syndirella.pipeline
===================

.. py:module:: syndirella.pipeline

.. autoapi-nested-parse::

   syndirella.run_pipeline.py

   This script contains the main pipeline for syndirella.



Attributes
----------

.. autoapisummary::

   syndirella.pipeline.logger


Functions
---------

.. autoapisummary::

   syndirella.pipeline.assert_scaffold_placement
   syndirella.pipeline.elaborate_from_cobbler_workshops
   syndirella.pipeline.start_elaboration
   syndirella.pipeline.elaborate_compound_with_manual_routes
   syndirella.pipeline.elaborate_compound_full_auto
   syndirella.pipeline.run_pipeline


Module Contents
---------------

.. py:data:: logger

.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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.


.. py:function:: 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']