CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_UA_level

CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_UA_level(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_csv_out=None, arg_axis_list=['C', 'CA', 'N'], arg_verbose=3)[source]

Computes the entropy calculations at the united atom (UA) level 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.

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_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_verbose (int, optional, default: 3) – Verbose level from 1-5

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