4.4.5. propka.energy

4.4.5.1. Energy calculations

Energy calculations.

Functions

angle_distance_factors([atom1, atom2, …])

Calculate distance and angle factors for three atoms for backbone interactions.

backbone_reorganization(_, conformation)

Perform calculations related to backbone reorganizations.

calculate_pair_weight(parameters, …)

Calculate the atom-pair based desolvation weight.

calculate_scale_factor(parameters, weight)

Calculate desolvation scaling factor.

calculate_weight(parameters, num_volume)

Calculate the atom-based desolvation weight.

check_buried(num_volume1, num_volume2)

Check to see if an interaction is buried

check_coo_arg_exception(group_coo, …)

Check for COO-ARG interaction atypical behavior.

check_coo_coo_exception(group1, group2, version)

Check for COO-COO hydrogen-bond atypical interaction behavior.

check_coo_his_exception(group1, group2, version)

Check for COO-HIS atypical interaction behavior

check_coulomb_pair(parameters, group1, …)

Checks if this Coulomb interaction should be done.

check_cys_cys_exception(group1, group2, version)

Check for CYS-CYS atypical interaction behavior

check_cys_his_exception(group1, group2, version)

Check for CYS-HIS atypical interaction behavior

check_exceptions(version, group1, group2)

Checks for atypical behavior in interactions between two groups.

check_oco_his_exception(group1, group2, version)

Check for OCO-HIS atypical interaction behavior

coulomb_energy(dist, weight, parameters)

Calculates the Coulomb interaction pKa shift based on Coulomb’s law.

electrostatic_interaction(group1, group2, …)

Calculate electrostatic interaction betwee two groups.

hydrogen_bond_energy(dist, dpka_max, cutoffs)

Calculate hydrogen-bond interaction pKa shift.

hydrogen_bond_interaction(group1, group2, …)

Calculate energy for hydrogen bond interactions between two groups.

radial_volume_desolvation(parameters, group)

Calculate desolvation terms for group.
propka.energy.angle_distance_factors(atom1=None, atom2=None, atom3=None, center=None)[source]

Calculate distance and angle factors for three atoms for backbone interactions.

NOTE - you need to use atom1 to be the e.g. ASP atom if distance is reset at return: [O1 – H2-N3].

Also generalized to be able to be used for residue ‘centers’ for C=O COO interactions.

Parameters

  • atom1 – first atom for calculation (could be None)

  • atom2 – second atom for calculation

  • atom3 – third atom for calculation

  • center – center point between atoms 1 and 2

Returns
[distance factor between atoms 1 and 2,

angle factor, distance factor between atoms 2 and 3]

propka.energy.backbone_reorganization(_, conformation)[source]

Perform calculations related to backbone reorganizations.

NOTE - this was described in the code as “adding test stuff” NOTE - this function does not appear to be used TODO - figure out why a similar function exists in version.py

Parameters

  • _ – not used

  • conformation – specific molecule conformation

propka.energy.calculate_pair_weight(parameters, num_volume1, num_volume2)[source]

Calculate the atom-pair based desolvation weight.

Parameters

  • num_volume1 – number of heavy atoms within first desolvation volume

  • num_volume2 – number of heavy atoms within second desolvation volume

Returns

desolvation weight

propka.energy.calculate_scale_factor(parameters, weight)[source]

Calculate desolvation scaling factor.

Parameters

  • parameters – parameters for desolvation calculation

  • weight – weight for scaling factor

Returns

scaling factor

propka.energy.calculate_weight(parameters, num_volume)[source]

Calculate the atom-based desolvation weight.

TODO - figure out why a similar function exists in version.py

Parameters

  • parameters – parameters for desolvation calculation

  • num_volume – number of heavy atoms within desolvation calculation volume

Returns

desolvation weight

propka.energy.check_buried(num_volume1, num_volume2)[source]

Check to see if an interaction is buried

Parameters

  • num_volume1 – number of buried heavy atoms in volume 1

  • num_volume2 – number of buried heavy atoms in volume 2

Returns

True if interaction is buried, False otherwise

propka.energy.check_coo_arg_exception(group_coo, group_arg, version)[source]

Check for COO-ARG interaction atypical behavior.

