parmed.rdkit.rdkit module

This package contains classes responsible for loading rdkit objects

class parmed.rdkit.rdkit.RDKit

Bases: object

Methods

from_sdf(filename[, structure])	Load SDF file to Structure
from_smiles(smiles[, coordinates])	Load smiles string to Structure
load(rmol)	Load a Mol object and return a populated Structure instance

static from_sdf(filename, structure=False)

Load SDF file to Structure

Parameters

filename: str

structurebool, default False

if True, return a Structure if False, return a list of Structure

static from_smiles(smiles, coordinates=True)

Load smiles string to Structure

Parameters

smilesstr, smiles

coordinatesbool, default True

if True, use `rdkit.Chem.AllChem.EmbedMultipleConfs to assign coordinates

Returns

parmStructure

static load(rmol)

Load a Mol object and return a populated Structure instance

Parameters

rmol: :class:`Mol`

RDKit Mol object to convert

Examples

>>> from rdkit import Chem
>>> import parmed as pmd
>>> mol = Chem.MolFromSmiles('Cc1ccccc1')
>>> struct = pmd.load_rdkit(mol)