Python rdMolDescriptors.CalcExactMolWt方法代码示例

# 需要导入模块: from rdkit.Chem import rdMolDescriptors [as 别名]
# 或者: from rdkit.Chem.rdMolDescriptors import CalcExactMolWt [as 别名]
def evaluate_chem_mol(mol):
    try:
        Chem.GetSSSR(mol)
        clogp = Crippen.MolLogP(mol)
        mw = MolDescriptors.CalcExactMolWt(mol)
        tpsa = Descriptors.TPSA(mol)
        ret_val = [
            True,
            320 < mw < 420,
            2 < clogp < 3,
            40 < tpsa < 60
        ]
    except:
        ret_val = [False] * 4

    return ret_val



# Same as above but decodes and check if a cached value could be used. 

# 需要导入模块: from rdkit.Chem import rdMolDescriptors [as 别名]
# 或者: from rdkit.Chem.rdMolDescriptors import CalcExactMolWt [as 别名]
def evaluate_chem_mol(mol):
    try:
        Chem.GetSSSR(mol)
        clogp = Crippen.MolLogP(mol)
        mw = MolDescriptors.CalcExactMolWt(mol)
        tpsa = Descriptors.TPSA(mol)
        ret_val = [
            True,
            320 < mw < 420,
            2 < clogp < 3,
            40 < tpsa < 60
        ]
    except:
        ret_val = [False] * 4
        
    return ret_val



# Same as above but decodes and check if a cached value could be used. 

# 需要导入模块: from rdkit.Chem import rdMolDescriptors [as 别名]
# 或者: from rdkit.Chem.rdMolDescriptors import CalcExactMolWt [as 别名]
def __init__(self, mol, atom_count=None, MW=None, Tb=None):
        if type(mol) == Chem.rdchem.Mol:
            self.rdkitmol = mol
        else:
            self.rdkitmol = Chem.MolFromSmiles(mol)
        if atom_count is None:
            self.rdkitmol_Hs = Chem.AddHs(self.rdkitmol)
            self.atom_count = len(self.rdkitmol_Hs.GetAtoms())
        else:
            self.atom_count = atom_count
        if MW is None:
            self.MW = rdMolDescriptors.CalcExactMolWt(self.rdkitmol_Hs)
        else:
            self.MW = MW
            
        self.counts, self.success, self.status = smarts_fragment(J_BIGGS_JOBACK_SMARTS_id_dict, rdkitmol=self.rdkitmol)
            
        if Tb is not None:
            self.Tb_estimated = self.Tb(self.counts)
        else:
            self.Tb_estimated = Tb 

# 需要导入模块: from rdkit.Chem import rdMolDescriptors [as 别名]
# 或者: from rdkit.Chem.rdMolDescriptors import CalcExactMolWt [as 别名]
def reward_target_mw(mol, target,ratio=40,max=4):
    """
    Reward for a target molecular weight
    :param mol: rdkit mol object
    :param target: float
    :return: float (-inf, max]
    """
    x = rdMolDescriptors.CalcExactMolWt(mol)
    reward = -1 * np.abs((x - target)/ratio) + max
    return reward

# TODO(Bowen): num rings is a discrete variable, so what is the best way to
# calculate the reward? 

# 需要导入模块: from rdkit.Chem import rdMolDescriptors [as 别名]
# 或者: from rdkit.Chem.rdMolDescriptors import CalcExactMolWt [as 别名]
def choose(self, mol):
        """Return the largest covalent unit.

        The largest fragment is determined by number of atoms (including hydrogens). Ties are broken by taking the
        fragment with the higher molecular weight, and then by taking the first alphabetically by SMILES if needed.

