Python AllChem.ReactionFromSmarts方法代碼示例

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def crossover_non_ring(parent_A, parent_B):

    for i in range(10):
        fragments_A = cut(parent_A)
        fragments_B = cut(parent_B)
        if fragments_A is None or fragments_B is None:
            return None
        rxn = AllChem.ReactionFromSmarts('[*:1]-[1*].[1*]-[*:2]>>[*:1]-[*:2]')
        new_mol_trial = []
        for fa in fragments_A:
            for fb in fragments_B:
                new_mol_trial.append(rxn.RunReactants((fa, fb))[0])

        new_mols = []
        for mol in new_mol_trial:
            mol = mol[0]
            if mol_ok(mol):
                new_mols.append(mol)

        if len(new_mols) > 0:
            return random.choice(new_mols)

    return None 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def TransformStringToImage(transform, retro=True, options=None,**kwargs):
    '''Wrapper function meant to take a SMARTS transform and return a PIL image
    of that transform.

    TODO: Need to improve generalization visually! Right now it still shows'''

    if not options:
        options = defaultDrawOptions()
        options.dotsPerAngstrom = 40

    # To generalize un-mapped atoms in transform, need to identify square brackets
    # without colon in the middle (e.g., [C]) and replace with dummy label [C:0] so
    # generalization display works
    old_tags = re.findall('\[[^:]+\]', transform)
    for old_tag in old_tags:
        new_tag = old_tag.replace(']', ':0]')
        transform = transform.replace(old_tag, new_tag)
    rxn = AllChem.ReactionFromSmarts(transform)
    return ReactionToImage(rxn, dummyAtoms=True, options=options, retro=retro, **kwargs) 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def initialize_rxn_from_smarts(reaction_smarts):
    # Initialize reaction
    rxn = AllChem.ReactionFromSmarts(reaction_smarts)
    rxn.Initialize()
    if rxn.Validate()[1] != 0:
        raise ValueError('validation failed')
    if PLEVEL >= 2: print('Validated rxn without errors')

    unmapped = 700
    for rct in rxn.GetReactants():
        rct.UpdatePropertyCache()
        Chem.AssignStereochemistry(rct)
        # Fill in atom map numbers
        for a in rct.GetAtoms():
            if not a.HasProp('molAtomMapNumber'):
                a.SetIntProp('molAtomMapNumber', unmapped)
                unmapped += 1
    if PLEVEL >= 2: print('Added {} map nums to unmapped reactants'.format(unmapped-700))
    if unmapped > 800:
        raise ValueError('Why do you have so many unmapped atoms in the template reactants?')

    return rxn 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def crossover_non_ring(parent_A,parent_B):
  for i in range(10):
    fragments_A = cut(parent_A)
    fragments_B = cut(parent_B)
    if fragments_A == None or fragments_B == None:
      return None
    rxn = AllChem.ReactionFromSmarts('[*:1]-[1*].[1*]-[*:2]>>[*:1]-[*:2]')
    new_mol_trial = []
    for fa in fragments_A:
      for fb in fragments_B:
        new_mol_trial.append(rxn.RunReactants((fa,fb))[0]) 
                                 
    new_mols = []
    for mol in new_mol_trial:
      mol = mol[0]
      if mol_OK(mol):
        new_mols.append(mol)
    
    if len(new_mols) > 0:
      return random.choice(new_mols)
    
