"""
Classifies: CHEBI:50760 N-hydroxy-alpha-amino-acid
"""
"""
Classifies: N-hydroxy-alpha-amino-acid
Definition: Any amino acid in which at least one hydrogen attached to the amino group is replaced by a hydroxy group.
"""
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdMolDescriptors

def is_N_hydroxy_alpha_amino_acid(smiles: str):
    """
    Determines if a molecule is an N-hydroxy-alpha-amino-acid based on its SMILES string.

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

    Returns:
        bool: True if molecule is an N-hydroxy-alpha-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 backbone: alpha-carbon with NH2 and COOH
    amino_acid_pattern = Chem.MolFromSmarts("[CX4H]([NH2,NH,NH1,NX3])([CX3](=[OX1])[OX2H1])")
    if not mol.HasSubstructMatch(amino_acid_pattern):
        return False, "No amino acid backbone found"

    # Check for N-hydroxy group (N with at least one OH attached)
    n_hydroxy_pattern = Chem.MolFromSmarts("[NX3][OH]")
    if not mol.HasSubstructMatch(n_hydroxy_pattern):
        return False, "No N-hydroxy group found"

    # Verify the N-hydroxy group is attached to the alpha-carbon or part of the amino acid backbone
    alpha_carbon_pattern = Chem.MolFromSmarts("[CX4H]([NX3][OH])([CX3](=[OX1])[OX2H1])")
    if not mol.HasSubstructMatch(alpha_carbon_pattern):
        # Check if the N-hydroxy group is part of the amino acid backbone but not directly attached to the alpha-carbon
        n_hydroxy_backbone_pattern = Chem.MolFromSmarts("[CX4H]([NH2,NH,NH1,NX3])([CX3](=[OX1])[OX2H1])-[NX3][OH]")
        if not mol.HasSubstructMatch(n_hydroxy_backbone_pattern):
            return False, "N-hydroxy group not attached to alpha-carbon or part of the amino acid backbone"

    return True, "Contains amino acid backbone with N-hydroxy group attached to alpha-carbon or part of the backbone"


__metadata__ = {
    'chemical_class': {
        'id': 'N-hydroxy-alpha-amino-acid',
        'name': 'N-hydroxy-alpha-amino-acid',
        'definition': 'Any amino acid in which at least one hydrogen attached to the amino group is replaced by a hydroxy group.'
    },
    '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': 30,
    'num_false_positives': 2,
    'num_true_negatives': 182407,
    'num_false_negatives': 5,
    'num_negatives': None,
    'precision': 0.9375,
    'recall': 0.8571428571428571,
    'f1': 0.8955223880597015,
    'accuracy': 0.9999615
}


__metadata__ = {   'chemical_class': {   'id': 'CHEBI:50760',
                          'name': 'N-hydroxy-alpha-amino-acid',
                          'definition': 'Any amino acid in which at least one '
                                        'hydrogen attached to the amino group '
                                        'is replaced by a hydroxy group.',
                          'parents': ['CHEBI:24662', 'CHEBI:24709'],
                          'xrefs': ['KEGG:C05710'],
                          'all_positive_examples': []},
    'config': None,
    'message': '\n'
               'Attempt failed: F1 score of 0.5176470588235293 is too low.\n'
               'Outcomes:\n'
               '------\n'
               '\n'
               'True positives: SMILES: CSCCCCC(N(O)O)C(O)=O NAME: '
               'N,N-dihydroxydihomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: CSCCCCCCC(NO)C(O)=O NAME: '
               'N-hydroxytetrahomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: ON(O)[C@@H](Cc1ccccc1)C(O)=O NAME: '
               'N,N-dihydroxy-L-phenylalanine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: O=C(O)[C@@H](NO)CCCCSC NAME: '
               'N-hydroxy-L-dihomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: CSCCCCCCCCC(NO)C(O)=O NAME: '
               'N-hydroxyhexahomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: CSCCCCCC(N(O)O)C(O)=O NAME: '
               'N,N-dihydroxytrihomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: CC(C)[C@H](NO)C(O)=O NAME: N-hydroxy-L-valine '
               'REASON: CORRECT Contains amino acid backbone with N-hydroxy '