        :param mol: The molecule to choose the largest fragment from.
        :type mol: rdkit.Chem.rdchem.Mol
        :return: The largest fragment.
        :rtype: rdkit.Chem.rdchem.Mol
        """
        log.debug('Running LargestFragmentChooser')
        # TODO: Alternatively allow a list of fragments to be passed as the mol parameter
        fragments = Chem.GetMolFrags(mol, asMols=True)
        largest = None
        for f in fragments:
            smiles = Chem.MolToSmiles(f, isomericSmiles=True)
            log.debug('Fragment: %s', smiles)
            organic = is_organic(f)
            if self.prefer_organic:
                # Skip this fragment if not organic and we already have an organic fragment as the largest so far
                if largest and largest['organic'] and not organic:
                    continue
                # Reset largest if it wasn't organic and this fragment is organic
                if largest and organic and not largest['organic']:
                    largest = None
            # Count atoms
            atoms = 0
            for a in f.GetAtoms():
                atoms += 1 + a.GetTotalNumHs()
            # Skip this fragment if fewer atoms than the largest
            if largest and atoms < largest['atoms']:
                continue
            # Skip this fragment if equal number of atoms but weight is lower
            weight = rdMolDescriptors.CalcExactMolWt(f)
            if largest and atoms == largest['atoms'] and weight < largest['weight']:
                continue
            # Skip this fragment if equal atoms and equal weight but smiles comes last alphabetically
            if largest and atoms == largest['atoms'] and weight == largest['weight'] and smiles > largest['smiles']:
                continue
            # Otherwise this is the largest so far
            log.debug('New largest fragment: %s (%s)', smiles, atoms)
            largest = {'smiles': smiles, 'fragment': f, 'atoms': atoms, 'weight': weight, 'organic': organic}
        return largest['fragment'] 

# 需要导入模块: from rdkit.Chem import rdMolDescriptors [as 别名]
# 或者: from rdkit.Chem.rdMolDescriptors import CalcExactMolWt [as 别名]
def choose(self, mol):
        """Return the largest covalent unit.

        The largest fragment is determined by number of atoms (including hydrogens). Ties are broken by taking the
        fragment with the higher molecular weight, and then by taking the first alphabetically by SMILES if needed.

        :param mol: The molecule to choose the largest fragment from.
        :type mol: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
        :return: The largest fragment.
        :rtype: :rdkit:`Mol <Chem.rdchem.Mol-class.html>`
        """
        log.debug("Running LargestFragmentChooser")
        # TODO: Alternatively allow a list of fragments to be passed as the mol parameter
        fragments = Chem.GetMolFrags(mol, asMols=True)
        largest = None
        for f in fragments:
            smiles = Chem.MolToSmiles(f, isomericSmiles=True)
            log.debug("Fragment: %s", smiles)
            organic = is_organic(f)
            if self.prefer_organic:
                # Skip this fragment if not organic and we already have an organic fragment as the largest so far
                if largest and largest["organic"] and not organic:
                    continue
                # Reset largest if it wasn't organic and this fragment is organic
                if largest and organic and not largest["organic"]:
                    largest = None
            # Count atoms
            atoms = 0
            for a in f.GetAtoms():
                atoms += 1 + a.GetTotalNumHs()
            # Skip this fragment if fewer atoms than the largest
            if largest and atoms < largest["atoms"]:
                continue
            # Skip this fragment if equal number of atoms but weight is lower
            weight = rdMolDescriptors.CalcExactMolWt(f)
            if largest and atoms == largest["atoms"] and weight < largest["weight"]:
                continue
            # Skip this fragment if equal atoms and equal weight but smiles comes last alphabetically
            if (
                largest
                and atoms == largest["atoms"]
                and weight == largest["weight"]
                and smiles > largest["smiles"]
            ):
                continue
            # Otherwise this is the largest so far
            log.debug("New largest fragment: %s (%s)", smiles, atoms)
            largest = {
                "smiles": smiles,
                "fragment": f,
                "atoms": atoms,
                "weight": weight,
                "organic": organic,
            }
        return largest["fragment"]


# ==============================================================================
# from .normalize import NORMALIZATIONS, MAX_RESTARTS, Normalizer
# ==============================================================================