schrodinger.application.desmond.stage.app.lambda_dynamics_analysis module

class schrodinger.application.desmond.stage.app.lambda_dynamics_analysis.LambdaDynamicsAnalysis(should_pack=True)

Bases: schrodinger.application.desmond.cmj.StageBase

Stage to handle analysis of Lambda Dynamics output data.

NAME = 'lambda_dynamics_analysis'

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

crunch()

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

schrodinger.application.desmond.stage.app.lambda_dynamics_analysis.calc_ddg_dataframe(mutation_dg_csv_fname: pathlib.Path, complex_dg_csv_fname: pathlib.Path) → pandas.core.frame.DataFrame

Merge the dG files output from the bound and unbound lambda dynamics workflow and calculate the ddG by finding their difference, and return a new dataframe displaying all three pieces of information

Parameters

• mutation_dg_csv_fname – path to the dg csv file output from the lambda dynamics mutation chain subworkflow

• complex_dg_csv_fname – path to the dg csv file output from the lambda dynamics complex subworkflow

Returns

a DataFrame containing the dG values at each site for the bound and unbound workflows and also the calculated ddG results