transformato.utils

Description

Functions

utils.check_switching_function()

There are three possibilities for the CHARMM/openMM switching functions: - vfswitch - switch - no-switch (not implemented — this will use vfswitch)

utils.get_bin_dir()

Returns the bin directory of this package

utils.get_structure_name(structure_name)
Parameters:

  • configuration (dict)

  • structure_name (str)

utils.get_test_output_dir()
utils.get_toppar_dir()
utils.isnotebook()
utils.load_config_yaml(input_dir, output_dir)
Return type:

dict

utils.map_lj_mutations_to_atom_idx()

returns a mapping between the mutations and the atom idx

Parameters:

lj_mutations (list of lj mutation objects) – [description]

Return type:

dict

utils.postprocessing(name='methane', engine='openMM', max_snapshots=300, num_proc=4, show_summary=False, different_path_for_dcd='', only_single_state='', analyze_traj_with='mdtraj', multiple_runs=0)

Performs postprocessing using either openMM or CHARMM and calculates the free energy estimate using MBAR.

Parameters:

  • configuration (dict) – Configuration file.

  • name (str, optional) – The name of the system as deposited in the configuration file. Defaults to “methane”.

  • engine (str, optional) – The MD engine, either openMM or CHARMM. Defaults to “openMM”.

  • max_snapshots (int, optional) – Maximum number of snapshots per lambda window. Defaults to 300.

  • show_summary (bool, optional) – Plot the accumulated free energy estimate and overlap plot. Defaults to False.

  • different_path_for_dcd (str, optional) – For debugging purpose only. Defaults to “”.

  • only_single_state (str, optional) – For debugging purpose only. Defaults to “”.

  • analyze_traj_with (str,optional) – Select package for loading trajectories (either mdanalysis or mdtraj). Defaults to mdtraj.

  • num_proc (int)

  • multiple_runs (int)

Returns:

[description]

Return type:

[type]

utils.psf_correction()

Correcting the issue with 2 missing spaces in the waterbox psf files and replacing the !NGRP statement so its possible that CHARMM, CHARMM_OpenMM and OpenMM can handle the correspoing psf file

Parameters:

str_object (StringIO)

utils.run_simulation(engine='openMM', only_vacuum=False)

Performs sampling given a list of directories with topology and parameter definitions

Parameters:

  • output_files (list) – List of directories with topology and parameter files in CHARMM format

  • engine (str, optional) – The MD engines used to perform the sampling. Defaults to “openMM”.

  • only_vacuum (bool, optional) – For debugging only. Defaults to False.