objects¶
Auxiliary functions for creating PyRosetta objects.
Functions¶
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Initialize a Pose object from a sequence, a .txt file containing the sequence or a PDB file. |
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Setup a PyRosetta MinMover object given the necessary parameters. |
Module Contents¶
- ensemblify.modelling.objects.setup_pose(input_structure, make_centroid=False)¶
Initialize a Pose object from a sequence, a .txt file containing the sequence or a PDB file.
If desired, the created Pose object is then changed to ‘centroid’ configuration.
- Parameters:
input_structure (
str) – Filepath to the input .pdb structure, .txt with sequence or the actual sequence string.make_centroid (
str, optional) – Whether to convert the Pose side-chains to centroid configuration. Defaults to False.
- Returns:
A PyRosetta Pose object initialized from the input structure/sequence.
- Return type:
pyrosetta.rosetta.core.pose.Pose
- ensemblify.modelling.objects.setup_minmover(scorefxn, min_id, tolerance, max_iters=None, dofs=('bb', 'chi'))¶
Setup a PyRosetta MinMover object given the necessary parameters.
- Parameters:
scorefxn (
pyrosetta.rosetta.core.scoring.ScoreFunction | str) – Score function that will be used during Pose minimization. If ScoreFunction id is provided instead, a ScoreFunction object is created automatically.min_id (
str) – Identifier for the used PyRosetta minimization algorithm.tolerance (
float) – Value for the MinMover tolerance.max_iters (
int) – Maximum iterations of the MinMover. Defaults to None, meaning the MinMover object’s default value.dofs (
tuple[str,str], optional) – Defines what angles to set as flexible during minimization. Defaults to backbone and sidechain, i.e. (‘bb’,’chi’).
- Returns:
A PyRosetta MinMover object setup with desired parameters.
- Return type:
pyrosetta.rosetta.protocols.minimization_packing.MinMover