CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_UA_level_multiprocess

CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_UA_level_multiprocess(arg_hostDataContainer, arg_outFile, arg_selector='all', arg_moutFile=None, arg_nmdFile=None, arg_fScale=1.0, arg_tScale=1.0, arg_temper=300.0, arg_verbose=3, arg_csv_out=None, arg_axis_list=['C', 'CA', 'N'], arg_thread=4)[source]

Computes the entropy calculations at the united atom (UA) level with multiple thread for a CodeEntropy.ClassCollection.DataContainer.DataContainer system. Each heavy atom with its covalently bonded H-atoms make a single bead. H-atoms are, however, treated explicitly. Determining rotation axes is part of the function. Translation axes for each bead by default is the C-Ca-N axes of the residue the bead is part of but can be specified. The rotation axes is a basis whose axes are directed along a sphereical-coordinate axes comprised of unit vectors along r,θ and Φ.

Warning

This uses multiprocess to spread workload across cores to speed up calculation. However, this will cause print and output to files not print in sequential order. For larger dataset running on multithread might result in reduced performance and excessive RAM use due to python GIL which data must be serialized.

Parameters:

  • arg_hostDataContainer (CodeEntropy.ClassCollection.DataContainer.DataContainer) – Data Container for CodeEntropy

  • arg_outFile (str, optional, default: None) – Path to a output file output is written via append mode if it is not None.

  • arg_selector (str, optional, default: “all”) – Selection string for MDanalysis.Universe.select_atoms.

  • arg_moutFile (str, optional, default: None) – Print matrices if path to a matrices out file is not None.

  • arg_nmdFile (str, optional, default: None) – Print modespectra if path to a spectra out file is not None.

  • arg_fScale (float, optional, default: 1.0) – Force scale.

  • arg_tScale (float, optional, default: 1.0) – Torque scale.

  • arg_temper (float, optional, default: 300.0) – Temperature in K

  • arg_verbose (int, optional, default: 3) – Verbose level from 1-5

  • arg_csv_out (str, optional, default: None) – Print entropy of each residue as sorted dataframe if path to a csv out file is not None.

  • arg_axis_list (list of str, optional, default: [‘C’, ‘CA’, ‘N’]) – The atom name of translational axis of each residue. They must be present at each residue of selected atom system

  • arg_thread (int, optional, default: 4) – Number of process to spawn for parallarization.

Returns:

  • entropyFF (float) – United-Atom level level Force-Force Entropy in J/mol/K

  • entropyTT (float) – United-Atom level level Torque-Torque Entropy in J/mol/K

  • result_df (pandas.DataFrame) – The FF and TT entropy for each residue at UA level sort by residue ID