OCDocker.Toolbox.Preparation module¶

Strategy Pattern implementation for molecule preparation.

This module provides an abstract interface and concrete implementations for preparing ligands and receptors using different tools (MGLTools, SPORES, OpenBabel).

Usage:

from OCDocker.Toolbox.Preparation import MGLToolsPreparationStrategy

class OCDocker.Toolbox.Preparation.PreparationStrategy[source]¶

Bases: ABC

Abstract base for ligand and receptor preparation backends.

Concrete strategies build external-tool command lines and run preparation with shared availability checks, output-directory creation, and overwrite handling.

get_ligand_command(input_path, output_path)[source]¶

Get the command list that would be used to prepare a ligand.

Parameters:

input_path (str) – Path to input ligand file
output_path (str) – Path to output prepared ligand file

Returns:

Command list that would be executed

Return type:

list[str]

get_receptor_command(input_path, output_path)[source]¶

Get the command list that would be used to prepare a receptor.

Parameters:

input_path (str) – Path to input receptor file
output_path (str) – Path to output prepared receptor file

Returns:

Command list that would be executed

Return type:

list[str]

abstractmethod prepare_ligand(input_path, output_path, log_file='', overwrite=False)[source]¶

Prepare a ligand molecule.

Parameters:

input_path (str) – Path to input ligand file
output_path (str) – Path to output prepared ligand file
log_file (str, optional) – Path to log file (empty to suppress)
overwrite (bool, optional) – Whether to overwrite existing output file (default is False)

Returns:

Error code or tuple of (error_code, stderr)

Return type:

Union[int, str, Tuple[int, str]]

abstractmethod prepare_receptor(input_path, output_path, log_file='', overwrite=False)[source]¶

Prepare a receptor molecule.

Parameters:

input_path (str) – Path to input receptor file
output_path (str) – Path to output prepared receptor file
log_file (str, optional) – Path to log file (empty to suppress)
overwrite (bool, optional) – Whether to overwrite existing output file (default is False)

Returns:

Error code or tuple of (error_code, stderr)

Return type:

Union[int, str, Tuple[int, str]]

class OCDocker.Toolbox.Preparation.MGLToolsPreparationStrategy[source]¶

Bases: PreparationStrategy

Prepare ligands and receptors with MGLTools scripts.

Uses prepare_ligand4.py and prepare_receptor4.py via the configured pythonsh interpreter from OCDocker.Config.ToolsConfig.

get_ligand_command(input_path, output_path)[source]¶

Get the command list that would be used to prepare a ligand.

Parameters:

input_path (str) – Path to input ligand file
output_path (str) – Path to output prepared ligand file

Returns:

Command list that would be executed

Return type:

list[str]

get_receptor_command(input_path, output_path)[source]¶

Get the command list that would be used to prepare a receptor.

Parameters:

input_path (str) – Path to input receptor file
output_path (str) – Path to output prepared receptor file

Returns:

Command list that would be executed

Return type:

list[str]

prepare_ligand(input_path, output_path, log_file='', overwrite=False)[source]¶

Prepare a ligand molecule.

Parameters:

input_path (str) – Path to input ligand file
output_path (str) – Path to output prepared ligand file
log_file (str, optional) – Path to log file (empty to suppress)
overwrite (bool, optional) – Whether to overwrite existing output file (default is False)

Returns:

Error code or tuple of (error_code, stderr)

Return type:

Union[int, str, Tuple[int, str]]

prepare_receptor(input_path, output_path, log_file='', overwrite=False)[source]¶

Prepare a receptor molecule.

Parameters:

input_path (str) – Path to input receptor file
output_path (str) – Path to output prepared receptor file
log_file (str, optional) – Path to log file (empty to suppress)
overwrite (bool, optional) – Whether to overwrite existing output file (default is False)

Returns:

Error code or tuple of (error_code, stderr)

Return type:

Union[int, str, Tuple[int, str]]

class OCDocker.Toolbox.Preparation.SPORESPreparationStrategy[source]¶

Bases: PreparationStrategy

Prepare receptors with the SPORES external tool.

Converts receptor structures to MOL2 and applies SPORES protonation and typing using the configured spores executable.

get_ligand_command(input_path, output_path)[source]¶

Get the command list that would be used to prepare a ligand.

Parameters:

input_path (str) – Path to input ligand file
output_path (str) – Path to output prepared ligand file

Returns:

Command list that would be executed

Return type:

list[str]

get_receptor_command(input_path, output_path)[source]¶

Get the command list that would be used to prepare a receptor.

Parameters:

input_path (str) – Path to input receptor file
output_path (str) – Path to output prepared receptor file

Returns:

Command list that would be executed (same as ligand for SPORES)

Return type:

list[str]

prepare_ligand(input_path, output_path, log_file='', overwrite=False)[source]¶

Prepare a ligand molecule.

Parameters:

input_path (str) – Path to input ligand file
output_path (str) – Path to output prepared ligand file
log_file (str, optional) – Path to log file (empty to suppress)
overwrite (bool, optional) – Whether to overwrite existing output file (default is False)

Returns:

Error code or tuple of (error_code, stderr)

Return type:

Union[int, str, Tuple[int, str]]

prepare_receptor(input_path, output_path, log_file='', overwrite=False)[source]¶

Prepare a receptor molecule.

Parameters:

input_path (str) – Path to input receptor file
output_path (str) – Path to output prepared receptor file
log_file (str, optional) – Path to log file (empty to suppress)
overwrite (bool, optional) – Whether to overwrite existing output file (default is False)

Return type:

int | str | Tuple[int, str]

class OCDocker.Toolbox.Preparation.OpenBabelPreparationStrategy[source]¶

Bases: PreparationStrategy

Prepare ligands and receptors with Open Babel.

Uses the configured obabel executable for format conversion and optional protonation when MGLTools is unavailable (e.g. Gnina workflows).

get_ligand_command(input_path, output_path)[source]¶

Get the command list that would be used to prepare a ligand.

Parameters:

input_path (str) – Path to input ligand file
output_path (str) – Path to output prepared ligand file

Returns:

Command list that would be executed (OpenBabel conversion)

Return type:

list[str]

get_receptor_command(input_path, output_path)[source]¶

Get the command list that would be used to prepare a receptor.

Parameters:

input_path (str) – Path to input receptor file
output_path (str) – Path to output prepared receptor file

Returns:

Command list that would be executed (OpenBabel conversion)

Return type:

list[str]

prepare_ligand(input_path, output_path, log_file='', overwrite=False)[source]¶

Prepare a ligand molecule.

Parameters:

input_path (str) – Path to input ligand file
output_path (str) – Path to output prepared ligand file
log_file (str, optional) – Path to log file (empty to suppress)
overwrite (bool, optional) – Whether to overwrite existing output file (default is False)

Returns:

Error code or tuple of (error_code, stderr)

Return type:

Union[int, str, Tuple[int, str]]

prepare_receptor(input_path, output_path, log_file='', overwrite=False)[source]¶

Prepare a receptor molecule.

Parameters:

input_path (str) – Path to input receptor file
output_path (str) – Path to output prepared receptor file
log_file (str, optional) – Path to log file (empty to suppress)
overwrite (bool, optional) – Whether to overwrite existing output file (default is False)

Returns:

Error code or tuple of (error_code, stderr)

Return type:

Union[int, str, Tuple[int, str]]