Fingerprints and Descriptors

mol2morgan_fp(mol, radius=2, nBits=2048)[source]

Convert an RDKit molecule to a Morgan fingerprint

Parameters:

mol (Mol) – RDKit molecule
radius (int) – fingerprint radius
nBits (int) – number of fingerprint bits

Return type:

ExplicitBitVect

Returns:

RDKit Morgan fingerprint

smi2morgan_fp(smi, radius=2, nBits=2048)[source]

Convert a SMILES to a Morgan fingerprint

Parameters:

smi (str) – SMILES
radius (int) – fingerprint radius
nBits (int) – number of fingerprint bits

Return type:

Optional[ExplicitBitVect]

Returns:

RDKit Morgan fingerprint

mol2numpy_fp(mol, radius=2, n_bits=2048)[source]

Convert an RDKit molecule to a numpy array with Morgan fingerprint bits Borrowed from https://iwatobipen.wordpress.com/2019/02/08/convert-fingerprint-to-numpy-array-and-conver-numpy-array-to-fingerprint-rdkit-memorandum/

Parameters:

mol (Mol) – RDKit molecule
radius (int) – fingerprint radius
n_bits (int) – number of fingerprint bits

Return type:

ndarray

Returns:

numpy array with RDKit fingerprint bits

smi2numpy_fp(smi, radius=2, nBits=2048)[source]

Convert a SMILES to a numpy array with Morgan fingerprint bits

Parameters:

smi (str) – SMILES string
radius (int) – fingerprint radius
nBits (int) – number of fingerprint bits

Return type:

ndarray

Returns:

numpy array with RDKit fingerprint bits

apply_func(name, mol)[source]

Apply an RDKit descriptor calculation to a molecule

Parameters:

name – descriptor name
mol – RDKit molecule

Returns:

class RDKitDescriptors[source]

Calculate RDKit descriptors

Initialize the RDKitDescriptors class.

Parameters:: self (RDKitDescriptors) – An instance of the RDKitDescriptors class
Returns:: None
Return type:: None

calc_mol(mol)[source]

Calculate descriptors for an RDKit molecule

Parameters:: mol (Mol) – RDKit molecule
Return type:: ndarray
Returns:: a numpy array with descriptors

calc_smiles(smiles)[source]

Calculate descriptors for a SMILES string

Parameters:: smiles (str) – SMILES string
Return type:: ndarray
Returns:: a numpy array with properties

pandas_smiles(smiles_list)[source]

Calculate descriptors for a list of SMILES strings and return them as a pandas DataFrame.

Parameters:: smiles_list (List[str]) – List of SMILES strings
Return type:: DataFrame
Returns:: DataFrame with calculated descriptors. Each row corresponds to a SMILES string and each column to a descriptor.

pandas_mols(mol_list)[source]

Calculate descriptors for a list of RDKit molecules and return them as a pandas DataFrame.

Parameters:: mol_list (List[Mol]) – List of RDKit molecules
Return type:: DataFrame
Returns:: DataFrame with calculated descriptors. Each row corresponds to a molecule and each column to a descriptor.

class RDKitProperties[source]

Calculate RDKit properties

calc_mol(mol)[source]

Calculate properties for an RDKit molecule

Parameters:: mol (Mol) – RDKit molecule
Return type:: ndarray
Returns:: a numpy array with properties

calc_smiles(smi)[source]

Calculate properties for a SMILES string

Parameters:: smi (str) – SMILES string
Return type:: Optional[ndarray]
Returns:: a numpy array with properties

pandas_smiles(smi_list)[source]

Calculates properties for a list of SMILES strings and returns them as a pandas DataFrame.

Parameters:: smi_list (List[str]) – List of SMILES strings
Returns:: DataFrame with calculated properties. Each row corresponds to a SMILES string and each column to a property.
Return type:: pd.DataFrame

pandas_mols(mol_list)[source]

Calculates properties for a list of RDKit molecules and returns them as a pandas DataFrame.

Parameters:: mol_list (List[Mol]) – List of RDKit molecules
Returns:: DataFrame with calculated properties. Each row corresponds to a molecule and each column to a property.
Return type:: pd.DataFrame

class Ro5Calculator[source]

A class used to calculate Lipinski’s Rule of Five properties for a given molecule.

Attributes

namesList[str]: A list of names of the properties to be calculated.
functionsList[Callable[[Mol], float]]: A list of functions used to calculate the properties.

Methods

calc_mol(mol: Mol) -> np.ndarray: Calculates properties for a RDKit molecule.
calc_smiles(smi: str) -> Optional[np.ndarray]: Calculates properties for a SMILES string.
pandas_smiles(smiles_list: List[str]) -> pd.DataFrame: Calculates properties for a list of SMILES strings and returns them as a pandas DataFrame.
pandas_mols(mol_list: List[Mol]) -> pd.DataFrame: Calculates properties for a list of RDKit molecules and returns them as a pandas DataFrame.

Initialize the Ro5Calculator class.

type self:: Ro5Calculator
param self:: An instance of the Ro5Calculator class
type self:: Ro5Calculator
return:: None
rtype:: None

calc_mol(mol)[source]

Calculate properties for a RDKit molecule

Parameters:: mol (Mol) – RDKit molecule
Returns:: a numpy array with properties
Return type:: np.ndarray

calc_smiles(smi)[source]

Calculate properties for a SMILES string

Parameters:: smi (str) – SMILES string
Returns:: a numpy array with properties
Return type:: Optional[np.ndarray]

pandas_smiles(smiles_list)[source]

Calculates properties for a list of SMILES strings and returns them as a pandas DataFrame.

Parameters:: smiles_list (List[str]) – List of SMILES strings
Returns:: DataFrame with calculated properties. Each row corresponds to a SMILES string and each column to a property.
Return type:: pd.DataFrame

pandas_mols(mol_list)[source]

Calculates properties for a list of RDKit molecules and returns them as a pandas DataFrame.

Parameters:: mol_list (List[Mol]) – List of RDKit molecules
Returns:: DataFrame with calculated properties. Each row corresponds to a molecule and each column to a property.
Return type:: pd.DataFrame