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"""Classes for handling modeling protocols.
"""
class Step:
"""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.software, self.ordered, self.name = 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)"
% (self.name or "Unnamed step",
"; ".join([self.method] + list(_get_flags())),
self.num_models_begin, self.num_models_end))
class Protocol:
"""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`.
:param str name: Optional name for the protocol
:param str details: Additional text describing the protocol
"""
def __init__(self, name=None, details=None):
self.name = name
self.details = details
#: All modeling steps (:class:`Step` objects)
self.steps = []
#: All analyses (:class:`~ihm.analysis.Analysis` objects)
self.analyses = []
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