  return None 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def __init__(self):
		self.rxns = [
			# Double bonds on aromatic rings (dist 1)
			AllChem.ReactionFromSmarts('[NH0:1]=[a:2][nH:3]>>[NH:1][a:2][nH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[a:2][nH:3]>>[NH2:1][a:2][nH0:3]'),
			AllChem.ReactionFromSmarts('[OH0:1]=[a:2][nH:3]>>[OH:1][a:2][nH0:3]'),
			# Double bonds on aromatic rings (dist 2)
			AllChem.ReactionFromSmarts('[NH0:1]=[a:2][a:4][nH:3]>>[NH:1][a:2][a:4][nH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[a:2][a:4][nH:3]>>[NH2:1][a:2][a:4][nH0:3]'),
			AllChem.ReactionFromSmarts('[OH0:1]=[a:2][a:4][nH:3]>>[OH:1][a:2][a:4][nH0:3]'),
			# Double bonds on aromatic rings (dist 2)
			AllChem.ReactionFromSmarts('[NH0:1]=[a:2][a:4][a:5][nH:3]>>[NH:1][a:2][a:4][a:5][nH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[a:2][a:4][a:5][nH:3]>>[NH2:1][a:2][a:4][a:5][nH0:3]'),
			AllChem.ReactionFromSmarts('[OH0:1]=[a:2][a:4][a:5][nH:3]>>[OH:1][a:2][a:4][a:5][nH0:3]'),
			# Iminol / amide 
			AllChem.ReactionFromSmarts('[NH0:1]=[C:2]-[OH:3]>>[NH1:1]-[C:2]=[OH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[C:2]-[OH:3]>>[NH2:1]-[C:2]=[OH0:3]'),
			# Thiourea
			AllChem.ReactionFromSmarts('[NH0:1]=[C:2]-[SH:3]>>[NH1:1]-[C:2]=[SH0:3]'),
			AllChem.ReactionFromSmarts('[NH1:1]=[C:2]-[SH:3]>>[NH2:1]-[C:2]=[SH0:3]'),
			# Azide
			AllChem.ReactionFromSmarts('[NH0:1][NH0:2]=[NH0;-:3]>>[NH0;-:1]=[NH0;+:2]=[NH0;-:3]'),
			# Cyanide salts
			AllChem.ReactionFromSmarts('([K,Na;H1:1].[C;X1;H0:2]#[N:3])>>[*;H0:1][*:2]#[N:3]'),
			AllChem.ReactionFromSmarts('([Cu:1].[C;X1;H0:2]#[N:3])>>[*:1][*:2]#[N:3]'),
			# Grinards
			AllChem.ReactionFromSmarts('([MgH+:1].[C;v3:2][*:3])>>[Mg+:1][*:2][*:3]'),
			# Coordinated tin
			AllChem.ReactionFromSmarts('([SnH4:1].[C;v3:2].[C;v3:3].[C;v3:4].[C;v3:5])>>[Sn:1]([*:2])([*:3])([*:4])[*:5]'),
			AllChem.ReactionFromSmarts('([SnH3:1].[C;v3:2].[C;v3:3].[C;v3:4])>>[Sn:1]([*:2])([*:3])[*:4]'),
			AllChem.ReactionFromSmarts('([SnH2:1].[C;v3:2].[C;v3:3])>>[Sn:1]([*:2])[*:3]'),
			AllChem.ReactionFromSmarts('([SnH1:1].[C;v3:2])>>[Sn:1][*:2]'),
		] 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def initialize_rxn_from_smarts(reaction_smarts):
    # Initialize reaction
    rxn = AllChem.ReactionFromSmarts(reaction_smarts)
    rxn.Initialize()
    if rxn.Validate()[1] != 0:
        raise ValueError('validation failed')
    if PLEVEL >= 2: print('Validated rxn without errors')


    # Figure out if there are unnecessary atom map numbers (that are not balanced)
    # e.g., leaving groups for retrosynthetic templates. This is because additional
    # atom map numbers in the input SMARTS template may conflict with the atom map
    # numbers of the molecules themselves
    prd_maps = [a.GetAtomMapNum() for prd in rxn.GetProducts() for a in prd.GetAtoms() if a.GetAtomMapNum()]

    unmapped = 700
    for rct in rxn.GetReactants():
        rct.UpdatePropertyCache()
        Chem.AssignStereochemistry(rct)
        # Fill in atom map numbers
        for a in rct.GetAtoms():
            if not a.GetAtomMapNum() or a.GetAtomMapNum() not in prd_maps:
                a.SetAtomMapNum(unmapped)
                unmapped += 1
    if PLEVEL >= 2: print('Added {} map nums to unmapped reactants'.format(unmapped-700))
    if unmapped > 800:
        raise ValueError('Why do you have so many unmapped atoms in the template reactants?')

    return rxn 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def setUp(self):
        for smiles in REACTION_SMILES_SAMPLE:
            ReactionModel.objects.create(rxn=smiles)
        for smarts in REACTION_SMARTS_SAMPLE:
            ReactionModel.objects.create(
                rxn=Chem.ReactionFromSmarts(str(smarts))) 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def from_db_value(self, value, expression, connection):
        if value is None:
            return value
        return Chem.ReactionFromSmarts(value, useSmiles=True) 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def to_python(self, value):
        if value is None or isinstance(value, Chem.ChemicalReaction):
            return value
        elif isinstance(value, str):
            # The string case. A reaction SMILES is expected.
            return Chem.ReactionFromSmarts(str(value), useSmiles=True)
        else:
            raise ValidationError("Invalid input for a ChemicalReaction instance") 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def crossover_ring(parent_A, parent_B):
    ring_smarts = Chem.MolFromSmarts('[R]')
    if not parent_A.HasSubstructMatch(ring_smarts) and not parent_B.HasSubstructMatch(ring_smarts):
        return None

