The ihm.protocol Python module

Classes for handling modeling protocols.

class ihm.protocol.Step(assembly, dataset_group, method, num_models_begin=None, num_models_end=None, software=None, script_file=None, multi_scale=False, multi_state=False, ordered=False, ensemble='default', name=None, description=None)[source]

A single step in a Protocol.

Parameters:

  • assembly (Assembly) – The part of the system modeled in this step

  • dataset_group (DatasetGroup) – The collection of datasets used in this modeling

  • method (str) – Description of the method used (e.g. “Monte Carlo”)

  • name (str) – A descriptive name for the step

  • num_models_begin (int) – The number of models at the beginning of the step

  • num_models_end (int) – The number of models at the end of the step

  • software (Software) – The software used in this step

  • script_file (Location) – Reference to the external file containing the script used in this step (usually a WorkflowFileLocation).

  • multi_scale (bool) – Indicates if the modeling is multi-scale

  • multi_state (bool) – Indicates if the modeling is multi-state

  • ordered (bool) – Indicates if the modeling is ordered

  • ensemble (bool) – Indicates if the modeling involves an ensemble; the default if unspecified is True iff the system contains at least one Ensemble.

  • description (str) – Additional text describing the step

class ihm.protocol.Protocol(name=None, details=None)[source]

A modeling protocol. Each protocol consists of a number of protocol steps (e.g. sampling, refinement) followed by a number of analyses.

Normally a protocol is passed to one or more Model objects, although unused protocols can still be included in the file if desired by adding them to orphan_protocols.

Parameters:

  • name (str) – Optional name for the protocol

  • details (str) – Additional text describing the protocol

analyses

All analyses (Analysis objects)

steps

All modeling steps (Step objects)