Python Chem.GetMolFrags方法代碼示例

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def validate_rdkit_mol(mol):
    """
    Sanitizes an RDKit molecules and returns True if the molecule is chemically
    valid.
    :param mol: an RDKit molecule 
    :return: True if the molecule is chemically valid, False otherwise
    """
    if rdc is None:
        raise ImportError('`validate_rdkit_mol` requires RDkit.')
    if len(rdc.GetMolFrags(mol)) > 1:
        return False
    try:
        rdc.SanitizeMol(mol)
        return True
    except ValueError:
        return False 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def cut(mol):
    if not mol.HasSubstructMatch(Chem.MolFromSmarts('[*]-;!@[*]')):
        return None

    bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[*]-;!@[*]')))  # single bond not in ring

    bs = [mol.GetBondBetweenAtoms(bis[0], bis[1]).GetIdx()]

    fragments_mol = Chem.FragmentOnBonds(mol, bs, addDummies=True, dummyLabels=[(1, 1)])

    try:
        return Chem.GetMolFrags(fragments_mol, asMols=True, sanitizeFrags=True)
    except ValueError:
        return None

    return None 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def remove(self, mol):
        """Return the molecule with specified fragments removed.

        :param mol: The molecule to remove fragments from.
        :type mol: rdkit.Chem.rdchem.Mol
        :return: The molecule with fragments removed.
        :rtype: rdkit.Chem.rdchem.Mol
        """
        log.debug('Running FragmentRemover')
        # Iterate FragmentPatterns and remove matching fragments
        for frag in self.fragments:
            # If nothing is left or leave_last and only one fragment, end here
            if mol.GetNumAtoms() == 0 or (self.leave_last and len(Chem.GetMolFrags(mol)) <= 1):
                break
            # Apply removal for this FragmentPattern
            removed = Chem.DeleteSubstructs(mol, frag.smarts, onlyFrags=True)
            if not mol.GetNumAtoms() == removed.GetNumAtoms():
                log.info('Removed fragment: %s', frag.name)
            if self.leave_last and removed.GetNumAtoms() == 0:
                # All the remaining fragments match this pattern - leave them all
                break
            mol = removed
        return mol 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def normalize(self, mol):
        """Apply a series of Normalization transforms to correct functional groups and recombine charges.

        A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
        until no further changes occur. If any changes occurred, we go back and start from the first Normalization
        again, in case the changes mean an earlier transform is now applicable. The molecule is returned once the entire
        series of Normalizations cause no further changes or if max_restarts (default 200) is reached.

        :param mol: The molecule to normalize.
        :type mol: rdkit.Chem.rdchem.Mol
        :return: The normalized fragment.
        :rtype: rdkit.Chem.rdchem.Mol
        """
        log.debug('Running Normalizer')
        # Normalize each fragment separately to get around quirky RunReactants behaviour
        fragments = []
        for fragment in Chem.GetMolFrags(mol, asMols=True):
            fragments.append(self._normalize_fragment(fragment))
        # Join normalized fragments into a single molecule again
        outmol = fragments.pop()
        for fragment in fragments:
            outmol = Chem.CombineMols(outmol, fragment)
        Chem.SanitizeMol(outmol)
        return outmol 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def keep_largest_fragment(sml):
    """Function that returns the SMILES sequence of the largest fragment for a input
    SMILES sequnce.

    Args:
        sml: SMILES sequence.
    Returns:
        canonical SMILES sequnce of the largest fragment.
    """
    mol_frags = Chem.GetMolFrags(Chem.MolFromSmiles(sml), asMols=True)
    largest_mol = None
    largest_mol_size = 0
    for mol in mol_frags:
        size = mol.GetNumAtoms()
        if size > largest_mol_size:
            largest_mol = mol
            largest_mol_size = size
    return Chem.MolToSmiles(largest_mol) 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def remove(self, mol):
        """Return the molecule with specified fragments removed.

