luna.wrappers.rdkit module

new_mol_from_block(block, mol_format, sanitize=True, removeHs=True)[source]

Read a molecule from a string block using RDKit.

Parameters

  • block (str) – The molecular string block.

  • mol_format (str) – The molecular format of block.

  • sanitize (bool) – If True (the default), sanitize the molecule.

  • removeHs (bool) – If True (the default), remove explict hydrogens from the molecule.

Returns

The parsed molecule or None in case the sanitization process fails.

Return type

rdkit.Chem.rdchem.Mol or None

Raises

IllegalArgumentError – If the provided molecular format is not accepted by RDKit.

Examples

>>> from luna.util.default_values import LUNA_PATH
>>> from luna.wrappers.rdkit import new_mol_from_block
>>> with open(f"{LUNA_PATH}/tutorial/inputs/GLY.sdf", "r") as IN:
...           mol_block = IN.read()
>>> rdk_mol = new_mol_from_block(block=mol_block, mol_format="sdf")
>>> print(rdk_mol.GetProp("_Name"))
GLY
read_mol_from_file(mol_file, mol_format, sanitize=True, removeHs=True)[source]

Read a molecule from mol_file using RDKit.

Parameters

  • mol_file (str) – The pathname of the molecular file to be read.

  • mol_format (str) – The molecular format of mol_file.

  • sanitize (bool) – If True (the default), sanitize the molecule.

  • removeHs (bool) – If True (the default), remove explict hydrogens from the molecule.

Returns

The parsed molecule or None in case the sanitization process fails.

Return type

rdkit.Chem.rdchem.Mol or None

Raises

IllegalArgumentError – If the provided molecular format is not accepted by RDKit.

Examples

>>> from luna.util.default_values import LUNA_PATH
>>> from luna.wrappers.rdkit import read_mol_from_file
>>> rdk_mol = read_mol_from_file(mol_file=f"{LUNA_PATH}/tutorial/inputs/ZINC000007786517.mol",
...                              mol_format="mol")
>>> print(rdk_mol.GetProp("_Name"))
 ZINC000007786517
read_multimol_file(mol_file, targets=None, mol_format=None, sanitize=True, removeHs=True)[source]

Read molecules from a multimolecular file using RDKit.

Parameters

  • mol_file (str) – The pathname of the molecular file to be read.

  • targets (iterable of str) – Only parses molecules, given by their ids, defined in targets.

  • mol_format (str, optional) – The molecular format of mol_file. If not provided, the format will be defined by the file extension.

  • sanitize (bool) – If True (the default), sanitize the molecule.

  • removeHs (bool) – If True (the default), remove explict hydrogens from the molecule.

Yields

tuple of (rdkit.Chem.rdchem.Mol, int) – A tuple containing the parsed molecule and its id.

Raises

IllegalArgumentError – If the provided or identified molecular format is not accepted by RDKit.

Examples

In this first example, we will read all molecules from a multimolecular file.

>>> from luna.util.default_values import LUNA_PATH
>>> from luna.wrappers.rdkit import read_multimol_file
>>> for mol_tuple in read_multimol_file(mol_file=f"{LUNA_PATH}/tutorial/inputs/ligands.mol2"):
...     print(mol_tuple[0].GetProp("_Name"))
 ZINC000343043015
 ZINC000065293174
 ZINC000575033470
 ZINC000096459890
 ZINC000012442563

Now, we will only read two molecules (ZINC000065293174, ZINC000096459890) from the same multimolecular file.

>>> from luna.util.default_values import LUNA_PATH
>>> from luna.wrappers.rdkit import read_multimol_file
>>> for mol_tuple in read_multimol_file(mol_file=f"{LUNA_PATH}/tutorial/inputs/ligands.mol2",
...                                     targets=["ZINC000065293174", "ZINC000096459890"]):
...     print(mol_tuple[0].GetProp("_Name"))
 ZINC000065293174
 ZINC000096459890