Boltzmann#

aleimi.boltzmann.arc_reader(arc: str)[source]#

This , for sure, will change in the future to a more object-oriented paradigm It reads a arc MOPAC file and give a tuple of

Parameters:

arc (str) – The arc file path

Returns:

A list of tuple sorted by energy. Each tuple contains:

  1. cells: conformer identifier,

  2. HeatsOfFormation_kcalmol: self-explanatory,

  3. CONTAINER__H: Coordinates numpy array of the heavy atoms with shape (Number of heavy atoms, 3),

  4. Class_E: The classic energy calculated during aleimi.confgen.main()

Return type:

list[tuple]

aleimi.boltzmann.main(file_path: str, Bd_rmsd: float = 1.0, Bd_E: float = 0.0, BOutPath: bool = True) → DataFrame[source]#

It reads the MOPAC output file (arc or out) and create a Boltzmann table

Parameters:

  • file_path (str) – MOPAC output (.arc or .out). It will be read with aleimi.boltzmann.arc_reader() or aleimi.boltzmann.out_reader() depending on the extension.

  • Bd_rmsd (float, optional) – RMSD to filter out redundant conformations, geometric filter, by default 1.0

  • Bd_E (float, optional) – Energy difference in kJ to filter out redundant conformations, geometric filter, by default 1.0, by default 0.0

  • BOutPath (bool, optional) – Directory to ouput the table {file_name}_boltzmann.csv”, by default True

Returns:

  • pd.DataFrame

  • A Table with columns –

    1. cell: conformer identifier,

    2. Class_E: Classic energy from the RDKit optimization. in this example is NaN because we did not perform this optimization,

    3. HeatOfFormation_kcal: self-explanatory [kcal/mol],

    4. Emin_Ei: Difference in energy between the lower and the i-th conformer in [kcal/mol],

    5. qi__Pi/Pmin__e^(Emin_Ei)/KbT: Boltzmann factors,

    6. Fraction_%__100*qi/q: Occupancy of each conformer,

Raises:

ValueError – _description_

aleimi.boltzmann.out_reader(out)[source]#

This , for sure, will change in the future to a more object-oriented paradigm It reads a out MOPAC file and give a tuple of

Parameters:

out (str) – The arc file path

Returns:

A list of tuple sorted by energy. Each tuple contains:

  1. cells: conformer identifier,

  2. HeatsOfFormation_kcalmol: self-explanatory,

  3. CONTAINER__H: Coordinates numpy array of the heavy atoms with shape (Number of heavy atoms, 3)

  4. Class_E: The classic energy calculated during aleimi.confgen.main()

Return type:

list[tuple]