Running tools¶

How to use this reference

This page contains information about each class and function in this module. This is meant as a detailed reference for this module. If you're looking an introduction, we recommend reviewing the How to section.

This module contains functions to start runs of various first-party tools on the Deep Origin platform

autodock_vina ¶

autodock_vina(
    *,
    database_id: str,
    row_id: str,
    search_space: dict,
    docking: dict,
    output_column_name: str,
    receptor_column_name: str,
    ligand_column_name: str
) -> str

starts an run of AutoDock Vina on the Deep Origin platform.

Parameters:

Name	Type	Description	Default
`database_id`	`str`	database ID or name of the database to source inputs from and write outputs to	required
`row_id`	`str`	row ID or name of the row to source inputs from and write outputs to.	required
`search_space`	`dict`	search space parameters. Must include keys 'center_x', 'center_y', 'center_z', 'size_x', 'size_y', and 'size_z'	required
`docking`	`dict`	docking parameters. Must include keys 'energy_range', 'exhaustiveness', and 'num_modes'	required
`output_column_name`	`str`	name of the column to write output file to	required
`receptor_column_name`	`str`	name of the column to source the receptor file from	required
`ligand_column_name`	`str`	name of the column to source the ligand file from	required

Returns:

Name	Type	Description
`str`	`str`	ID of the job. This ID can be used to query status.

ligand_prep ¶

ligand_prep(
    *,
    database_id: str,
    row_id: str,
    output_column_name: str,
    ligand_column_name: str
) -> str

starts a run of Ligand Prep (Meeko) on the Deep Origin platform.

Parameters:

Name	Type	Description	Default
`database_id`	`str`	ID or HID of the database	required
`row_id`	`str`	ID or HID of the row	required
`output_column_name`	`str`	name of the column to write results to (the prepared ligand)	required
`ligand_column_name`	`str`	name of the column in the database that contains the input ligand	required

Returns:

Name	Type	Description
`str`	`str`	ID of the job. This ID can be used to query status.

receptor_prep ¶

receptor_prep(
    *,
    database_id: str,
    row_id: str,
    output_column_name: str,
    receptor_column_name: str,
    add_missing_residues: Optional[bool] = True,
    add_missing_atoms: Optional[bool] = True,
    add_missing_hydrogens: Optional[bool] = True,
    ph: Optional[float] = 7.4,
    remove_heterogens: Optional[bool] = True,
    remove_water: Optional[bool] = True
) -> str

starts a run of Receptor Prep (PDBFixer) on the Deep Origin platform.

Parameters:

Name	Type	Description	Default
`database_id`	`str`	ID or HID of the database	required
`row_id`	`str`	ID or HID of the row	required
`output_column_name`	`str`	name of the column to write results to (the prepared ligand)	required
`receptor_column_name`	`str`	name of the column in the database that contains the input ligand	required
`add_missing_residues`	`bool`	whether to add missing residues. Defaults to True.	`True`
`add_missing_atoms`	`bool`	whether to add missing atoms. Defaults to True.	`True`
`add_missing_hydrogens`	`bool`	whether to add missing hydrogens. Defaults to True.	`True`
`ph`	`float`	pH value. Defaults to 7.4.	`7.4`
`remove_heterogens`	`bool`	whether to remove heterogens. Defaults to True.	`True`
`remove_water`	`bool`	whether to remove water. Defaults to True.	`True`

Returns:

Name	Type	Description
`str`	`str`	ID of the job. This ID can be used to query status.