4.4.4. propka.determinants¶
4.4.4.1. Working with Determinants¶
Functions to manipulate propka.determinant.Determinant
objects.
See also
Functions
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Add the Coulomb interaction (an acid pair). |
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Add the Coulomb interaction (a base pair). |
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Add non-iterative Coulomb determinants and perturbations. |
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Add the Coulomb interaction (an acid-base pair). |
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Add determinants and perturbations for distance(R1,R2) < coulomb_cutoff. |
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Add side-chain determinants and perturbations. |
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Set determinants between titrable and backbone groups. |
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Add side-chain and coulomb determinants/perturbations to all residues. |
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Add ion determinants and perturbations. |
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propka.determinants.
add_coulomb_acid_pair
(object1, object2, value)[source]¶ Add the Coulomb interaction (an acid pair).
The higher pKa is raised.
- Parameters
object1 – first part of pair
object2 – second part of pair
value – determinant value
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propka.determinants.
add_coulomb_base_pair
(object1, object2, value)[source]¶ Add the Coulomb interaction (a base pair).
The lower pKa is lowered.
- Parameters
object1 – first part of pair
object2 – second part of pair
value – determinant value
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propka.determinants.
add_coulomb_determinants
(group1, group2, distance, version)[source]¶ Add non-iterative Coulomb determinants and perturbations.
- Parameters
group1 – first group to add
group2 – second group to add
distance – distance between groups
version – version object
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propka.determinants.
add_coulomb_ion_pair
(object1, object2, value)[source]¶ Add the Coulomb interaction (an acid-base pair).
The pKa of the acid is lowered & the pKa of the base is raised.
- Parameters
object1 – first part of pair
object2 – second part of pair
value – determinant value
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propka.determinants.
add_determinants
(group1, group2, distance, version)[source]¶ Add determinants and perturbations for distance(R1,R2) < coulomb_cutoff.
- Parameters
group1 – first group to add
group2 – second group to add
distance – distance between groups
version – version object
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propka.determinants.
add_sidechain_determinants
(group1, group2, version=None)[source]¶ Add side-chain determinants and perturbations.
NOTE - res_num1 > res_num2
- Parameters
group1 – first group to add
group2 – second group to add
version – version object
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propka.determinants.
set_backbone_determinants
(titratable_groups, backbone_groups, version)[source]¶ Set determinants between titrable and backbone groups.
- Parameters
titratable_groups – list of titratable groups
backbone_groups – list of backbone groups
version – version object
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propka.determinants.
set_determinants
(propka_groups, version=None, options=None)[source]¶ Add side-chain and coulomb determinants/perturbations to all residues.
NOTE - backbone determinants are set separately
- Parameters
propka_groups – groups to adjust
version – version object
options – options object