propka.iterative

Working with Determinants

Iterative functions for pKa calculations. These appear to mostly involve propka.determinant.Determinant instances.

Functions

add_determinants(iterative_interactions, version)

Add determinants iteratively.

add_iterative_acid_pair(object1, object2, ...)

Add the Coulomb 'iterative' interaction (an acid pair).

add_iterative_base_pair(object1, object2, ...)

Add the Coulomb 'iterative' interaction (a base pair).

add_iterative_ion_pair(object1, object2, ...)

Add the Coulomb 'iterative' interaction (an acid-base pair)

add_to_determinant_list(group1, group2, ...)

Add iterative determinantes to the list.

find_iterative(pair, iteratives)

Find the 'iteratives' that correspond to the groups in 'pair'.

Classes

Iterative(group)

Iterative class - pKa values and references of iterative groups.
class propka.iterative.Iterative(group: Group)[source]

Iterative class - pKa values and references of iterative groups.

NOTE - this class has a fake determinant list, true determinants are made after the iterations are finished.

propka.iterative.add_determinants(iterative_interactions: List[list], version: Version)[source]

Add determinants iteratively.

The iterative pKa scheme. Later it is all added in ‘calculateTotalPKA’

Parameters:

  • iterative_interactions – list of iterative interactions

  • version – version object

  • _ – options object

propka.iterative.add_iterative_acid_pair(object1: Iterative, object2: Iterative, interaction: list)[source]

Add the Coulomb ‘iterative’ interaction (an acid pair).

The higher pKa is raised with QQ+HB The lower pKa is lowered with HB

Parameters:

  • object1 – first object in pair

  • object2 – second object in pair

  • interaction – list with [values, annihilation]

propka.iterative.add_iterative_base_pair(object1: Iterative, object2: Iterative, interaction: list)[source]

Add the Coulomb ‘iterative’ interaction (a base pair).

The lower pKa is lowered

Parameters:

  • object1 – first object in pair

  • object2 – second object in pair

  • interaction – list with [values, annihilation]

propka.iterative.add_iterative_ion_pair(object1: Iterative, object2: Iterative, interaction: list, version: Version)[source]

Add the Coulomb ‘iterative’ interaction (an acid-base pair)

the pKa of the acid is lowered & the pKa of the base is raised

Parameters:

  • object1 – first object in pair

  • object2 – second object in pair

  • interaction – list with [values, annihilation]

  • version – version object

propka.iterative.add_to_determinant_list(group1: Group, group2: Group, distance: float, iterative_interactions: List[list], version: Version)[source]

Add iterative determinantes to the list.

[[R1, R2], [side-chain, coulomb], [A1, A2]], …

NOTE - sign is determined when the interaction is added to the iterative

object!

NOTE - distance < coulomb_cutoff here

Parameters:

  • group1 – first group in pair

  • group2 – second group in pair

  • distance – distance between groups

  • iterative_interactions – interaction list to modify

  • version – version object

propka.iterative.find_iterative(pair: Sequence[Group], iteratives: Iterable[Iterative]) → Tuple[Iterative, Iterative][source]

Find the ‘iteratives’ that correspond to the groups in ‘pair’.

Parameters:

  • pair – groups to match

  • iteratives – list of iteratives to search

Returns:

  1. first matched iterative

  2. second matched iterative