syndirella.check_inputs

syndirella.check_inputs.py

This module contains the functions used to check the inputs for running the pipeline.

Attributes

`check_csv`(→ None)	Make sure that the csv path exists, can be read, and contains the required columns.
`metadata_dict`(→ Dict)	Get the metadata dictionary from the metadata file, checking that it contains the required columns.
`check_template_paths`(→ Set[str])	Get the exact template paths, checking that they exist in the template directory.
`fill_in_product`(→ None)	Fill in the scaffold for the given step.
`check_route`(→ None)	Checks that the route is in the correct format and fills in missing products if needed.
`check_manual`(→ None)	Check that the manual dataframe is in the correct format, otherwise raise errors.
`check_hit_names`(→ None)	Check that the hit names are found within SDF.
`check_apo_template`(→ None)	Check that the template is actually apo (containing no LIG).
`format_additional_info`(→ Dict[str, Any])	This function is used to format the additional info from the dataframe into a dictionary.
`get_exact_hit_names`(→ List[str])	Get the exact hit name to use for placement.
`get_template_path`(→ str)	Get the exact template path to use for placement.
`check_additional_columns`(→ None)	Check that the additional columns are in the csv.
`format_manual_route`(→ Tuple[List[Tuple[Any, Any]], ...)	Format route to output reactants, reaction names, and products.
`check_pipeline_inputs`(→ None)	Check the inputs for the pipeline.

syndirella.check_inputs.check_csv(csv_path: str) → None[source]: Make sure that the csv path exists, can be read, and contains the required columns.

syndirella.check_inputs.metadata_dict(metadata_path: str, long_code_column: str = 'Long code') → Dict[source]: Get the metadata dictionary from the metadata file, checking that it contains the required columns.

syndirella.check_inputs.check_template_paths(template_dir: str, csv_path: str, metadata_path: str) → Set[str][source]: Get the exact template paths, checking that they exist in the template directory.

syndirella.check_inputs.fill_in_product(row: pandas.Series, step: int) → None[source]: Fill in the scaffold for the given step.

syndirella.check_inputs.check_route(i: int, row: pandas.Series) → None[source]: Checks that the route is in the correct format and fills in missing products if needed.

syndirella.check_inputs.check_manual(csv_path: str) → None[source]: Check that the manual dataframe is in the correct format, otherwise raise errors.

syndirella.check_inputs.check_hit_names(csv_path: str, hits_path: str, metadata_path: str, long_code_column: str) → None[source]: Check that the hit names are found within SDF.

syndirella.check_inputs.check_apo_template(template_path: str) → None[source]: Check that the template is actually apo (containing no LIG).

syndirella.check_inputs.format_additional_info(row: pandas.Series, additional_columns: List[str]) → Dict[str, Any][source]: This function is used to format the additional info from the dataframe into a dictionary.

syndirella.check_inputs.get_exact_hit_names(row: pandas.Series, metadata_path: str, hits_path: str) → List[str][source]: Get the exact hit name to use for placement.

syndirella.check_inputs.get_template_path(template_dir: str, template: str, metadata_path: str) → str[source]: Get the exact template path to use for placement.

syndirella.check_inputs.check_additional_columns(csv_path: str, additional_columns: List[str]) → None[source]: Check that the additional columns are in the csv.

syndirella.check_inputs.format_manual_route(row: pandas.Series) → Tuple[List[Tuple[Any, Any]], List[Any], int][source]: Format route to output reactants, reaction names, and products.

syndirella.check_inputs.check_pipeline_inputs(*, csv_path: str, template_dir: str, hits_path: str, metadata_path: str, additional_columns: List[str], manual_routes: bool, long_code_column: str) → None[source]: Check the inputs for the pipeline.