4.4.2. propka.coupled_groups¶
4.4.2.1. Coupling between groups¶
Describe and analyze energetic coupling between groups.
Classes
Groups that are coupled without covalent bonding. |
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class
propka.coupled_groups.NonCovalentlyCoupledGroups[source]¶ Groups that are coupled without covalent bonding.
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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
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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)
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get_interaction_factor(interaction_energy)[source]¶ Get scaling factor related to interaction energy.
- Parameters
interaction_energy – interaction energy
- Returns
float value of scaling factor
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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
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identify_non_covalently_coupled_groups(conformation, verbose=True)[source]¶ Find coupled residues in protein.
- Parameters
conformation – protein conformation to test
verbose – verbose output (boolean)
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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
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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.
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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
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print_out_swaps(conformation)[source]¶ Print out something having to do with coupling interactions.
- Parameters
conformation – conformation to print
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print_system(conformation, system)[source]¶ Print out something about the system.
- Parameters
conformation – conformation to print
system – system to print
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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
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