        :param mol: The molecule to remove fragments from.
        :type mol: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
        :return: The molecule with fragments removed.
        :rtype: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
        """
        log.debug("Running FragmentRemover")
        # Iterate FragmentPatterns and remove matching fragments
        for frag in self.fragments:
            # If nothing is left or leave_last and only one fragment, end here
            if mol.GetNumAtoms() == 0 or (
                self.leave_last and len(Chem.GetMolFrags(mol)) <= 1
            ):
                break
            # Apply removal for this FragmentPattern
            removed = Chem.DeleteSubstructs(mol, frag.smarts, onlyFrags=True)
            if not mol.GetNumAtoms() == removed.GetNumAtoms():
                log.info("Removed fragment: %s", frag.name)
            if self.leave_last and removed.GetNumAtoms() == 0:
                # All the remaining fragments match this pattern - leave them all
                break
            mol = removed
        return mol 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def normalize(self, mol):
        """Apply a series of Normalization transforms to correct functional groups and recombine charges.

        A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
        until no further changes occur. If any changes occurred, we go back and start from the first Normalization
        again, in case the changes mean an earlier transform is now applicable. The molecule is returned once the entire
        series of Normalizations cause no further changes or if max_restarts (default 200) is reached.

        :param mol: The molecule to normalize.
        :type mol: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
        :return: The normalized fragment.
        :rtype: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
        """
        log.debug("Running Normalizer")
        # Normalize each fragment separately to get around quirky RunReactants behaviour
        fragments = []
        for fragment in Chem.GetMolFrags(mol, asMols=True):
            fragments.append(self._normalize_fragment(fragment))
        # Join normalized fragments into a single molecule again
        outmol = fragments.pop()
        for fragment in fragments:
            outmol = Chem.CombineMols(outmol, fragment)
        Chem.SanitizeMol(outmol)
        return outmol 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def cut_ring(mol):

    for i in range(10):
        if random.random() < 0.5:
            if not mol.HasSubstructMatch(Chem.MolFromSmarts('[R]@[R]@[R]@[R]')):
                return None
            bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[R]@[R]@[R]@[R]')))
            bis = ((bis[0], bis[1]), (bis[2], bis[3]),)
        else:
            if not mol.HasSubstructMatch(Chem.MolFromSmarts('[R]@[R;!D2]@[R]')):
                return None
            bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[R]@[R;!D2]@[R]')))
            bis = ((bis[0], bis[1]), (bis[1], bis[2]),)

        bs = [mol.GetBondBetweenAtoms(x, y).GetIdx() for x, y in bis]

        fragments_mol = Chem.FragmentOnBonds(mol, bs, addDummies=True, dummyLabels=[(1, 1), (1, 1)])

        try:
            fragments = Chem.GetMolFrags(fragments_mol, asMols=True, sanitizeFrags=True)
            if len(fragments) == 2:
                return fragments
        except ValueError:
            return None

    return None 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def _check_matches_fragment(self, mol):
        matches = frozenset(frozenset(match) for match in mol.GetSubstructMatches(self._smarts))
        fragments = frozenset(frozenset(frag) for frag in Chem.GetMolFrags(mol))
        if matches & fragments:
            self.log.log(self.level, self.message, {'smarts': self.smarts}) 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def run(self, mol):
        for fp in self.fragments:
            matches = frozenset(frozenset(match) for match in mol.GetSubstructMatches(fp.smarts))
            fragments = frozenset(frozenset(frag) for frag in Chem.GetMolFrags(mol))
            if matches & fragments:
                self.log.info('%s is present', fp.name) 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def clean_charges(mol):
    """
    This hack should not be needed anymore, but is kept just in case

    """

    Chem.SanitizeMol(mol)
    #rxn_smarts = ['[N+:1]=[*:2]-[C-:3]>>[N+0:1]-[*:2]=[C-0:3]',
    #              '[N+:1]=[*:2]-[O-:3]>>[N+0:1]-[*:2]=[O-0:3]',
    #              '[N+:1]=[*:2]-[*:3]=[*:4]-[O-:5]>>[N+0:1]-[*:2]=[*:3]-[*:4]=[O-0:5]',
    #              '[#8:1]=[#6:2]([!-:6])[*:3]=[*:4][#6-:5]>>[*-:1][*:2]([*:6])=[*:3][*:4]=[*+0:5]',
    #              '[O:1]=[c:2][c-:3]>>[*-:1][*:2][*+0:3]',
    #              '[O:1]=[C:2][C-:3]>>[*-:1][*:2]=[*+0:3]']

