propka.determinants

Working with Determinants

Functions to manipulate propka.determinant.Determinant objects.

See also

propka.determinant

Functions

add_coulomb_acid_pair(object1, object2, value)

Add the Coulomb interaction (an acid pair).

add_coulomb_base_pair(object1, object2, value)

Add the Coulomb interaction (a base pair).

add_coulomb_determinants(group1, group2, ...)

Add non-iterative Coulomb determinants and perturbations.

add_coulomb_ion_pair(object1, object2, value)

Add the Coulomb interaction (an acid-base pair).

add_determinants(group1, group2, distance, ...)

Add determinants and perturbations for distance(R1,R2) < coulomb_cutoff.

add_sidechain_determinants(group1, group2, ...)

Add side-chain determinants and perturbations.

set_backbone_determinants(titratable_groups, ...)

Set determinants between titrable and backbone groups.

set_determinants(propka_groups, version[, ...])

Add side-chain and coulomb determinants/perturbations to all residues.

set_ion_determinants(conformation_container, ...)

Add ion determinants and perturbations.
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

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

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

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

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

propka.determinants.add_sidechain_determinants(group1: Group, group2: Group, version: Version)[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

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

propka.determinants.set_determinants(propka_groups: List[Group], version: Version, 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

propka.determinants.set_ion_determinants(conformation_container, version)[source]

Add ion determinants and perturbations.

Parameters:

  • conformation_container – conformation to set

  • version – version object