pyrosetta.toolbox.atom_pair_energy Namespace Reference

Functions
def	etable_atom_pair_energies (res1, atom_index_1, res2, atom_index_2, sfxn)
def	_atom_pair_energy_table (sfxn, score_type, residue_1, residue_2, threshold=0.)
def	dump_atom_pair_energy_table (sfxn, score_type, residue_1, residue_2, output_filename)
def	print_atom_pair_energy_table (sfxn, score_type, residue_1, residue_2, threshold)
def	_reisude_pair_energies (res, pose, sfxn, score_type, threshold=0.)
def	dump_residue_pair_energies (res, pose, sfxn, score_type, output_filename)
def	print_residue_pair_energies (res, pose, sfxn, score_type, threshold)

Function Documentation

_atom_pair_energy_table()

def pyrosetta.toolbox.atom_pair_energy._atom_pair_energy_table (   sfxn,   score_type,   residue_1,   residue_2,   threshold = 0.  )

private

Compute the pairwise atom pair energies for two residues and yield the result
for each atom on residue 1.

Args:
    sfxn (pyrosetta.ScoreFunction): the scorefunction to use
    score_type (str): the term of the scorefunction to yield
    residue_1 (pyrosetta.rosetta.core.conformation.Residue): residue 1
    residue_2 (pyrosetta.rosetta.core.conformation.Residue): residue 2
    threshold (float): Minimum absolute value of a score term to include.
        Defaults to 0.

Yields:
    list: a list of tuples containing the atom index of residue 2 and the value
    of the score term representing all interatomic interactions of a particular
    atom on residue 1.

References pyrosetta.toolbox.atom_pair_energy.etable_atom_pair_energies(), pyrosetta.tests.distributed.test_dask.format, join(), print(), range, and basic::options::OptionKeys::in::file.zip.

Referenced by pyrosetta.toolbox.atom_pair_energy.dump_atom_pair_energy_table(), and pyrosetta.toolbox.atom_pair_energy.print_atom_pair_energy_table().

_reisude_pair_energies()

def pyrosetta.toolbox.atom_pair_energy._reisude_pair_energies (   res,   pose,   sfxn,   score_type,   threshold = 0.  )

private

Compute the scores of a particular residue with all other residues in a Pose
and yield them.

Args:
    res (int): Pose-numbered index of the residue of interest
    pose (pyrosetta.Pose): the target Pose
    sfxn (pyrosetta.ScoreFunction): the scorefunction to use
    score_type (str): the term of the scorefunction to return
    threshold (float): Minimum absolute value of a score term to include.
        Defaults to 0.

Yields:
    tuple: (i, score) where i is a Pose-numbered residue and score is the score of
        residue i with the user-specified residue, res.

References ObjexxFCL.abs(), and range.

Referenced by pyrosetta.toolbox.atom_pair_energy.dump_residue_pair_energies(), and pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies().

dump_atom_pair_energy_table()

def pyrosetta.toolbox.atom_pair_energy.dump_atom_pair_energy_table	(		sfxn,
			score_type,
			residue_1,
			residue_2,
			output_filename
	)

Compute of all pairwise atom pair energies for the complete list of atoms
contained by residue_1 and residue_2 using a specified score_type in the provided
sfxn and write the results to a csv file.

Notes:
    Only non-zero scores are written

Args:
    sfxn (pyrosetta.ScoreFunction): the scorefunction to use
    score_type (str): the term of the scorefunction to consider
    residue_1 (pyrosetta.rosetta.core.conformation.Residue): residue 1
    residue_2 (pyrosetta.rosetta.core.conformation.Residue): residue 2
    output_filename (str): name of the file to which the results will be written

References pyrosetta.toolbox.atom_pair_energy._atom_pair_energy_table(), basic::options::OptionKeys::in::file.list, basic::database.open(), and str().

dump_residue_pair_energies()

def pyrosetta.toolbox.atom_pair_energy.dump_residue_pair_energies	(		res,
			pose,
			sfxn,
			score_type,
			output_filename
	)

Compute the scores of a particular residue with all other residues in a Pose
and write the results to a csv file.

Notes:
    Only non-zero scores are returned

Args:
    res (int): Pose-numbered index of the residue of interest
    pose (pyrosetta.Pose): the target Pose
    sfxn (pyrosetta.ScoreFunction): the scorefunction to use
    score_type (str): the term of the scorefunction to return
    output_filename (str): name of the file to which the results will be written

References pyrosetta.toolbox.atom_pair_energy._reisude_pair_energies(), basic::options::OptionKeys::in::file.list, basic::database.open(), and str().

etable_atom_pair_energies()

def pyrosetta.toolbox.atom_pair_energy.etable_atom_pair_energies	(		res1,
			atom_index_1,
			res2,
			atom_index_2,
			sfxn
	)

Compute the energy of two atoms and return the LJ, solvation and electrostatic
terms.

Args:
    res1 (pyrosetta.rosetta.core.conformation.Residue): the residue that contains the
        first atom of interest.
    atom_index_1 (int): index of the desired atom in residue 1
    res2 (pyrosetta.rosetta.core.conformation.Residue): the residue that contains the
        second atom of interest.
    atom_index_2 (int): index of the desired atom in residue 2

Returns:
    tuple: values of the lj_atr, lj_rep, fa_solv, and fa_elec potentials.

Usage: lj_atr, lj_rep, solv=etable_atom_pair_energies(res1, atom_index_1, res2, atom_index_2, sfxn)
    Description: given a pair of atoms (specified using a pair of residue objects and
    atom indices) and scorefunction, use the precomputed 'etable' to return
    LJ attractive, LJ repulsive, and LK solvation energies

References numeric.distance_squared().

Referenced by pyrosetta.toolbox.atom_pair_energy._atom_pair_energy_table().

print_atom_pair_energy_table()

def pyrosetta.toolbox.atom_pair_energy.print_atom_pair_energy_table	(		sfxn,
			score_type,
			residue_1,
			residue_2,
			threshold
	)

Compute of all pairwise atom pair energies for the complete list of atoms
contained by residue_1 and residue_2 using a specified score_type in the provided
sfxn and print the values that exceed some threshold value.

Args:
    sfxn (pyrosetta.ScoreFunction): the scorefunction to use
    score_type (str): the term of the scorefunction to consider
    residue_1 (pyrosetta.rosetta.core.conformation.Residue): residue 1
    residue_2 (pyrosetta.rosetta.core.conformation.Residue): residue 2
    threshold (float): Minimum absolute value of a score term to include.
        Defaults to 0.

References pyrosetta.toolbox.atom_pair_energy._atom_pair_energy_table(), pyrosetta.tests.distributed.test_dask.format, and print().

print_residue_pair_energies()

def pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies	(		res,
			pose,
			sfxn,
			score_type,
			threshold
	)

Compute the scores of a particular residue with all other residues in a Pose
and print the values that exceed some threshold value.

Args:
    res (int): Pose-numbered index of the residue of interest
    pose (pyrosetta.Pose): the target Pose
    sfxn (pyrosetta.ScoreFunction): the scorefunction to use
    score_type (str): the term of the scorefunction to return
    threshold (float): Minimum absolute value of a score term to include.
        Defaults to 0.

References pyrosetta.toolbox.atom_pair_energy._reisude_pair_energies(), pyrosetta.tests.distributed.test_dask.format, and print().