4.4.5. propka.energy¶
4.4.5.1. Energy calculations¶
Energy calculations.
Functions
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Calculate distance and angle factors for three atoms for backbone interactions. |
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Perform calculations related to backbone reorganizations. |
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Calculate the atom-pair based desolvation weight. |
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Calculate desolvation scaling factor. |
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Calculate the atom-based desolvation weight. |
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Check to see if an interaction is buried |
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Check for COO-ARG interaction atypical behavior. |
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Check for COO-COO hydrogen-bond atypical interaction behavior. |
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Check for COO-HIS atypical interaction behavior |
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Checks if this Coulomb interaction should be done. |
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Check for CYS-CYS atypical interaction behavior |
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Check for CYS-HIS atypical interaction behavior |
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Checks for atypical behavior in interactions between two groups. |
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Check for OCO-HIS atypical interaction behavior |
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Calculates the Coulomb interaction pKa shift based on Coulomb’s law. |
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Calculate electrostatic interaction betwee two groups. |
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Calculate hydrogen-bond interaction pKa shift. |
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Calculate energy for hydrogen bond interactions between two groups. |
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Calculate desolvation terms for group. |
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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]
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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
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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
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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
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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
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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
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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
Boolean indicating atypical behavior,
value associated with atypical interaction (None if Boolean is False)
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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
Boolean indicating atypical behavior,
value associated with atypical interaction (None if Boolean is False)
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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
Boolean indicating atypical behavior,
value associated with atypical interaction (None if Boolean is False)
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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
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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
Boolean indicating atypical behavior,
value associated with atypical interaction (None if Boolean is False)
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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
Boolean indicating atypical behavior,
value associated with atypical interaction (None if Boolean is False)
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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
Boolean indicating atypical behavior,
value associated with atypical interaction (None if Boolean is False)
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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
Boolean indicating atypical behavior,
value associated with atypical interaction (None if Boolean is False)
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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
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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)
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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
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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