pyrosetta.bindings.energies Namespace Reference

Functions
def	_residue_selection_to_1ind (selection, total_count)
def	residue_pair_energies_array (energies, from_residue_selection=None, to_residue_selection=None)
def	residue_onebody_energies_array (energies, residue_selection=None, out=None)
def	residue_total_energies_array (energies, residue_selection=None, out=None)
def	total_energies_array (energies, out=None)
def	active_total_energies (energies)
def	nonzero_weights (energies, out=None)
def	nonzero_weights_dtype (weights)
def	energies_total_score (energy_table, energy_weights)

Variables
list	__all__

Detailed Description

Utility functions related to rosetta energies.

Function Documentation

_residue_selection_to_1ind()

def pyrosetta.bindings.energies._residue_selection_to_1ind (   selection,   total_count  )

private

Referenced by pyrosetta.bindings.energies.residue_onebody_energies_array(), pyrosetta.bindings.energies.residue_pair_energies_array(), and pyrosetta.bindings.energies.residue_total_energies_array().

active_total_energies()

def pyrosetta.bindings.energies.active_total_energies

(

energies

)

References run_backbone.float, and sum().

Referenced by pyrosetta.bindings.pose.PoseScoreAccessor.all(), pyrosetta.bindings.scores.energies.EnergiesAccessor.all(), and pyrosetta.bindings.pose.PoseScoreAccessor.energies().

energies_total_score()

def pyrosetta.bindings.energies.energies_total_score	(		energy_table,
			energy_weights
	)

Convert energy term struct array into total score array via given weights.
energies - Struct array with energy term fields.
energy_weights - dict of energy weights.
returns - total_score float array of energies.shape.

Referenced by pyrosetta.bindings.energies.residue_pair_energies_array().

nonzero_weights()

def pyrosetta.bindings.energies.nonzero_weights	(		energies,
			out = None
	)

Gets energy terms weights in the given energies object.
returns:
    { score_term : score_weight }

References pyrosetta.bindings.energies.nonzero_weights_dtype().

Referenced by header(), print_verbose_ddgs(), pyrosetta.bindings.energies.residue_pair_energies_array(), and weights().

nonzero_weights_dtype()

def pyrosetta.bindings.energies.nonzero_weights_dtype

(

weights

)

Referenced by pyrosetta.bindings.energies.nonzero_weights(), pyrosetta.bindings.energies.residue_onebody_energies_array(), pyrosetta.bindings.energies.residue_total_energies_array(), and pyrosetta.bindings.energies.total_energies_array().

residue_onebody_energies_array()

def pyrosetta.bindings.energies.residue_onebody_energies_array	(		energies,
			residue_selection = None,
			out = None
	)

Gets table of energy terms with non-zero weight on a per-residue basis.
returns:
    structure_array of shape n_residue, with per-score-term entries

References pyrosetta.bindings.energies._residue_selection_to_1ind(), ObjexxFCL.len(), pyrosetta.bindings.energies.nonzero_weights_dtype(), range, and sum().

residue_pair_energies_array()

def pyrosetta.bindings.energies.residue_pair_energies_array	(		energies,
			from_residue_selection = None,
			to_residue_selection = None
	)

Generate pair energy table from the given energies object.
returns: energy_table - 2d energy type structured array.
            shape - (energies.size, energies.size)
            dtype - [(<type>, float)] for every nonzero weight energy type.

References pyrosetta.bindings.energies._residue_selection_to_1ind(), pyrosetta.bindings.energies.energies_total_score(), ObjexxFCL.len(), basic::options::OptionKeys::in::file.list, pyrosetta.bindings.energies.nonzero_weights(), range, binder.split(), and str().

residue_total_energies_array()

def pyrosetta.bindings.energies.residue_total_energies_array	(		energies,
			residue_selection = None,
			out = None
	)

Gets table of energy terms with non-zero weight on a per-residue basis.
returns:
    structure_array of shape n_residue, with per-score-term entries

References pyrosetta.bindings.energies._residue_selection_to_1ind(), ObjexxFCL.len(), pyrosetta.bindings.energies.nonzero_weights_dtype(), and range.

total_energies_array()

def pyrosetta.bindings.energies.total_energies_array	(		energies,
			out = None
	)

Get total structured dtype with non-zero energies.

References pyrosetta.bindings.energies.nonzero_weights_dtype().

Variable Documentation

__all__

list pyrosetta.bindings.energies.__all__

private

Initial value:

=  [
    "residue_pair_energies_array",
    "residue_onebody_energies_array",
    "residue_total_energies_array",
    "total_energies_array",
    "nonzero_weights",
    "nonzero_weights_dtype",
    "energies_total_score",
]