CodeEntropy.ClassCollection.PoseidonClass.Poseidon.run_analysis

Poseidon.run_analysis(temperature=298.0, entropyEnergy=True, level_list=['moleculeLevel'], solvent=None, water='WAT', verbose=False, weighting=None, forceUnits='kJ')[source]

Perform analysis using poseidon

Parameters:

  • temperature (float, Optional, default: 298.0) – Temperature for system.

  • entropyEnergy (Bool, Optional, default: True) – Run entropy and energy analysis.

  • level_list (list of str, Optional, default: [‘moleculeLevel’]) – Choose and refine the level of analyiss: moleculeLevel, residLevel_resname, atomLevel, soluteContacts.

  • solvent (str, Optional, default: None) – Resname for solvent.

  • water (str or list of str, Optional, default: ‘WAT’) – Resname for water.

  • verbose (bool, Optional, default: False) – Print out progress of each step.

  • weighting (str or None, Optional, default: None) – Get weighing for each frame if the simulation is biased.

  • forceUnits (str, Optional, default: ‘kJ’) – Units of forces, kJ or Kcal.

Returns:

solventData: dataframe that contains the result for solvent soluteData: dataframe that contains the result for solute contactMatrix: dataframe that contains the contact matrix

Return type:

Tuple of DataFrame, for each level analysed