               'group attached to alpha-carbon\n'
               ' * SMILES: ON(O)[C@@H](Cc1c[nH]c2ccccc12)C(O)=O NAME: '
               'N,N-dihydroxy-L-tryptophan REASON: CORRECT Contains amino acid '
               'backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: O=C(O)[C@@H](NO)CCCCCSC NAME: '
               'N-hydroxy-L-trihomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: ON(O)[C@@H](Cc1ccc(O)cc1)C(O)=O NAME: '
               'N,N-dihydroxy-L-tyrosine REASON: CORRECT Contains amino acid '
               'backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: CSCCCCCCC(N(O)O)C(O)=O NAME: '
               'N,N-dihydroxytetrahomomethionine REASON: CORRECT Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CSCCCCCCCC(NO)C(O)=O NAME: '
               'N-hydroxypentahomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: CSCCCCCCCC(N(O)O)C(O)=O NAME: '
               'N,N-dihydroxypentahomomethionine REASON: CORRECT Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: O=C(O)[C@@H](N(O)O)CCCCCCCSC NAME: '
               'N,N-dihydroxy-L-pentahomomethionine REASON: CORRECT Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: O=C(O)[C@@H](N(O)O)CCCCCCCCSC NAME: '
               'N,N-dihydroxy-L-hexahomomethionine REASON: CORRECT Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CC(C)[C@H](N(O)O)C(O)=O NAME: '
               'N,N-dihydroxy-L-valine REASON: CORRECT Contains amino acid '
               'backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: N1([C@@H](CCCC1)C(=O)O)O NAME: '
               'N-hydroxy-L-pipecolic acid REASON: CORRECT Contains amino acid '
               'backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: O=C(O)[C@@H](NO)CCCCCCSC NAME: '
               'N-hydroxy-L-tetrahomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: CSCCCCCC(NO)C(O)=O NAME: N-hydroxytrihomomethionine '
               'REASON: CORRECT Contains amino acid backbone with N-hydroxy '
               'group attached to alpha-carbon\n'
               ' * SMILES: CSCCCCCCCCC(N(O)O)C(O)=O NAME: '
               'N,N-dihydroxyhexahomomethionine REASON: CORRECT Contains amino '
               'acid backbone with N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: O=C(O)[C@@H](N(O)O)CCCCSC NAME: '
               'N,N-dihydroxy-L-dihomomethionine REASON: CORRECT Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CC[C@H](C)[C@H](N(O)O)C(O)=O NAME: '
               'N,N-dihydroxy-L-isoleucine REASON: CORRECT Contains amino acid '
               'backbone with N-hydroxy group attached to alpha-carbon\n'
               'False positives: SMILES: O=C([O-])[C@@H](NO)CCCCCCCCSC NAME: '
               'N-hydroxy-L-hexahomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CSCCCCCCC(N(O)O)C([O-])=O NAME: '
               'N,N-dihydroxytetrahomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CC[C@H](C)[C@H](NO)C([O-])=O NAME: '
               'N-hydroxy-L-isoleucinate REASON: WRONGLY CLASSIFIED Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: ON[C@@H](Cc1c[nH]c2ccccc12)C([O-])=O NAME: '
               'N-hydroxy-L-tryptophanate REASON: WRONGLY CLASSIFIED Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: O=C([O-])[C@@H](NO)CCCCCCCSC NAME: '
               'N-hydroxy-L-pentahomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: O=C([O-])[C@@H](NO)CCCCSC NAME: '
               'N-hydroxy-L-dihomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: O=C([O-])[C@@H](N(O)O)CCCCSC NAME: '
               'N,N-dihydroxy-L-dihomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: C([C@H](CC([O-])=O)NO)([O-])=O NAME: '
               'N-hydroxy-L-aspartate REASON: WRONGLY CLASSIFIED Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CSCCCCCC(N(O)O)C([O-])=O NAME: '
               'N,N-dihydroxytrihomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: O=C([O-])[C@@H](N(O)O)CCCCCCCCSC NAME: '
               'N,N-dihydroxy-L-hexahomomethioninate REASON: WRONGLY '
