schrodinger.application.desmond.stage.app.lambda_dynamics module

class schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMapper(*args, **kwargs)

Bases: schrodinger.application.desmond.cmj.StructureStageBase

Generate the mutant proteins and map the forcefield terms to prepare for lambda dynamics simulations.

This stage expects a mutations file as well as a cms file to be passed from a previous stage that has run through both the build_geometry and assign_forcefield stages. The output file from this stage will be a cms file with the original protein system and additional lambda dynamics information stored in the s_fep_TITRATION_STATES property.

NAME = 'lambda_dynamics_mapper'

PARAM = <schrodinger.utils.sea.sea.Map object>

collect_inputfile() → List[str]

Return the input file needed from the launch directory.

run(jobname: str, input_fname: str) → Optional[str]

Parameters

• jobname – Jobname for this stage.

• input_fname – Filename for the input structure.

Returns

Filename for the output structure or None if there was an error generating the output.

class schrodinger.application.desmond.stage.app.lambda_dynamics.LambdaDynamicsMdLauncher(should_pack=True)

Bases: schrodinger.application.desmond.stage.launcher.Multisim

Generate the adaptive pmf coefficients to be added to the md subjob msj and launch the md subjob for the lambda dynamics workflow.

This stage expects a lambda dynamics cms produced from the LambdaDynamicsMapper stage to be passed from a previous stage. The output of this stage will be a .yaml file containing the adaptive pmf coefficients for the job, the completed md subjob msj, the cfg for the md subjob, and the output from the md subjob.

NAME = 'lambda_dynamics_md_launcher'

PARAM = <schrodinger.utils.sea.sea.Map object>

collect_inputfile() → List[str]

Return the input file needed from the launch directory.

crunch()

This is where jobs of this stage are created. This function should be overriden by the subclass.

hook_captured_successful_job(job: schrodinger.application.desmond.cmj.Job)