repESP.util module

Constants and convenience functions for interacting with the library

angstrom_per_bohr = 0.5291772086

The conversion factor from Bohr radii (a₀) to angstrom (Å)

Value used by Gaussian 09, based on: P. J. Mohr, B. N. Taylor, and D. B. Newell, “CODATA Recommended Values of the Fundamental Physical Constants: 2006,” Rev. Mod. Phys., 80 (2008) 633-730. DOI: 10.1103/RevModPhys.80.633.

Type:float
list_from_dict(dict_: Dict[int, T1], length: int, default: T2 = None, one_indexed: bool = False) → List[Union[T1, T2]][source]

Convenience function for creating lists from dictionaries

For sparse data or certain user input it may be easier to represent properties of a list (e.g. equivalence information for each atom in a molecule) as a dictionary. However, many interfaces of this library expect lists and thus this convenience function is provided for the conversion.

Example

>>> list_from_dict({1: "foo"}, 3, "bar")
["bar", "foo", "bar"]
Parameters:
  • dict_ (typing.Dict[int, T1]) –

    The dictionary mapping the index of the desired list to its property, which is of the generic type T1. If this argument contains keys outside the range of valid indices in the desired list, the input is not valid; no errors will be raised but these keys will be ignored.

    Valid indices are integer values of i that fulfil 0 <= i < length if one_indexed is False and 0 < i <= length otherwise.

  • length (int) – The length of the desired list.
  • default (T2, optional) – The value to be used in the output list when the index is not included in the dict_ argument. The type of this value is not required to be of the same type T1 as the values of dict_. Defaults to None.
  • one_indexed (bool, optional) – Whether the list indices in the keys of the input dict_ are counting from one. Defaults to False, meaning they are counting from zero.
Returns:

A list of items of the given length with values specified in dict_.
Return type:

typing.List[Union[T1, T2]]
mask_from_list(list_: List[int], length: int, value_if_present: T1 = True, value_if_absent: T2 = False, one_indexed: bool = False) → List[Union[T1, T2]][source]

Convenience function for creating masks from lists

For sparse data or certain user input it may be easier to represent properties of a list (e.g. whether each atom belongs to a methyl or methylene group) as a list of elements which have a certain value of the property. However, some interfaces of this library expect complete lists (‘masks’) and thus this convenience function is provided for the conversion.

Example

>>> mask_from_list([1], 3)
[False, True, False]

Note that the same output can always be achieved with the list_from_dict function.

>>> list_from_dict({1: True}, 3, False)
[False, True, False]

The difference is that list_from_dict allows more than two values in the output list. When only two values are needed, mask_from_list has a more convenient input format.

Parameters:
  • list_ (typing.List[int]) –

    The list of indices, for which the corresponding values in the resulting list are to have value_if_present as the value (and value_if_absent otherwise).

    If this argument contains values outside the range of valid indices in the desired list, the input is not valid; no errors will be raised but these keys will be ignored.

    Valid indices are integer values of i that fulfil 0 <= i < length if one_indexed is False and 0 < i <= length otherwise.

  • length (int) – The length of the desired list.
  • value_if_present (T1, optional) – The value to be assigned to the element of the output list if the corresponding argument is present in the list_ argument. Defaults to True.
  • value_if_absent (T2, optional) – The value to be assigned to the element of the output list if the corresponding argument is absent from the list_ argument. Defaults to False.
  • one_indexed (bool, optional) – Whether the list indices in the keys of the input dict_ are counting from one. Defaults to False, meaning they are counting from zero.
Returns:

A list of length length with values equal to value_if_present if the corresponding item is in the input list_ and value_if_absent otherwise.
Return type:

typing.List[Union[T1, T2]]