3=CC=CC=C3)CC(=O)N)C '
               'NAME: Anabaenopeptin 850 REASON: WRONGLY CLASSIFIED Contains '
               'amino acid functional groups and an aromatic ring integrated '
               'into the backbone\n'
               ' * SMILES: C[C@](N)(CC1=CN=CN1)C(O)=O NAME: '
               'alpha-methyl-L-histidine REASON: WRONGLY CLASSIFIED Contains '
               'amino acid functional groups and an aromatic ring integrated '
               'into the backbone\n'
               'False negatives: SMILES: C1=COC(=C1)NC(=O)C2=CC=C(C=C2)N NAME: '
               '4-amino-N-(2-furanyl)benzamide REASON: MISSED No carboxyl '
               'group found\n'
               ' * SMILES: CNC(=O)c1ccccc1N NAME: N-Methylanthranilamide '
               'REASON: MISSED No carboxyl group found\n'
               ' * SMILES: '
               'CC1=NC(=CC=C1)NC(=O)C2=CC(=C(C=C2)N(C)C3CCCCC3)[N+](=O)[O-] '
               'NAME: '
               '4-[cyclohexyl(methyl)amino]-N-(6-methyl-2-pyridinyl)-3-nitrobenzamide '
               'REASON: MISSED No carboxyl group found\n'
               ' * SMILES: '
               'O(N1C(=O)CCC1=O)C(=O)C2=C(C(=C(N(C([2H])([2H])[2H])C([2H])([2H])[2H])C(=C2[2H])[2H])[2H])[2H] '
               'NAME: DMABA-d10 NHS ester REASON: MISSED No carboxyl group '
               'found\n'
               ' * SMILES: CC(=NNC(=O)C1=CC=CC=C1N)CC(=O)NC2=CC3=C(C=C2)OCO3 '
               'NAME: '
               '2-amino-N-[[4-(1,3-benzodioxol-5-ylamino)-4-oxobutan-2-ylidene]amino]benzamide '
               'REASON: MISSED No carboxyl group found\n'
               ' * SMILES: CC1=C(C=CC(=C1)I)NC2=C(C(=C(C=C2C(=O)NOCC3CC3)F)F)F '
               'NAME: '
               'N-(cyclopropylmethoxy)-3,4,5-trifluoro-2-(4-iodo-2-methylanilino)benzamide '
               'REASON: MISSED No carboxyl group found\n'
               ' * SMILES: '
               'O(N1C(=O)CCC1=O)C(=O)C2=C(C(=C(N(C)C)C(=C2[2H])[2H])[2H])[2H] '
               'NAME: DMABA-d4 NHS ester REASON: MISSED No carboxyl group '
               'found\n'
               ' * SMILES: O=C(ON1C(CC(OC(=O)C)CC1(C)C)(C)C)C2=CC=C(N)C=C2 '
               'NAME: Benzoic acid, 4-amino-, '
               '4-acetoxy-2,2,6,6-tetramethyl-1-piperidinyl ester REASON: '
               'MISSED No carboxyl group found\n'
               ' * SMILES: CC(=NNC(=O)C1=CC=C(C=C1)N(C)C)C2=CC(=CC=C2)OC NAME: '
               '4-(dimethylamino)-N-[1-(3-methoxyphenyl)ethylideneamino]benzamide '
               'REASON: MISSED No carboxyl group found\n'
               ' * SMILES: C1=CC(=C(C=C1I)F)NC2=C(C=CC(=C2F)F)C(=O)NOCC(CO)O '
               'NAME: '
               'N-(2,3-dihydroxypropoxy)-3,4-difluoro-2-(2-fluoro-4-iodoanilino)benzamide '
               'REASON: MISSED No carboxyl group 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': 'OC[C@H]1O[C@H](C[C@@H]1O)N1C=NC2=C1N=CNC[C@H]2O',
                                     'name': 'pentostatin',
                                     'reason': 'No carboxyl group found'},
                                 {   'smiles': 'O1C(CCC=2C1=CC(OC3OC(C(O)C(O)C3O)C(O)=O)=C(C2OC)C=4C(=O)C=5C(OC4)=CC(O)=C(O)C5)(C)C',
                                     'name': '6-{[6-(6,7-dihydroxy-4-oxo-4H-chromen-3-yl)-5-methoxy-2,2-dimethyl-3,4-dihydro-2H-1-benzopyran-7-yl]oxy}-3,4,5-trihydroxyoxane-2-carboxylic '
                                             'acid',
                                     'reason': 'No amino group found'},
                                 {   'smiles': 'O=C1O[C@@H]([C@@H](OC)C=CC=C(C[C@@H](C)[C@@H]([C@@H]([C@@H]([C@@H](C=C(C=C1OC)C)C)O)C)O)C)[C@H]([C@@H](O)[C@@H]([C@@]2(O[C@H](/C=C/C)[C@@H](C)[C@@H](C2)OC3OC(C(O)C(C3)O)C)O)C)C',
                                     'name': 'Concanamycin D',
                                     'reason': 'No amino group found'},
                                 {   'smiles': 'O1[C@@H](O[C@@H]2[C@@H](O)[C@@H](O[C@@H]([C@@H]2O)CO)O[C@H]3[C@H](O)[C@@H](NC(=O)C)C(O[C@@H]3CO)O)[C@H](NC(=O)C)[C@@H](O[C@@H]4O[C@@H]([C@H](O)[C@H](O)[C@H]4O)CO)[C@H](O[C@@H]5O[C@H]([C@@H](O)[C@@H](O)[C@@H]5O)C)[C@H]1CO',
