schrodinger.application.desmond.msj_generator.lambda_dynamics module¶

class schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: Optional[str] = None, salt_concentration: Optional[float] = 0.0, membrane: Optional[str] = None, sim_time: Optional[int] = 5000, equilibration_time: Optional[int] = None, sim_time_complex: Optional[int] = None, sim_time_solvent: Optional[int] = None, sim_time_vacuum: Optional[int] = None, sim_time_fragment: Optional[int] = None, max_walltime: int = 0, lambda_windows: Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: Optional[int] = None, core_hopping_lambda_windows: Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: Optional[str] = None, ff_structure_file: Optional[str] = None, restraints_file: Optional[str] = None, pmf_coefficients_fname: Optional[str] = None, mutations_filename: str = 'mutations.txt', mutation_chain_asl: Optional[str] = None, order: int = 5, softcore_enabled: bool = True, linear_schedule: bool = False, n_segments: int = 20, adapt_iterations: int = 4, adapt_interval: float = 2000.0, phs: List[float] = <factory>, pH: float = 7.0)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.SimLegParams

pmf_coefficients_fname: Optional[str] = None¶

mutations_filename: str = 'mutations.txt'¶

mutation_chain_asl: Optional[str] = None¶

order: int = 5¶

softcore_enabled: bool = True¶

linear_schedule: bool = False¶

n_segments: int = 20¶

adapt_iterations: int = 4¶

adapt_interval: float = 2000.0¶

phs: List[float]¶

pH: float = 7.0¶

__init__(forcefield: str = 'S-OPLS', rand_seed: int = 2014, ensemble: str = 'NPT', buffer_width: float = 0.0, molecules: int = 64, water_model: typing.Optional[str] = None, salt_concentration: typing.Optional[float] = 0.0, membrane: typing.Optional[str] = None, sim_time: typing.Optional[int] = 5000, equilibration_time: typing.Optional[int] = None, sim_time_complex: typing.Optional[int] = None, sim_time_solvent: typing.Optional[int] = None, sim_time_vacuum: typing.Optional[int] = None, sim_time_fragment: typing.Optional[int] = None, max_walltime: int = 0, lambda_windows: typing.Optional[int] = None, custom_charge_mode: str = 'assign', charged_lambda_windows: typing.Optional[int] = None, core_hopping_lambda_windows: typing.Optional[int] = None, h_mass: bool = True, concatenate: bool = True, skip_legs: typing.List = <factory>, ffbuilder: bool = False, modify_dihe: bool = False, minimize_volume: bool = False, rest_asl: str = 'asl: atom.%s 1', ff_host: typing.Optional[str] = None, ff_structure_file: typing.Optional[str] = None, restraints_file: typing.Optional[str] = None, pmf_coefficients_fname: typing.Optional[str] = None, mutations_filename: str = 'mutations.txt', mutation_chain_asl: typing.Optional[str] = None, order: int = 5, softcore_enabled: bool = True, linear_schedule: bool = False, n_segments: int = 20, adapt_iterations: int = 4, adapt_interval: float = 2000.0, phs: typing.List[float] = <factory>, pH: float = 7.0) → None¶

class schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsWorkflowParams(sim_params: schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams = <factory>)¶

Bases: schrodinger.application.desmond.msj_generator.workflow_params.WorkflowParams

sim_params: schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams¶

__init__(sim_params: schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsSimLegParams = <factory>) → None¶

class schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsMsjGenerator(jobname: str, cd_params: Dict[str, object], **kwargs)¶

Bases: schrodinger.application.desmond.msj_generator.common.BaseMsjGenerator

Msj generator class for the Lambda Dynamics workflow.

This class generates a main job msj from the template lambda_dynamics.msj and sets the user-supplied mutations_filename option in the LambdaDynamicsMapper stage and sets the job command and pmf_coefficients option for the LambdaDynamicsMdLauncher stage. This class also generates a md subjob msj from the lambda_dynamics_md.msj.

TEMPLATE_MSJ = 'lambda_dynamics.msj'¶

TEMPLATE_MD_MSJ = 'lambda_dynamics_md.msj'¶

WorkflowParamsCls¶: alias of schrodinger.application.desmond.msj_generator.lambda_dynamics.LambdaDynamicsWorkflowParams

__init__(jobname: str, cd_params: Dict[str, object], **kwargs)¶

# TODO consider renaming cpus to gpus or more generic slots :param jobname: The jobname.

Parameters: cd_params – A dictionary with cpus set to the number of gpu slots to use, and ‘mps_factor` set to the number of processes per GPU.

write_main_msj() → str¶: Write the main msj for the workflow.

write_md_msj() → str¶: Write the md msj for the workflow.

generate_main_msj() → schrodinger.application.desmond.multisim.parser.Msj¶: Generate the main msj for the workflow.

generate_md_msj() → schrodinger.application.desmond.multisim.parser.Msj¶: Generate the md msj for the workflow.