schrodinger.application.transforms.enumerators.synthesize module

class schrodinger.application.transforms.enumerators.synthesize.Synthesize(core_smarts: str, depth: int = 1, dedupe_routes: bool = False, max_routes: Optional[int] = None, max_products_per_route: int = 100, max_tries_per_route: Optional[int] = None, reagent_libraries: Optional[List[pathlib.Path]] = None, seed: Optional[int] = None)

Bases: apache_beam.transforms.ptransform.PTransform

Enumerates unique sanitized molecules from a combinatorial synthesis using routes based on the input molecules using the default reaction dictionary and reagent library.

If the maximum number of products is less than the total number of combinations the route synthesis will be done by random sampling, which may yield fewer products than requested, otherwise a systematic set of unique products will be yielded.

__init__(core_smarts: str, depth: int = 1, dedupe_routes: bool = False, max_routes: Optional[int] = None, max_products_per_route: int = 100, max_tries_per_route: Optional[int] = None, reagent_libraries: Optional[List[pathlib.Path]] = None, seed: Optional[int] = None)
Parameters

  • core_smarts – the SMARTS that the products should have and needs to be part of the input molecule

  • depth – the maximum depth of the retrosynthetic routes to use

  • dedupe_routes – whether to deduplicate the routes

  • max_products_per_route – the maximum number of products try to synthesize for each input molecule per route. Use 0 to force an exhaustive synthesis.

  • max_tries_per_route – the maximum number of tries to synthesize products for each input molecule per route. If None, the number of tries is automatically determined. If 0, the synthesis will be exhaustive.

  • reagent_libraries – the optional reagent libraries to use. If None or an empty list, the default reagent library will be used.

  • seed – seed for random number generator. If None, the random number generator will not be seeded.

expand(pcoll)
class schrodinger.application.transforms.enumerators.synthesize.EnumerateRoutes(core_smarts: str, depth: int = 1, dedup: bool = False)

Bases: apache_beam.transforms.ptransform.PTransform

Enumerates synthesis routes for core_smarts containing molecules using the default reaction dictionary.

if dedup is True, the routes will be deduplicated based on their one-line representation.

__init__(core_smarts: str, depth: int = 1, dedup: bool = False)
expand(pcoll)
class schrodinger.application.transforms.enumerators.synthesize.DeduplicateRoutes(label: Optional[str] = None)

Bases: apache_beam.transforms.ptransform.PTransform

A PTransform that deduplicates the route nodes based on their one-line representation.

expand(route_nodes)
class schrodinger.application.transforms.enumerators.synthesize.EvaluateRoutes(max_products_per_route: int = 100, max_tries_per_route: Optional[int] = None, reagent_libraries: Optional[List[pathlib.Path]] = None, seed: Optional[int] = None)

Bases: apache_beam.transforms.ptransform.PTransform

A PTransform that returns unique sanitized molecules after applying the synthesis reactions to the input molecules.

The products may be generated by random sampling if max_products_per_route is not zero and the number of products is less than the total number of combinations, otherwise a systematic set of unique products will be yielded.

__init__(max_products_per_route: int = 100, max_tries_per_route: Optional[int] = None, reagent_libraries: Optional[List[pathlib.Path]] = None, seed: Optional[int] = None)
expand(pcoll)
class schrodinger.application.transforms.enumerators.synthesize.SystematicSynthesize(core_smarts: str, max_routes: Optional[int] = None, max_reactions_per_route: Optional[int] = None)

Bases: apache_beam.transforms.ptransform.PTransform

Enumerates unique sanitized molecules from a combinatorial synthesis of unique routes of depth 1, based on the input molecules with fixed frozen heavy core atoms using the default reaction dictionary and reagent library.

The number of routes used may be limited my max_routes, and the number of reactions per route may be limited by max_reactions_per_route.

The route synthesis will be done systematically.

__init__(core_smarts: str, max_routes: Optional[int] = None, max_reactions_per_route: Optional[int] = None)
expand(pcoll)