implicit_solvent_ddm.config

Dataclass to make life a little easier, which defines config properties, sub-properties, and types in a config.py file. Using a dataclass rather a dictionary ensures all key values pairs are read in (YAML config) before initiating the workflow.

Functions

workflow(job, config)

Classes

AmberMasks(receptor_mask, ligand_mask)	AMBER masks to denote receptor/host and guest atoms
BasicMD(method_type[, md_template_mdin])	Parameters to run a basic Molecular Dynamics (MD) simulation.
Config(workflow, system_settings, ...[, ...])	Encapsulates user-specified configuration parameters for the simulation workflow.
EndStateMethod(endstate_method_type, ...)	Defines the strategy for simulating endstates: either a long MD simulation or Replica Exchange Molecular Dynamics (REMD).
FlatBottomRestraints([flat_bottom_width, ...])	Parameters for flat-bottom distance restraints between receptor and ligand atoms.
IntermediateStateArgs(...[, ...])	Parameter arguments used for intermediate simulation steps within the thermodynamic cycle.
NumberOfCoresPerSystem(complex_ncores, ...)	Number of cores specified for respected host, guest and complex simulation.
ParameterFiles(complex_parameter_filename, ...)	Stores and manages AMBER parameter and coordinate file paths for MD simulations.
REMD(method_type[, remd_template_mdin, ...])	Parameters for running Replica Exchange Molecular Dynamics (REMD).
SystemSettings([mpi_command, ...])	SystemSettings defines system-level parameters for MD simulations.
Workflow([setup_workflow, ...])	Defines the configuration for a modular computational workflow.