4.4.2. propka.coupled_groups

4.4.2.1. Coupling between groups

Describe and analyze energetic coupling between groups.

Classes

NonCovalentlyCoupledGroups()

Groups that are coupled without covalent bonding.

class propka.coupled_groups.NonCovalentlyCoupledGroups[source]

Groups that are coupled without covalent bonding.

get_free_energy_diff_factor(energy1, energy2)[source]

Get scaling factor for difference between free energies.

Parameters
  • energy1 – first energy to compare

  • energy2 – second energy to compare

Returns

float value of scaling factor

static get_interaction(group1, group2, include_side_chain_hbs=True)[source]

Get interaction energy between two groups.

Parameters
  • group1 – first group for interaction

  • group2 – second group for interaction

  • include_side_chain_hbs – include sidechain hydrogen bonds in energy

Returns

interaction energy (float)

get_interaction_factor(interaction_energy)[source]

Get scaling factor related to interaction energy.

Parameters

interaction_energy – interaction energy

Returns

float value of scaling factor

get_pka_diff_factor(pka1, pka2)[source]

Get scaling factor for difference between intrinsic pKa values.

Parameters
  • pka1 – first pKa to compare

  • pka2 – second pKa to compare

Returns

float value of scaling factor

identify_non_covalently_coupled_groups(conformation, verbose=True)[source]

Find coupled residues in protein.

Parameters
  • conformation – protein conformation to test

  • verbose – verbose output (boolean)

is_coupled_protonation_state_probability(group1, group2, energy_method, return_on_fail=True)[source]

Check whether two groups are energetically coupled.

Parameters
  • group1 – first group for interaction

  • group2 – second group for interaction

  • energy_method – function for calculating energy

  • return_on_fail – return if part of the calculation fails

Returns

dictionary describing coupling

static make_data_to_string(data, group1, group2)[source]

Describe interaction between groups.

Parameters
  • data – data about interactions

  • group1 – first group

  • group2 – second group

Returns

formatted string with information.

print_determinants_section(system, tag)[source]

Print determinants of system.

Parameters
  • system – set of groups

  • tag – something to add to output

Returns

string with summary

print_out_swaps(conformation)[source]

Print out something having to do with coupling interactions.

Parameters

conformation – conformation to print

print_system(conformation, system)[source]

Print out something about the system.

Parameters
  • conformation – conformation to print

  • system – system to print

swap_interactions(groups1, groups2, include_side_chain_hbs=True)[source]

Swap interactions between two groups.

Parameters
  • group1 – first group to swap

  • group2 – second group to swap

static tagged_format(tag, str_, labels)[source]

Tag a string.

Parameters
  • tag – tag to add

  • str – string to tag

  • labels – labels to replace

Returns

tagged string

static transfer_determinant(determinants1, determinants2, label1, label2)[source]

Transfer information between two sets of determinants.

Parameters
  • determinants1 – determinant list

  • determinants2 – determinant list

  • label1 – label for list 1

  • label2 – label for list 2