4.4.6. propka.iterative¶
4.4.6.1. Working with Determinants¶
Iterative functions for pKa calculations. These appear to mostly
involve propka.determinant.Determinant instances.
Functions
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Add determinants iteratively. |
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Add the Coulomb ‘iterative’ interaction (an acid pair). |
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Add the Coulomb ‘iterative’ interaction (a base pair). |
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Add the Coulomb ‘iterative’ interaction (an acid-base pair) |
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Add iterative determinantes to the list. |
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Find the ‘iteratives’ that correspond to the groups in ‘pair’. |
Classes
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Iterative class - pKa values and references of iterative groups. |
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class
propka.iterative.Iterative(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.
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propka.iterative.add_determinants(iterative_interactions, version, _=None)[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
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propka.iterative.add_iterative_acid_pair(object1, object2, interaction)[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]
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propka.iterative.add_iterative_base_pair(object1, object2, interaction)[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]
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propka.iterative.add_iterative_ion_pair(object1, object2, interaction, 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
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propka.iterative.add_to_determinant_list(group1, group2, distance, iterative_interactions, 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