opencadd.structure.core.Structure.from_smiles

classmethod Structure.from_smiles(smiles, sanitize=True, addHs=True, generate_coordinates=True, numConfs=1, rdkit_kwargs={}, **kwargs)

Create a Universe from a SMILES string with rdkit

Parameters

  • smiles (str) – SMILES string

  • sanitize (bool (optional, default True)) – Toggle the sanitization of the molecule

  • addHs (bool (optional, default True)) – Add all necessary hydrogens to the molecule

  • generate_coordinates (bool (optional, default True)) – Generate 3D coordinates using RDKit’s AllChem.EmbedMultipleConfs() function. Requires adding hydrogens with the addHs parameter

  • numConfs (int (optional, default 1)) – Number of frames to generate coordinates for. Ignored if generate_coordinates=False

  • rdkit_kwargs (dict (optional)) – Other arguments passed to the RDKit EmbedMultipleConfs() function

  • kwargs (dict) – Parameters passed on Universe creation

Returns

universe – contains atom names and topology information (bonds) derived from the input SMILES string; coordinates are included if generate_coordinates was set to True

Return type

Universe

Examples

To create a Universe with 10 conformers of ethanol:

>>> u = mda.Universe.from_smiles('CCO', numConfs=10)
>>> u
<Universe with 9 atoms>
>>> u.trajectory
<RDKitReader with 10 frames of 9 atoms>

To use a different conformer generation algorithm, like ETKDGv3:

>>> u = mda.Universe.from_smiles('CCO', rdkit_kwargs=dict(
                                 params=AllChem.ETKDGv3()))
>>> u.trajectory
<RDKitReader with 1 frames of 9 atoms>

New in version 2.0.0.