Molecule

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Wandb class for 3D Molecular data.

Molecule(
    data_or_path: Union[str, 'TextIO'],
    caption: Optional[str] = None,
    **kwargs
) -> None
Args
data_or_path(string, io) Molecule can be initialized from a file name or an io object.
caption(string) Caption associated with the molecule for display.

Methods

from_rdkit

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@classmethod
from_rdkit(
    data_or_path: "RDKitDataType",
    caption: Optional[str] = None,
    convert_to_3d_and_optimize: bool = (True),
    mmff_optimize_molecule_max_iterations: int = 200
) -> "Molecule"

Convert RDKit-supported file/object types to wandb.Molecule.

Args
data_or_path(string, rdkit.Chem.rdchem.Mol) Molecule can be initialized from a file name or an rdkit.Chem.rdchem.Mol object.
caption(string) Caption associated with the molecule for display.
convert_to_3d_and_optimize(bool) Convert to rdkit.Chem.rdchem.Mol with 3D coordinates. This is an expensive operation that may take a long time for complicated molecules.
mmff_optimize_molecule_max_iterations(int) Number of iterations to use in rdkit.Chem.AllChem.MMFFOptimizeMolecule

from_smiles

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@classmethod
from_smiles(
    data: str,
    caption: Optional[str] = None,
    sanitize: bool = (True),
    convert_to_3d_and_optimize: bool = (True),
    mmff_optimize_molecule_max_iterations: int = 200
) -> "Molecule"

Convert SMILES string to wandb.Molecule.

Args
data(string) SMILES string.
caption(string) Caption associated with the molecule for display
sanitize(bool) Check if the molecule is chemically reasonable by the RDKit’s definition.
convert_to_3d_and_optimize(bool) Convert to rdkit.Chem.rdchem.Mol with 3D coordinates. This is an expensive operation that may take a long time for complicated molecules.
mmff_optimize_molecule_max_iterations(int) Number of iterations to use in rdkit.Chem.AllChem.MMFFOptimizeMolecule
Class Variables
SUPPORTED_RDKIT_TYPES
SUPPORTED_TYPES

Last modified March 6, 2025