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.