    rxn_smarts1 = ['[*:1]~[1*].[1*]~[*:2]>>[*:1]-[*:2]', '[*:1]~[1*].[1*]~[*:2]>>[*:1]=[*:2]']
    rxn_smarts2 = ['([*:1]~[1*].[1*]~[*:2])>>[*:1]-[*:2]', '([*:1]~[1*].[1*]~[*:2])>>[*:1]=[*:2]']

    for i in range(10):
        fragments_A = cut_ring(parent_A)
        fragments_B = cut_ring(parent_B)

        if fragments_A is None or fragments_B is None:
            return None

        new_mol_trial = []
        for rs in rxn_smarts1:
            rxn1 = AllChem.ReactionFromSmarts(rs)
            new_mol_trial = []
            for fa in fragments_A:
                for fb in fragments_B:
                    new_mol_trial.append(rxn1.RunReactants((fa, fb))[0])

        new_mols = []
        for rs in rxn_smarts2:
            rxn2 = AllChem.ReactionFromSmarts(rs)
            for m in new_mol_trial:
                m = m[0]
                if mol_ok(m):
                    new_mols += list(rxn2.RunReactants((m,)))

        new_mols2 = []
        for m in new_mols:
            m = m[0]
            if mol_ok(m) and ring_OK(m):
                new_mols2.append(m)

        if len(new_mols2) > 0:
            return random.choice(new_mols2)

    return None 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def mutate(mol, mutation_rate):
    if random.random() > mutation_rate:
        return mol

    try:
        Chem.Kekulize(mol, clearAromaticFlags=True)
    except ValueError:
        return mol

    p = [0.15, 0.14, 0.14, 0.14, 0.14, 0.14, 0.15]
    for i in range(10):
        rxn_smarts_list = 7 * ['']
        rxn_smarts_list[0] = insert_atom()
        rxn_smarts_list[1] = change_bond_order()
        rxn_smarts_list[2] = delete_cyclic_bond()
        rxn_smarts_list[3] = add_ring()
        rxn_smarts_list[4] = delete_atom()
        rxn_smarts_list[5] = change_atom(mol)
        rxn_smarts_list[6] = append_atom()
        rxn_smarts = np.random.choice(rxn_smarts_list, p=p)

        # print 'mutation',rxn_smarts

        rxn = AllChem.ReactionFromSmarts(rxn_smarts)

        new_mol_trial = rxn.RunReactants((mol,))

        new_mols = []
        for m in new_mol_trial:
            m = m[0]
            # print Chem.MolToSmiles(mol),mol_ok(mol)
            if co.mol_ok(m) and co.ring_OK(m):
                new_mols.append(m)

        if len(new_mols) > 0:
            return random.choice(new_mols)

    return None 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def run_rxn(rxn_smarts, mol):
    new_mol_list = []
    patt = rxn_smarts.split('>>')[0]
    # work on a copy so an un-kekulized version is returned
    # if the molecule is not changed
    mol_copy = Chem.Mol(mol)
    try:
        Chem.Kekulize(mol_copy)
    except ValueError:
        pass
    if mol_copy.HasSubstructMatch(Chem.MolFromSmarts(patt)):
        rxn = AllChem.ReactionFromSmarts(rxn_smarts)
        new_mols = rxn.RunReactants((mol_copy,))
        for new_mol in new_mols:
            try:
                Chem.SanitizeMol(new_mol[0])
                new_mol_list.append(new_mol[0])
            except ValueError:
                pass
        if len(new_mol_list) > 0:
            new_mol = random.choice(new_mol_list)
            return new_mol
        else:
            return mol
    else:
        return mol 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def transform(self):
        log.debug('Loading Normalization transform: %s', self.name)
        return AllChem.ReactionFromSmarts(str(self.transform_str)) 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def fingerprint_reactions(reactions, fp_dim):
    fps = []
    for r in reactions:
        rxn = AllChem.ReactionFromSmarts(r)
        # fp = AllChem.CreateDifferenceFingerprintForReaction(rxn)
        fp = AllChem.CreateStructuralFingerprintForReaction(rxn)
        fold_factor = fp.GetNumBits()//fp_dim
        fp = DataStructs.FoldFingerprint(fp, fold_factor)
        fps.append(fp)
    return fps 

# 需要導入模塊: from rdkit.Chem import AllChem [as 別名]
# 或者: from rdkit.Chem.AllChem import ReactionFromSmarts [as 別名]
def transform(mol, rule):
    """Apply transformation rule to a molecule to get reactants"""
    rxn = AllChem.ReactionFromSmarts(rule)
    results = rxn.RunReactants([mol])

    # Only look at first set of results (TODO any reason not to?)
    results = results[0]
    reactants = [Chem.MolToSmiles(smi) for smi in results]
    return reactants