propka.coupled_groups
Coupling between groups
Describe and analyze energetic coupling between groups.
Classes
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: Group, group2: Group, 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