    rxn_smarts = ['[#6,#7:1]1=[#6,#7:2][#6,#7:3]=[#6,#7:4][CX3-,NX3-:5][#6,#7:6]1=[#6,#7:7]>>'
                  '[#6,#7:1]1=[#6,#7:2][#6,#7:3]=[#6,#7:4][-0,-0:5]=[#6,#7:6]1[#6-,#7-:7]',
                  '[#6,#7:1]1=[#6,#7:2][#6,#7:3](=[#6,#7:4])[#6,#7:5]=[#6,#7:6][CX3-,NX3-:7]1>>'
                  '[#6,#7:1]1=[#6,#7:2][#6,#7:3]([#6-,#7-:4])=[#6,#7:5][#6,#7:6]=[-0,-0:7]1']

    fragments = Chem.GetMolFrags(mol,asMols=True,sanitizeFrags=False)

    for i, fragment in enumerate(fragments):
        for smarts in rxn_smarts:
            patt = Chem.MolFromSmarts(smarts.split(">>")[0])
            while fragment.HasSubstructMatch(patt):
                rxn = AllChem.ReactionFromSmarts(smarts)
                ps = rxn.RunReactants((fragment,))
                fragment = ps[0][0]
                Chem.SanitizeMol(fragment)
        if i == 0:
            mol = fragment
        else:
            mol = Chem.CombineMols(mol, fragment)

    return mol 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def _check_matches_fragment(self, mol):
        matches = frozenset(
            frozenset(match) for match in mol.GetSubstructMatches(self._smarts)
        )
        fragments = frozenset(frozenset(frag) for frag in Chem.GetMolFrags(mol))
        if matches & fragments:
            self.log.log(self.level, self.message, {"smarts": self.smarts}) 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def run(self, mol):
        for fp in self.fragments:
            matches = frozenset(
                frozenset(match) for match in mol.GetSubstructMatches(fp.smarts)
            )
            fragments = frozenset(frozenset(frag) for frag in Chem.GetMolFrags(mol))
            if matches & fragments:
                self.log.info("%s is present", fp.name) 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def cut(mol):
  if not mol.HasSubstructMatch(Chem.MolFromSmarts('[*]-;!@[*]')): 
  	return None
  bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[*]-;!@[*]'))) #single bond not in ring
  #print bis,bis[0],bis[1]
  bs = [mol.GetBondBetweenAtoms(bis[0],bis[1]).GetIdx()]

  fragments_mol = Chem.FragmentOnBonds(mol,bs,addDummies=True,dummyLabels=[(1, 1)])

  try:
    fragments = Chem.GetMolFrags(fragments_mol,asMols=True)
    return fragments
  except:
    return None 

# 需要導入模塊: from rdkit import Chem [as 別名]
# 或者: from rdkit.Chem import GetMolFrags [as 別名]
def cut_ring(mol):
  for i in range(10):
    if random.random() < 0.5:
      if not mol.HasSubstructMatch(Chem.MolFromSmarts('[R]@[R]@[R]@[R]')): 
      	return None
      bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[R]@[R]@[R]@[R]')))
      bis = ((bis[0],bis[1]),(bis[2],bis[3]),)
    else:
      if not mol.HasSubstructMatch(Chem.MolFromSmarts('[R]@[R;!D2]@[R]')): 
      	return None
      bis = random.choice(mol.GetSubstructMatches(Chem.MolFromSmarts('[R]@[R;!D2]@[R]')))
      bis = ((bis[0],bis[1]),(bis[1],bis[2]),)
    
    #print bis
    bs = [mol.GetBondBetweenAtoms(x,y).GetIdx() for x,y in bis]

    fragments_mol = Chem.FragmentOnBonds(mol,bs,addDummies=True,dummyLabels=[(1, 1),(1,1)])

    try:
      fragments = Chem.GetMolFrags(fragments_mol,asMols=True)
    except:
      return None

    if len(fragments) == 2:
      return fragments
    
  return None