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Rosetta
2019.07
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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.dump_atom_pair_energy_table(), pyrosetta.toolbox.atom_pair_energy.etable_atom_pair_energies(), pyrosetta.tests.distributed.test_dask.format, fmt.join(), fmt.print(), basic::options::OptionKeys::relax::range.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().
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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 basic::options::OptionKeys::relax::range.range.
Referenced by pyrosetta.toolbox.atom_pair_energy.dump_residue_pair_energies(), and pyrosetta.toolbox.atom_pair_energy.print_residue_pair_energies().
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, and basic::database.open().
Referenced by pyrosetta.toolbox.atom_pair_energy._atom_pair_energy_table().
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, and basic::database.open().
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().
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 fmt.print().
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 fmt.print().