Source code for ihm.protocol

"""Classes for handling modeling protocols.

[docs] class Step(object): """A single step in a :class:`Protocol`. :param assembly: The part of the system modeled in this step :type assembly: :class:`~ihm.Assembly` :param dataset_group: The collection of datasets used in this modeling :type dataset_group: :class:`~ihm.dataset.DatasetGroup` :param str method: Description of the method used (e.g. "Monte Carlo") :param str name: A descriptive name for the step :param int num_models_begin: The number of models at the beginning of the step :param int num_models_end: The number of models at the end of the step :param software: The software used in this step :type software: :class:`~ihm.Software` :param script_file: Reference to the external file containing the script used in this step (usually a :class:`~ihm.location.WorkflowFileLocation`). :type script_file: :class:`~ihm.location.Location` :param bool multi_scale: Indicates if the modeling is multi-scale :param bool multi_state: Indicates if the modeling is multi-state :param bool ordered: Indicates if the modeling is ordered :param bool ensemble: Indicates if the modeling involves an ensemble; the default if unspecified is True iff the system contains at least one :class:`~ihm.model.Ensemble`. :param str description: Additional text describing the step """ def __init__(self, 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): self.assembly = assembly self.dataset_group = dataset_group self.method = method self.num_models_begin = num_models_begin self.num_models_end = num_models_end self.multi_scale, self.multi_state = multi_scale, multi_state, self.ordered, = software, ordered, name self.ensemble = ensemble self.script_file = script_file self.description = description def _get_report(self): def _get_flags(): if self.multi_scale: yield "multi-scale" if self.multi_state: yield "multi-state" if self.ordered: yield "ordered" return ("%s (%s) (%s->%s models)" % ( or "Unnamed step", "; ".join([self.method] + list(_get_flags())), self.num_models_begin, self.num_models_end))
[docs] class Protocol(object): """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 :class:`~ihm.model.Model` objects, although unused protocols can still be included in the file if desired by adding them to :attr:`~ihm.System.orphan_protocols`. """ def __init__(self, name=None): = name #: All modeling steps (:class:`Step` objects) self.steps = [] #: All analyses (:class:`~ihm.analysis.Analysis` objects) self.analyses = []