syndirella.pipeline

syndirella.run_pipeline.py

This script contains the main pipeline for syndirella.

Attributes

logger

Functions

assert_scaffold_placement(...)	Assert that the scaffold can be placed for any stereoisomers. If not, raise an error.
elaborate_from_cobbler_workshops(cobbler_workshops, ...)	Does elaboration once the cobbler workshops are created.
start_elaboration(→ Tuple[float, ...)	Starts the elaboration of a single compound.
elaborate_compound_with_manual_routes(product, ...[, ...])	This function is used to elaborate a single compound using a manually defined route.
elaborate_compound_full_auto(product, hits, ...[, ...])	This function is used to elaborate a single compound.
run_pipeline(settings)	Run the whole syndirella pipeline! 👑

Module Contents

syndirella.pipeline.logger

syndirella.pipeline.assert_scaffold_placement(scaffold: str, template_path: str, hits_path: str, hits_names: List[str], output_dir: str, scaffold_place_num: int) → Dict[syndirella.error.Chem.Mol, str]

Assert that the scaffold can be placed for any stereoisomers. If not, raise an error.

syndirella.pipeline.elaborate_from_cobbler_workshops(cobbler_workshops: List[syndirella.route.CobblersWorkshop.CobblersWorkshop], template_path: str, hits_path: str, hits: List[str], batch_num: int, csv_path: str, output_dir: str, scaffold_placements: Dict[syndirella.error.Chem.Mol, str], additional_info=None)

Does elaboration once the cobbler workshops are created.

syndirella.pipeline.start_elaboration(product: str, template_path: str, hits_path: str, hits: List[str], output_dir: str, scaffold_place_num: int, no_scaffold_place: bool) → Tuple[float, Dict[syndirella.error.Chem.Mol, str | None] | Dict]

Starts the elaboration of a single compound.

syndirella.pipeline.elaborate_compound_with_manual_routes(product: str, reactants: List[Tuple[str, str]], reaction_names: List[str], num_steps: int, hits: List[str], template_path: str, hits_path: str, batch_num: int, output_dir: str, csv_path: str, atom_diff_min: int, atom_diff_max: int, scaffold_place_num: int, scaffold_place: bool, no_scaffold_place: bool, additional_info=None)

This function is used to elaborate a single compound using a manually defined route.

syndirella.pipeline.elaborate_compound_full_auto(product: str, hits: List[str], template_path: str, hits_path: str, batch_num: int, output_dir: str, csv_path: str, atom_diff_min: int, atom_diff_max: int, scaffold_place_num: int, scaffold_place: bool, no_scaffold_place: bool, additional_info=None)

This function is used to elaborate a single compound.

syndirella.pipeline.run_pipeline(settings: Dict)

Run the whole syndirella pipeline! 👑

OUTDATED DOCSTRING: Settings dict should have these keys:

csv_path=settings[‘input’], output_dir=settings[‘output’], template_dir=settings[‘templates’], hits_path=settings[‘hits_path’], metadata_path=settings[‘metadata’], batch_num=settings[‘batch_num’], additional_columns=[‘compound_set’], # Will always be compound_set manual_routes=settings[‘manual’], atom_diff_min=settings[‘atom_diff_min’], atom_diff_max=settings[‘atom_diff_max’]