movers

Custom Mover classes created from the PyRosetta Mover class.

Classes

SetRandomDihedralsMover

Custom PyRosetta Mover object that sets random dihedral angles in target residues, taken from

Functions

setup_mover(mover_id, databases, variance, log_file)

Create custom PyRosetta Mover.

Module Contents

class ensemblify.generation.ensemble_utils.movers.SetRandomDihedralsMover(databases, variance, log_file)

Custom PyRosetta Mover object that sets random dihedral angles in target residues, taken from a given database.

Inherits from pyrosetta.rosetta.protocols.moves.Mover.

Parameters:

• databases (dict[str, dict[str, pandas.DataFrame]])

• variance (float)

• log_file (str)

databases

All the available databases to sample from. Mapping of database_ids to databases nested dicts, that map residue 1lettercodes to dihedral angle values dataframes.

Type:

dict

variance

New dihedral angle values inserted into sampling regions are sampled from a Gaussian distribution centered on the value found in database and percentage variance equal to this value.

Type:

float

log_file

Path to .log file for warnings or error messages related to sampling.

Type:

str

get_name()

Return the name of this mover.

apply(pose, target_resnum, database_id, secondary_structure, sampling_mode)

Apply the mover to a Pose, on the given residue number (PyRosetta Pose numbering).

Parameters:

• pose (pyrosetta.rosetta.core.pose.Pose) – Pose on which the mover will be applied.

• target_resnum (int) – Residue number where to apply the mover (PyRosetta Pose numbering).

• database_id (str) – Identifier for which database to sample from.

• secondary_structure (str, optional) – Which secondary structure element to force in this target region. If None, sample database without restraint.

• sampling_mode (str) – Whether to sample the database considering neighbouring residues (‘TRIPEPTIDE’) or not (‘SINGLERESIDUE’).

ensemblify.generation.ensemble_utils.movers.setup_mover(mover_id, databases, variance, log_file)

Create custom PyRosetta Mover.

Setup Mover object given a database to sample from and a mover id.

Parameters:

• mover_id (str) – Identifier for which CustomMover to create.

• databases (dict[str,dict[str,pd.DataFrame]]) – Mapping of database_ids to databases nested dicts, that map residue 1lettercodes to dihedral angle values dataframes.

• variance (float) – New dihedral angle values inserted into sampling regions are sampled from a Gaussian distribution centered on the value found in database and percentage variance equal to this value.

• log_file (str) – Path to .log file for warnings or error messages related to sampling.

Returns:

Custom PyRosetta Mover object.

Return type:

pyrosetta.rosetta.protocols.moves.Mover