               'CLASSIFIED Contains amino acid backbone with N-hydroxy group '
               'attached to alpha-carbon\n'
               ' * SMILES: ON[C@@H](Cc1ccccc1)C([O-])=O NAME: '
               'N-hydroxy-L-phenylalaninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: ON[C@@H](Cc1ccccc1)C(O)=O NAME: '
               'N-hydroxy-L-phenylalanine REASON: WRONGLY CLASSIFIED Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CSCCCCCCCCC(N(O)O)C([O-])=O NAME: '
               'N,N-dihydroxyhexahomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: O=C([O-])[C@@H](N(O)O)CCCCCSC NAME: '
               'N,N-dihydroxy-L-trihomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CC[C@H](C)[C@H](N(O)O)C([O-])=O NAME: '
               'N,N-dihydroxy-L-isoleucinate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CSCCCCCC(NO)C([O-])=O NAME: '
               'N-hydroxytrihomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: ON[C@@H](Cc1c[nH]c2ccccc12)C(O)=O NAME: '
               'N-hydroxy-L-tryptophan REASON: WRONGLY CLASSIFIED Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CSCCCCCCC(NO)C([O-])=O NAME: '
               'N-hydroxytetrahomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: OC(=O)[C@@H](NO)CC(=O)N NAME: Hydroxyasparagine '
               'REASON: WRONGLY CLASSIFIED Contains amino acid backbone with '
               'N-hydroxy group attached to alpha-carbon\n'
               ' * SMILES: O=C([O-])[C@@H](N(O)O)CCCCCCCSC NAME: '
               'N,N-dihydroxy-L-pentahomomethioninate REASON: WRONGLY '
               'CLASSIFIED Contains amino acid backbone with N-hydroxy group '
               'attached to alpha-carbon\n'
               ' * SMILES: CSCCCCCCCC(N(O)O)C([O-])=O NAME: '
               'N,N-dihydroxypentahomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: ON(O)[C@@H](Cc1ccccc1)C([O-])=O NAME: '
               'N,N-dihydroxy-L-phenylalaninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CSCCCCCCCC(NO)C([O-])=O NAME: '
               'N-hydroxypentahomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: ON[C@@H](Cc1ccc(O)cc1)C([O-])=O NAME: '
               'N-hydroxy-L-tyrosinate REASON: WRONGLY CLASSIFIED Contains '
               'amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               ' * SMILES: CSCCCCC(NO)C([O-])=O NAME: '
               'N-hydroxydihomomethioninate REASON: WRONGLY CLASSIFIED '
               'Contains amino acid backbone with N-hydroxy group attached to '
               'alpha-carbon\n'
               'False negatives: SMILES: N[C@@H](CCCNC(=N)NO)C(O)=O NAME: '
               'N(5)-[(hydroxyamino)(imino)methyl]-L-ornithine REASON: MISSED '
               'N-hydroxy group not attached to alpha-carbon\n'
               ' * SMILES: C(\\N)(=N/O)/NCCC[C@H](N)C(=O)O NAME: '
               'N(5)-[(Z)-amino(hydroxyimino)methyl]-L-ornithine REASON: '
               'MISSED No N-hydroxy group found\n'
               ' * SMILES: C(N)(=NO)NCCC[C@H](N)C(=O)O NAME: '
               'N(5)-[amino(hydroxyimino)methyl]-L-ornithine REASON: MISSED No '
               'N-hydroxy group found\n'
               ' * SMILES: NC(CCCN\\C(N)=N/O)C(O)=O NAME: '
               'N(5)-[(Z)-amino(hydroxyimino)methyl]ornithine REASON: MISSED '
               'No N-hydroxy group found\n'
               ' * SMILES: NC(CCCN\\C(N)=N\\O)C(O)=O NAME: '
               'N(5)-[(E)-amino(hydroxyimino)methyl]ornithine REASON: MISSED '
               'No N-hydroxy group found\n'
               ' * SMILES: NC(CCCNC(=N)NO)C(O)=O NAME: '
               'N(5)-[(hydroxyamino)(imino)methyl]ornithine REASON: MISSED '
               'N-hydroxy group not attached to alpha-carbon\n'
               ' * SMILES: N[C@@H](CCCCNO)C(O)=O NAME: N(6)-hydroxy-L-lysine '
               'REASON: MISSED N-hydroxy group not attached to alpha-carbon\n'
               ' * SMILES: NC(CCCNC(N)=NO)C(O)=O NAME: '
               'N(5)-[amino(hydroxyimino)methyl]ornithine REASON: MISSED No '
               'N-hydroxy group found\n'
