IsomerCollection#

class maize.utilities.chem.chem.IsomerCollection(molecules: Sequence[Isomer])[source]#

Bases: object

Represents a collection of isomers / enumerations of a molecule.

Parameters:: molecules – Molecules part of the collection and sharing a common topology

__init__(molecules: Sequence[Isomer]) → None[source]#

Methods

`__init__`(molecules)
`embed`([n_conformers])	Generate a 3D embedding of all isomers.
`from_sdf`(file)	Create an isomer collection from an SDF file containing different isomers or conformers.
`from_smiles`(smiles[, max_isomers, sanitize, ...])	Create an isomer collection from a SMILES string.
`remove_isomer`(isomer)	Remove isomer from collection
`to_sdf`(path)	Write all isomers to an SDF file.
`to_smiles`()	return smiles for an isomer collection

Attributes

`best_score`	The best score among all isomers / conformers
`inchi`	Returns the InChI key for the molecule
`n_isomers`	Number of contained isomers
`scored`	Whether the isomers have been scored
`smiles`

classmethod from_smiles(smiles: str, max_isomers: int = 8, sanitize: bool = True, timeout: int = 10) → Self[source]#

Create an isomer collection from a SMILES string.

Parameters:

smiles – The SMILES string to initialize the collection with
max_isomers – Maximum number of isomers to generate
sanitize – Whether to sanitize the molecule
timeout – Timeout in seconds before failing stereoisomer generation

Returns:

IsomerCollection instance

Return type:

IsomerCollection

Raises:

ChemistryException – If there was an error parsing the SMILES code

See also

steps.mai.molecule.Gypsum: A more advanced approach of generating any kind of isomer or high-energy conformers

classmethod from_sdf(file: Path) → Self[source]#

Create an isomer collection from an SDF file containing different isomers or conformers.

Parameters:: file – The SDF file input
Returns:: IsomerCollection instance
Return type:: IsomerCollection
Raises:: ChemistryException – If there was an error parsing the SMILES code

property n_isomers: int#: Number of contained isomers

property scored: bool#: Whether the isomers have been scored

property best_score: float#: The best score among all isomers / conformers

property inchi: str#: Returns the InChI key for the molecule

to_sdf(path: Path) → None[source]#

Write all isomers to an SDF file.

Parameters:: path – Output file path

to_smiles() → List[str][source]#: return smiles for an isomer collection

embed(n_conformers: int = 1) → None[source]#

Generate a 3D embedding of all isomers.

Parameters:: n_conformers – Number of conformers to generate
Raises:: ChemistryException – If there was an error generating the embeddings

remove_isomer(isomer: Isomer) → None[source]#: Remove isomer from collection