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wandb.data_types.Molecule
Wandb class for 3D Molecular data
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Molecule(
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data_or_path: Union[str, 'TextIO'],
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**kwargs
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) -> None
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Arguments
Text
data_or_path
(string, io) Molecule can be initialized from a file name or an io object.

Methods

from_rdkit

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@classmethod
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from_rdkit(
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data_or_path: "RDKitDataType",
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convert_to_3d_and_optimize: bool = (True),
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mmff_optimize_molecule_max_iterations: int = 200
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) -> "Molecule"
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Convert RDKit-supported file/object types to wandb.Molecule
Arguments
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data_or_path
(string, rdkit.Chem.rdchem.Mol) Molecule can be initialized from a file name or an rdkit.Chem.rdchem.Mol object.
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
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from_smiles(
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data: str,
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sanitize: bool = (True),
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convert_to_3d_and_optimize: bool = (True),
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mmff_optimize_molecule_max_iterations: int = 200
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) -> "Molecule"
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Convert SMILES string to wandb.Molecule
Arguments
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data
string SMILES string.
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
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SUPPORTED_RDKIT_TYPES
SUPPORTED_TYPES