rdkit_to_params.rdkitside package

Submodules

rdkit_to_params.rdkitside.utilities module

class rdkit_to_params.rdkitside.utilities.DummyMasker(mol: Mol, placekeeper_zahl: int = 6, blank_Gasteiger: bool = True)

Bases: object

A context manager that allows operations on a mol containing dummy atoms (R/*) that otherwise would raise an RDKit error. It simply masks and unmasks the dummy atoms.

>>> mol = Chem.MolFromSmiles('*CCC(C)C')
>>> with DummyMasker(mol):
>>>     AllChem.EmbedMolecule(mol)

The input options for dummy maker are mol (Chem.Mol), placekeeper_zahl (Z for atomic number), and blank_Gasteiger to make the dummy atom’s ‘_GasteigerCharge’ property zero if present. The Zahl of the placekeeping element will affect the Gasteiger partial chargers of nearby atoms though.

__init__(mol: Mol, placekeeper_zahl: int = 6, blank_Gasteiger: bool = True)

mask()

unmask()

rdkit_to_params.rdkitside.utilities.neutralise(*args, **kwargs)

rdkit_to_params.rdkitside.utilities.neutralize(mol: <module 'rdkit.Chem' from '/home/docs/checkouts/readthedocs.org/user_builds/rdkit-to-params/envs/latest/lib/python3.8/site-packages/rdkit/Chem/__init__.py'>) → <module 'rdkit.Chem' from '/home/docs/checkouts/readthedocs.org/user_builds/rdkit-to-params/envs/latest/lib/python3.8/site-packages/rdkit/Chem/__init__.py'>

Alters the protonation of tne molecule to be that at pH 7. Not great, but does the job.

• Protonates amines, but not aromatic bound amines.

• Deprotonates carboxylic acid, phosphoric acid and sulfuric acid, without ruining esters.

Module contents

The functionality is too big for a single class so was split into functional units.

• init contains the various entry points

• rename deals with atom renaming

• prep labels atoms etc. for conversion

• convert converts the mol into params entries