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 5, 2025