TIES_MD.ties_analysis package

Subpackages

• TIES_MD.ties_analysis.engines package
  • Submodules
  • TIES_MD.ties_analysis.engines.namd module
    • NAMD
      • NAMD.collate_data()
      • NAMD.run_analysis()
    • get_iter()
    • get_replica()
    • get_window()
    • read_alch_file()
  • TIES_MD.ties_analysis.engines.openmm module
    • Lambdas
      • Lambdas.update_attrs_from_schedule()
    • OpenMM
      • OpenMM.collate_data()
      • OpenMM.run_analysis()
    • get_replica()
    • get_window()
  • Module contents
• TIES_MD.ties_analysis.methods package
  • Submodules
  • TIES_MD.ties_analysis.methods.FEP module
    • MBAR_Analysis
      • MBAR_Analysis.analysis()
      • MBAR_Analysis.decorrelate_data()
      • MBAR_Analysis.plot_overlap_mat()
      • MBAR_Analysis.replica_analysis()
  • TIES_MD.ties_analysis.methods.TI module
    • TI_Analysis
      • TI_Analysis.analysis()
      • TI_Analysis.intergrate()
      • TI_Analysis.plot_du_by_dl()
    • compute_bs_error()
    • get_lam_diff()
  • Module contents

Submodules

TIES_MD.ties_analysis.config module

class TIES_MD.ties_analysis.config.Config(analysis_cfg='./analysis.cfg')

Bases: object

Class that reads the config file and set options.

Parameters:

analysis_cfg – path to file containing general analysis params

get_options()

Function to print options stored in config class

Returns:

None

TIES_MD.ties_analysis.config.read_config(config_file)

Function that is reading config file and build dict of options.

Parameters:

config_file – str, path to a config file

Returns:

dict, containing all options to run analysis

TIES_MD.ties_analysis.ties_analysis module

class TIES_MD.ties_analysis.ties_analysis.Analysis(cfg)

Bases: object

Class that is setting up all engines and methods for analysis.

Parameters:

cfg – dict, holding all options

run()

Function to run the analysis.

Returns:

None

TIES_MD.ties_analysis.ties_analysis.main()

Main function where we chose to setup or run analysis.

Returns:

None

TIES_MD.ties_analysis.ties_analysis.make_exp(verbose=True)

TIES_MD.ties_analysis.ties_analysis.nice_print(string)

Function to print to terminal with padding.

Parameters:

string – str to format

Returns:

None

Module contents