tcutility.analysis.vdd package

Submodules

tcutility.analysis.vdd.charge module

class VDDCharge(atom_index, atom_symbol, charge, frag_index)

Bases: object

atom_index: int

atom_symbol: str

charge: float

frag_index: int

change_unit(ratio)

tcutility.analysis.vdd.manager module

change_unit_decorator(func)

create_vdd_charge_manager(results)

Create a VDDChargeManager from a Result object.

Return type:

VDDChargeManager

class VDDChargeManager(vdd_charges, is_fragment_calculation, calc_dir, mol_charge)

Bases: object

Class to manage the VDD charges. It can be used to print the VDD charges in a nice table and write them to a text file or excel file.

vdd_charges: Dict[str, List[VDDCharge]]

is_fragment_calculation: bool

calc_dir: Path

mol_charge: int

name: str

unit: str

irreps: List[str]

charge_is_conserved()

Check if the total charge of the molecule is conserved. The total charge is the sum of the VDD charges.

Return type:

bool

change_unit(new_unit)

Change the unit of the VDD charges. Available units are “me” (mili-electrons) and “e” (electrons).

Return type:

None

get_vdd_charges()

Get the VDD charges in the specified unit ([me] or [e]).

Return type:

Dict[str, List[VDDCharge]]

get_summed_vdd_charges(irreps=None)

Get the summed VDD charges per fragment for the specified unit ([me] or [e]).

Return type:

Dict[str, Dict[str, float]]

get_vdd_charges_dataframe()

Get the VDD charges as a pandas DataFrame in a specified unit ([me] or [e]).

Return type:

DataFrame

get_summed_vdd_charges_dataframe()

Get the summed VDD charges as a pandas DataFrame in a specified unit ([me] or [e]).

Return type:

DataFrame

get_vdd_charges_table()

Return type:

str

get_summed_vdd_charges_table()

Return type:

str

static write_to_txt(output_dir, managers, unit='me')

Write the VDD charges to a text file. It is a static method because multiple managers can be written to the same file.

Return type:

None

write_to_excel(output_file=None)

Write the VDD charges to an excel file. Results are written to two sheets: “VDD charges” and “Summed VDD charges”.

Return type:

None

plot_vdd_charges_per_atom(output_file=None, unit='me')

Plot the VDD charges as a bar graph for each irrep.

Return type:

None

Module contents