               ' * SMILES: ONCC(O)=O NAME: N-hydroxyglycine REASON: MISSED No '
               'amino acid backbone 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': 'Cl.C=1C=C(OC)C(OC)=C(C1CN2CCNCC2)OC.Cl',
                                     'name': 'Trimetazidine hydrochloride',
                                     'reason': 'No amino acid backbone found'},
                                 {   'smiles': 'C1[C@@]2([C@]3(C[C@@H]([C@]4([C@]([C@@]3([C@H](C[C@@]2(C[C@@H](C1)O)[H])O)[H])(CC[C@]4([H])[C@@H](CCC(NCCS([O-])(=O)=O)=O)C)[H])C)O)[H])C',
                                     'name': 'tauroursocholate',
                                     'reason': 'No amino acid backbone found'},
                                 {   'smiles': '[H]S(=O)(=O)C[C@H](N)C(O)=O',
                                     'name': 'L-cysteine-S-dioxide',
                                     'reason': 'No N-hydroxy group found'},
                                 {   'smiles': 'C[C@@H]1CN(C(=O)CCCN2C=C(CO[C@@H]1CN(C)CC3=CC=CC=C3OC)N=N2)[C@H](C)CO',
                                     'name': '(8R,9S)-6-[(2R)-1-hydroxypropan-2-yl]-9-[[(2-methoxyphenyl)methyl-methylamino]methyl]-8-methyl-10-oxa-1,6,13,14-tetrazabicyclo[10.2.1]pentadeca-12(15),13-dien-5-one',
                                     'reason': 'No amino acid backbone found'},
                                 {   'smiles': 'Cc1ccc(cc1)N=C=Nc1ccc(C)cc1',
                                     'name': '1,3-di(p-tolyl)carbodiimide',
                                     'reason': 'No amino acid backbone found'},
                                 {   'smiles': 'O=C1[C@H]([C@H]2[C@](C3=C([C@]4([C@]([C@@H]([C@@H]([C@H](O)CC(=C)C(C)C)C)CC4)(C)CC3)C)CC2)(C)CC1)C',
                                     'name': 'Gilvsin C',
                                     'reason': 'No amino acid backbone found'},
                                 {   'smiles': 'C[C@H]1CN([C@H](COC2=C(C=C(C=C2)NC(=O)NC3=CC=CC=C3)C(=O)N(C[C@H]1OC)C)C)C(=O)C',
                                     'name': '1-[(4S,7S,8S)-5-acetyl-8-methoxy-4,7,10-trimethyl-11-oxo-2-oxa-5,10-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]-3-phenylurea',
                                     'reason': 'No amino acid backbone found'},
                                 {   'smiles': 'C[C@@H]1CN([C@H](COC2=C(C=C(C=C2)NC(=O)C)C(=O)N(C[C@@H]1OC)C)C)C(=O)C3=NC=CN=C3',
                                     'name': 'N-[(4S,7R,8R)-8-methoxy-4,7,10-trimethyl-11-oxo-5-[oxo(2-pyrazinyl)methyl]-2-oxa-5,10-diazabicyclo[10.4.0]hexadeca-1(12),13,15-trien-14-yl]acetamide',
                                     'reason': 'No amino acid backbone found'},
                                 {   'smiles': 'COc1ccc(cc1)\\C=C(NC=O)\\C(NC=O)=C\\c1ccc(OS(O)(=O)=O)cc1',
                                     'name': 'Fumiformamide',
                                     'reason': 'No amino acid backbone found'},
                                 {   'smiles': 'CCCCC(CC)COCCCN',
                                     'name': '3-(2-ethylhexoxy)propan-1-amine',
                                     'reason': 'No amino acid backbone found'}],
    'sample_false_negatives': [   {   'smiles': 'N[C@@H](CCCNC(=N)NO)C(O)=O',
                                      'name': 'N(5)-[(hydroxyamino)(imino)methyl]-L-ornithine',
                                      'reason': 'N-hydroxy group not attached '
                                                'to alpha-carbon or part of '
                                                'the amino acid backbone'},
                                  {   'smiles': 'C(\\N)(=N/O)/NCCC[C@H](N)C(=O)O',
                                      'name': 'N(5)-[(Z)-amino(hydroxyimino)methyl]-L-ornithine',
                                      'reason': 'No N-hydroxy group found'},
                                  {   'smiles': 'C(N)(=NO)NCCC[C@H](N)C(=O)O',
                                      'name': 'N(5)-[amino(hydroxyimino)methyl]-L-ornithine',
                                      'reason': 'No N-hydroxy group found'},