                                     'name': 'N-[(3R,4R,5S,6R)-5-[(2S,3R,4S,5S,6R)-4-[(2S,3R,4R,5S,6R)-3-Acetamido-6-(hydroxymethyl)-4-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-5-[(2S,3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxyoxan-2-yl]oxy-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2,4-dihydroxy-6-(hydroxymethyl)oxan-3-yl]acetamide',
                                     'reason': 'No aromatic ring found'},
                                 {   'smiles': 'O=C(O)[C@]1([C@H]2[C@@](OC=3C=C4C5=C(C=CC=C5)NC4=CC3CC2)(CC[C@@H]1O)C)C',
                                     'name': 'Oxiamycin',
                                     'reason': 'No amino group found'},
                                 {   'smiles': 'C1CCC(C1)CC#CC2=CC=C(C=C2)[C@@H]3[C@@H]4CN(CC(=O)N4[C@@H]3CO)C(=O)C5=CC=C(C=C5)F',
                                     'name': '(6R,7R,8S)-7-[4-(3-cyclopentylprop-1-ynyl)phenyl]-4-[(4-fluorophenyl)-oxomethyl]-8-(hydroxymethyl)-1,4-diazabicyclo[4.2.0]octan-2-one',
                                     'reason': 'No carboxyl group found'},
                                 {   'smiles': 'S(=O)(C(SSCCC)CC)CCC',
                                     'name': 'Propyl 1-(propylsulfinyl)propyl '
                                             'disulfide',
                                     'reason': 'No amino group found'},
                                 {   'smiles': 'ClC=1C(=O)[C@@H]([C@@](O)(C/C=C\\CCCCC)C1)C[C@H](OC(=O)C)[C@@H](OC(=O)C)CCCC(OC)=O',
                                     'name': 'punaglandin 6',
                                     'reason': 'No amino group found'},
                                 {   'smiles': 'CCCCCCCCCCCCCCCCCCCCCCCC[C@H](O)C(=O)N[C@@H](COP(O)(=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@H]1O)[C@H](O)[C@@H](O)CCCCCCCCCCCCCC',
                                     'name': 'Ins-1-P-Cer(t18:0/2-OH-26:0)',
                                     'reason': 'No aromatic ring found'},
                                 {   'smiles': 'CCC(C)(C)C(=O)OC1CC(C=C2C1[C@H]([C@H](C=C2)C)CC[C@@H]3CC(CC(=O)O3)O)C',
                                     'name': '2,2-dimethylbutanoic acid '
                                             '[(7S,8S)-8-[2-[(2R)-4-hydroxy-6-oxo-2-oxanyl]ethyl]-3,7-dimethyl-1,2,3,7,8,8a-hexahydronaphthalen-1-yl] '
                                             'ester',
                                     'reason': 'No amino group found'}],
    'sample_false_negatives': [   {   'smiles': 'N[C@H](CC1=CC=C(CC(O)=O)C=C1)C(O)=O',
                                      'name': '4-(carboxymethyl)-D-phenylalanine',
                                      'reason': 'Aromatic ring not integrated '
                                                'into amino acid structure'},
                                  {   'smiles': 'O(N1C(=O)CCC1=O)C(=O)C2=C(C(=C(N(C([2H])([2H])[2H])C([2H])([2H])[2H])C(=C2[2H])[2H])[2H])[2H]',
                                      'name': 'DMABA-d10 NHS ester',
                                      'reason': 'No carboxyl group found'},
                                  {   'smiles': 'OC(=O)[C@@H](N)CC1=C(C(=C(C(=C1[2H])[2H])[2H])[2H])[2H]',
                                      'name': 'L-phenylalanine-d5',
                                      'reason': 'Aromatic ring not integrated '
                                                'into amino acid structure'},
                                  {   'smiles': 'N[C@H](Cc1ccccc1)C(O)=O',
                                      'name': 'D-phenylalanine',
                                      'reason': 'Aromatic ring not integrated '
                                                'into amino acid structure'},
                                  {   'smiles': 'NC(CC1=CC=C(CC(O)=O)C=C1)C(O)=O',
                                      'name': '4-(carboxymethyl)phenylalanine',
