atom_pair_energy

pyrosetta.toolbox.atom_pair_energy._atom_pair_energy_table(sfxn, score_type, residue_1, residue_2, threshold=0.0)

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.

pyrosetta.toolbox.atom_pair_energy._reisude_pair_energies(res, pose, sfxn, score_type, threshold=0.0)

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.

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

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

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

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.

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.