Uses the two shortest unique distances (involving 2+2 atoms)

Parameters

  • group_coo – COO group

  • group_arg – ARG group

  • version – version object

Returns

  1. Boolean indicating atypical behavior,

  2. value associated with atypical interaction (None if Boolean is False)

propka.energy.check_coo_coo_exception(group1, group2, version)[source]

Check for COO-COO hydrogen-bond atypical interaction behavior.

Parameters

  • group1 – first group for check

  • group2 – second group for check

  • version – version object

Returns

  1. Boolean indicating atypical behavior,

  2. value associated with atypical interaction (None if Boolean is False)

propka.energy.check_coo_his_exception(group1, group2, version)[source]

Check for COO-HIS atypical interaction behavior

Parameters

  • group1 – first group for check

  • group2 – second group for check

  • version – version object

Returns

  1. Boolean indicating atypical behavior,

  2. value associated with atypical interaction (None if Boolean is False)

propka.energy.check_coulomb_pair(parameters, group1, group2, dist)[source]

Checks if this Coulomb interaction should be done.

NOTE - this is a propka2.0 hack TODO - figure out why a similar function exists in version.py

Parameters

  • parameters – parameters for Coulomb calculations

  • group1 – first interacting group

  • group2 – second interacting group

  • dist – distance between groups

Returns

Boolean

propka.energy.check_cys_cys_exception(group1, group2, version)[source]

Check for CYS-CYS atypical interaction behavior

Parameters

  • group1 – first group for check

  • group2 – second group for check

  • version – version object

Returns

  1. Boolean indicating atypical behavior,

  2. value associated with atypical interaction (None if Boolean is False)

propka.energy.check_cys_his_exception(group1, group2, version)[source]

Check for CYS-HIS atypical interaction behavior

Parameters

  • group1 – first group for check

  • group2 – second group for check

  • version – version object

Returns

  1. Boolean indicating atypical behavior,

  2. value associated with atypical interaction (None if Boolean is False)

propka.energy.check_exceptions(version, group1, group2)[source]

Checks for atypical behavior in interactions between two groups. Checks are made based on group type.

TODO - figure out why a similar function exists in version.py

Parameters

  • version – version object

  • group1 – first group for check

  • group2 – second group for check

Returns

  1. Boolean indicating atypical behavior,

  2. value associated with atypical interaction (None if Boolean is False)

propka.energy.check_oco_his_exception(group1, group2, version)[source]

Check for OCO-HIS atypical interaction behavior

Parameters

  • group1 – first group for check

  • group2 – second group for check

  • version – version object

Returns

  1. Boolean indicating atypical behavior,

  2. value associated with atypical interaction (None if Boolean is False)

propka.energy.coulomb_energy(dist, weight, parameters)[source]

Calculates the Coulomb interaction pKa shift based on Coulomb’s law.

Parameters

  • dist – distance for electrostatic interaction

  • weight – scaling of dielectric constant

  • parameters – parameter object for calculation

Returns

pKa shift

propka.energy.electrostatic_interaction(group1, group2, dist, version)[source]

Calculate electrostatic interaction betwee two groups.

Parameters

  • group1 – first interacting group

  • group2 – second interacting group

  • dist – distance between groups

  • version – version-specific object with parameters and functions

Returns

electrostatic interaction energy or None (if no interaction is appropriate)

propka.energy.hydrogen_bond_energy(dist, dpka_max, cutoffs, f_angle=1.0)[source]

Calculate hydrogen-bond interaction pKa shift.

Parameters

  • dist – distance for hydrogen bond

  • dpka_max – maximum pKa value shift

  • cutoffs – array with max and min distance values

  • f_angle – angle scaling factor

Returns

pKa shift value

propka.energy.hydrogen_bond_interaction(group1, group2, version)[source]

Calculate energy for hydrogen bond interactions between two groups.

Parameters

  • group1 – first interacting group

  • group2 – second interacting group

  • version – an object that contains version-specific parameters

Returns

hydrogen bond interaction energy

propka.energy.radial_volume_desolvation(parameters, group)[source]

Calculate desolvation terms for group.

Parameters

  • parameters – parameters for desolvation calculation

  • group – group of atoms for calculation