                                      'reason': 'Aromatic ring not integrated '
                                                'into amino acid structure'},
                                  {   'smiles': 'N[C@@H](CC1=CC=C(CC(O)=O)C=C1)C(O)=O',
                                      'name': '4-(carboxymethyl)-L-phenylalanine',
                                      'reason': 'Aromatic ring not integrated '
                                                'into amino acid structure'},
                                  {   'smiles': 'NC(Cc1ccccc1)C(O)=O',
                                      'name': 'phenylalanine',
                                      'reason': 'Aromatic ring not integrated '
                                                'into amino acid structure'},
                                  {   'smiles': 'O(N1C(=O)CCC1=O)C(=O)C2=C(C(=C(N(C)C)C(=C2[2H])[2H])[2H])[2H]',
                                      'name': 'DMABA-d4 NHS ester',
                                      'reason': 'No carboxyl group found'},
                                  {   'smiles': 'O=C(ON1C(CC(OC(=O)C)CC1(C)C)(C)C)C2=CC=C(N)C=C2',
                                      'name': 'Benzoic acid, 4-amino-, '
                                              '4-acetoxy-2,2,6,6-tetramethyl-1-piperidinyl '
                                              'ester',
                                      'reason': 'No carboxyl group found'},
                                  {   'smiles': 'C=1C(=C(C=C(Cl)C1)NC2=CC=CC=C2C(=O)[O-])C([O-])=O.[Na+].[Na+]',
                                      'name': 'Lobenzarit disodium',
                                      'reason': 'No carboxyl group found'}],
    'attempt': 2,
    'reasoning': 'The previous code had a few issues that led to false '
                 'positives and false negatives:\n'
                 '\n'
                 '1. **False Positives**: The code incorrectly classified some '
                 'molecules as aromatic amino acids because it only checked '
                 'for the presence of an aromatic ring and amino/carboxyl '
                 'groups, without ensuring that the aromatic ring was properly '
                 'integrated into the amino acid backbone. This led to '
                 'molecules with separate aromatic rings and amino acid groups '
                 'being misclassified.\n'
                 '\n'
                 '2. **False Negatives**: The code missed some aromatic amino '
                 'acids because it required the aromatic ring to be directly '
                 'connected to the amino acid backbone. This excluded cases '
                 'where the aromatic ring was part of a side chain or where '
                 'the carboxyl group was not in the expected form (e.g., '
                 'esters or amides).\n'
                 '\n'
                 '### Improvements:\n'
                 '1. **Aromatic Ring Integration**: We need to ensure that the '
                 'aromatic ring is part of the amino acid structure, either in '
                 'the backbone or in a side chain.\n'
                 '2. **Carboxyl Group Flexibility**: We should allow for more '
                 'flexible carboxyl group patterns, including esters and '
                 'amides, which are common in amino acids.\n'
                 '3. **Amino Group Flexibility**: Similarly, we should allow '
                 'for more flexible amino group patterns, including secondary '
                 'and tertiary amines.\n'
                 '\n'
                 'Here is the improved code:',
    'success': True,
    'best': True,
    'error': '',
    'stdout': None,
    'num_true_positives': 76,
    'num_false_positives': 100,
    'num_true_negatives': 434,
    'num_false_negatives': 12,
    'num_negatives': None,
    'precision': 0.4318181818181818,
    'recall': 0.8636363636363636,
    'f1': 0.5757575757575758,
    'accuracy': 0.819935691318328,
    'negative_predictive_value': 0.9730941704035875}