Contexts

ContextValidator

Base class for validating simulation contexts.

extra_anions(value, context)

Validate extra_anions

extra_cations(value, context)

Validate extra_cations

validate(context_manager)

Validate contexts for simulations.

PARAMETER	DESCRIPTION
context_manager	A simulation context manager to validate. TYPE: SimulationContextManager

RETURNS	DESCRIPTION
bool	If the context is valid.

write(value, context)

Validate write

SimulationContextManager(yaml_path=None, **kwargs)

Contexts for setting up molecular simulations.

PARAMETER	DESCRIPTION
yaml_path	Path to YAML file to load into the context. TYPE: str | None DEFAULT: None

anion_identity = 'Cl-'

Identity of the anion in the system.

cation_identity = 'Na+'

Identity of the cation in the system.

compute_platform = 'mpi'

Desired platform to run simulations on.

Options:

• mpi: Message passing interface for central processing units (CPUs).
• cuda: Compute Unified Device Architecture (CUDA) for graphics processing units (GPUs).

coord_path = None

Path to coordinate file for current stage.

cpu_cores = None

Number of CPU cores to use if requested

extra_anions = 0

Number of extra anions to add to the system.

extra_cations = 0

Number of extra cations to add to the system.

ff_dna = None

Molecular mechanics force fields for DNA.

ff_glycam = None

Molecular mechanics force fields for sugars

ff_ions = None

Molecular mechanics force fields for ions.

ff_lipid = None

Molecular mechanics force fields for lipids.

ff_protein = None

Molecular mechanics force field used to describe polypeptides.

ff_rna = None

Molecular mechanics force fields for RNA.

ff_small_molecule = None

Molecular mechanics force fields for small molecules.

ff_water = None

Molecular mechanics force fields for water.

input_dir = None

Path to input directory for current stage.

input_kwargs = None

Simulation keyword arguments for input files.

input_path = None

Path to input file for current stage.

neutralize_charge = True

Flag to determine if system charge should be neutralized by placing additional ions.

output_dir = None

Path to output directory for current stage.

output_path = None

Path to output file for current stage.

prev_coordinate_path = None

Path to coordinate file of previous stage

prev_restart_path = None

Path to restart file from previous stage or initial coordinates.

ref_coord_path = None

Path to reference coordinate file. This is often used for enforcing restraints.

restart_path = None

Path to restart file for this stage.

run_path = None

Path to run file.

sbatch_options = None

sbatch options for a slurm submission script. Some common options are: job-name, nodes, ntasks-per-node, cpus-per-task, gpus, gres, cpus-per-gpu, chdir, output, error, time, clusters, partition, account.

These options are written in the format of #SBATCH --{key}={value}.

scratch_dir = None

Specify path for scratch directory if desired. If None, we do not use scratch.

slurm_lines = None

Lines for a slurm submission script.

slurm_path = None

Path to slurm submission file.

solvent_ionic_strength = 0.15

Ionic strength of the solvent in mole/L.

solvent_padding = 10.0

Padding between solute and box edge to fill with solvent in Angstroms.

splits = 1

Split simulation stage into several chunks.

stage_name = None

Name or label for simulation stage.

stages = None

Contexts for successive stages. Stage \(i > 0\) is assumed to be restarted from stage \(i - 1\).

submit = False

Submit the job.

system_charge = 0

Net charge of the molecular system.

topo_path = None

Path to topology file.

verbosity = None

Verbosity level for logging.

work_dir = None

Working directory for preparing calculations.

write = False

Write files.

write_dir = None

Write directory.

yaml_path = yaml_path

Path of YAML file that was loaded. Defaults to None.

__enter__()

Enter the context and return the current context as a dictionary.

__exit__(exc_type, exc_value, exc_tb)

Exit the context.

PARAMETER	DESCRIPTION
exc_type	Type of the exception.
exc_value	Value of the exception.
exc_tb	Traceback information.

from_yaml(yaml_path)

Load context information from a YAML file. This will only update data contained in the YAML file.

PARAMETER	DESCRIPTION
yaml_path	Path to YAML file to load. TYPE: str | None

get()

Retrieve the context.

RETURNS	DESCRIPTION
dict[str, Any]	A dictionary representing the current context.

update(attr_dict)

Update attributes with values from the provided dictionary.

PARAMETER	DESCRIPTION
attr_dict	Dictionary containing attribute names and their TYPE: dict[str, Any]

cli_validate_yaml_context()

Command-line interface for validating YAML context files.

run_context_yaml_validator(yaml_path, validator_obj_string)

Validate YAML context.

PARAMETER	DESCRIPTION
yaml_path	Path to YAML file. TYPE: str
validator_obj_string	String to validator object. TYPE: str

RETURNS	DESCRIPTION
bool	If the YAML context is valid.