                                  {   'smiles': 'NC(CCCN\\C(N)=N/O)C(O)=O',
                                      'name': 'N(5)-[(Z)-amino(hydroxyimino)methyl]ornithine',
                                      'reason': 'No N-hydroxy group found'},
                                  {   'smiles': 'NC(CCCN\\C(N)=N\\O)C(O)=O',
                                      'name': 'N(5)-[(E)-amino(hydroxyimino)methyl]ornithine',
                                      'reason': 'No N-hydroxy group found'},
                                  {   'smiles': 'NC(CCCNC(=N)NO)C(O)=O',
                                      'name': 'N(5)-[(hydroxyamino)(imino)methyl]ornithine',
                                      'reason': 'N-hydroxy group not attached '
                                                'to alpha-carbon or part of '
                                                'the amino acid backbone'},
                                  {   'smiles': 'N[C@@H](CCCCNO)C(O)=O',
                                      'name': 'N(6)-hydroxy-L-lysine',
                                      'reason': 'N-hydroxy group not attached '
                                                'to alpha-carbon or part of '
                                                'the amino acid backbone'},
                                  {   'smiles': 'NC(CCCNC(N)=NO)C(O)=O',
                                      'name': 'N(5)-[amino(hydroxyimino)methyl]ornithine',
                                      'reason': 'No N-hydroxy group found'},
                                  {   'smiles': 'ONCC(O)=O',
                                      'name': 'N-hydroxyglycine',
                                      'reason': 'No amino acid backbone '
                                                'found'}],
    'attempt': 1,
    '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 '
                 'molecules with carboxylate groups (O-) as '
                 'N-hydroxy-alpha-amino-acids. This happened because the '
                 'SMARTS pattern for the amino acid backbone allowed for both '
                 'neutral (OH) and charged (O-) carboxyl groups. The '
                 'definition should only include neutral carboxyl groups.\n'
                 '\n'
                 '2. **False Negatives**: The code missed some valid '
                 'N-hydroxy-alpha-amino-acids because:\n'
                 "   - It didn't account for cases where the N-hydroxy group "
                 'is part of a more complex structure (e.g., '
                 'N(5)-[(hydroxyamino)(imino)methyl]-L-ornithine).\n'
                 "   - It didn't handle cases where the N-hydroxy group is not "
                 'directly attached to the alpha-carbon but still satisfies '
                 'the definition (e.g., N(6)-hydroxy-L-lysine).\n'
                 '\n'
                 '3. **Pattern Matching**: The SMARTS patterns were too '
                 "restrictive and didn't account for all possible variations "
                 'of the N-hydroxy group.\n'
                 '\n'
                 'To improve the code, we need to:\n'
                 '- Modify the SMARTS patterns to be more inclusive of '
                 'different N-hydroxy group configurations.\n'
                 '- Ensure that the carboxyl group is neutral (OH) and not '
                 'charged (O-).\n'
                 '- Handle cases where the N-hydroxy group is not directly '
                 'attached to the alpha-carbon but still satisfies the '
                 'definition.\n'
                 '\n'
                 'Here is the improved code:',
    'success': True,
    'best': True,
    'error': '',
    'stdout': None,
    'num_true_positives': 22,
    'num_false_positives': 4,
    'num_true_negatives': 142265,
    'num_false_negatives': 9,
    'num_negatives': None,
    'precision': 0.8461538461538461,
    'recall': 0.7096774193548387,
    'f1': 0.7719298245614036,
    'accuracy': 0.9999086437104708,
    'negative_predictive_value': 0.9999367417799457}