Prep

Module defining an abstract base class for simulation preparation steps and a concrete implementation for Amber.

SimPrep()

Bases: ABC

Standardized framework for preparing files for molecular simulation runs.

This abstract base class defines the interface for preparing input files, run scripts, and other necessary files for executing molecular dynamics simulations. Concrete implementations of this class should be created for specific simulation packages (e.g., Amber, GROMACS) to handle their unique input file formats, command-line arguments, and workflow requirements.

The SimPrep class provides a set of abstract methods that outline the essential steps involved in simulation preparation. These methods cover configuration preprocessing, input file generation, SLURM script creation, and the construction of the command to execute the simulation. By adhering to this framework, different simulation preparation workflows can be managed in a consistent and modular manner within Simlify.

get_stage_input_lines(simlify_config, **kwargs)

Prepares the lines for a single simulation stage's input file.

This abstract class method is responsible for generating the content of the input file required by the simulation engine for a particular stage of the simulation. The generated lines should be formatted according to the input file syntax of the target simulation package. Implementations in concrete subclasses will define how the input file content is generated based on the provided SimlifyConfig.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing options and parameters relevant to the current simulation stage. TYPE: SimlifyConfig

RETURNS	DESCRIPTION
Collection[str]	A collection (e.g., a list) of strings, where each string represents a line in the input file for the simulation stage. The lines should typically not include the newline character (\n) at the end.

RAISES	DESCRIPTION
NotImplementedError	If this abstract method is called directly. Subclasses must provide their own implementation.

get_stage_run_command(simlify_config, **kwargs)

Prepares the bash command to execute a single simulation stage.

This abstract class method is responsible for constructing the command that will be executed in a shell environment (e.g., bash) to run the simulation for a given stage. This command will typically involve invoking the simulation engine executable with the appropriate input file and any necessary command-line arguments. The specific command will vary depending on the simulation package and the configuration settings.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing options and parameters relevant to the current simulation stage, including the path to the input file and any execution settings. TYPE: SimlifyConfig

RETURNS	DESCRIPTION
Collection[str]	A collection (e.g., a list) of strings, where each string represents a part of the bash command to run the simulation stage. These parts might be joined together with spaces to form the complete command.

RAISES	DESCRIPTION
NotImplementedError	If this abstract method is called directly. Subclasses must provide their own implementation.

Notes

It is expected that the prepare_sim_config method has been called prior to this method to ensure that the simlify_config object is properly prepared.

prepare(simlify_config, **kwargs)

Runs all necessary steps to prepare the simulations based on the provided configuration.

This abstract class method serves as the main entry point for the simulation preparation process. It should call the other preparation methods in the correct order to generate all required input files, run scripts, and any other necessary files for the entire simulation workflow, which might consist of multiple stages.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing all the necessary options and parameters for the simulation. TYPE: SimlifyConfig

prepare_sim_config(simlify_config, **kwargs)

Preprocesses and validates the simulation configuration for a specific simulation package.

This abstract static method is responsible for performing any necessary preprocessing and validation of the SimlifyConfig object before the simulation preparation proceeds. This step is crucial for ensuring that all required parameters are set, paths are correct, and the configuration is consistent with the requirements of the target simulation package. Implementations of this method in concrete subclasses should handle the specific configuration needs of their respective simulation engines.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing options and parameters for the simulation. This object might be modified in-place during the preprocessing and validation. TYPE: SimlifyConfig

RETURNS	DESCRIPTION
SimlifyConfig	The potentially modified Simlify configuration object after preprocessing and validation.

RAISES	DESCRIPTION
NotImplementedError	If this abstract method is called directly. Subclasses must provide their own implementation.

prepare_slurm(file_path, simlify_config, write=True, **kwargs)

Prepares the lines for a SLURM submission script.

This class method generates the content for a SLURM (Simple Linux Utility for Resource Management) submission script based on the SLURM configuration specified in the SimlifyConfig. The generated script can be used to submit the simulation job to a SLURM-managed cluster.

PARAMETER	DESCRIPTION
file_path	The full path to the file where the SLURM submission script will be written if `write: The Simlify configuration object containing the SLURM-specific settings (e.g., number of nodes, tasks per node, time limit). TYPE: str
write	A boolean flag indicating whether to write the generated SLURM script to the specified file_path. Defaults to True. If False, the lines of the script are returned but not written to disk. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
list[str]	A list of strings, where each string represents a line in the generated SLURM submission script, including the newline character (\n) at the end of each line.

Notes

The SLURM configuration is typically defined within the simlify_config.slurm attribute, which is expected to be an object with a render method that generates the script content.

prepare_stage(simlify_config, run_commands=None, write=True, **kwargs)

Prepares the input files for a single simulation stage and builds the bash commands to run it.

This abstract class method orchestrates the preparation of a single stage in the simulation workflow. It typically involves generating the input file content using get_stage_input_lines, optionally writing this content to a file, and then constructing the command to run the simulation for this stage using get_stage_run_command.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing options and parameters relevant to the current simulation stage. TYPE: SimlifyConfig
run_commands	A list of bash commands accumulated from previous stages. The commands for the current stage will be appended to this list. Defaults to None, in which case a new list is created. TYPE: list[str] | None DEFAULT: None
write	A boolean flag indicating whether to write the input file to disk. Defaults to True. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
tuple[list[str], list[str]]	A tuple containing two lists: - The lines of the input file generated for this stage. - The updated list of bash commands, including the command(s) for this stage.

RAISES	DESCRIPTION
NotImplementedError	If this abstract method is called directly. Subclasses must provide their own implementation.