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"""Classes for handling the analysis of a modeling run.
"""
from ihm.util import _text_choice_property
class Step:
"""A single step in an :class:`Analysis`.
Normally one of the more specific derived classes is used;
see :class:`FilterStep`, :class:`ClusterStep`, :class:`RescoreStep`,
:class:`ValidationStep`, and :class:`EmptyStep`, although this base
class can be used for a generic 'other' step.
:param str feature: feature energy/score;RMSD;dRMSD;other
: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 assembly: The part of the system analyzed in this step
:type assembly: :class:`~ihm.Assembly`
:param dataset_group: The collection of datasets used in this analysis,
if applicable
:type dataset_group: :class:`~ihm.dataset.DatasetGroup`
: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 str details: Additional text describing this step
"""
type = 'other'
def _get_report(self):
return ("%s (%s->%s models)"
% (self.type, self.num_models_begin, self.num_models_end))
def __init__(self, feature, num_models_begin, num_models_end,
assembly=None, dataset_group=None, software=None,
script_file=None, details=None):
self.assembly, self.dataset_group = assembly, dataset_group
self.feature, self.software = feature, software
self.num_models_begin = num_models_begin
self.num_models_end = num_models_end
self.script_file = script_file
self.details = details
feature = _text_choice_property(
"feature", ["energy/score", "RMSD", "dRMSD", "other", "none"],
doc="The feature used in the analysis, if applicable")
class FilterStep(Step):
"""A single filtering step in an :class:`Analysis`.
See :class:`Step` for a description of the parameters.
"""
type = 'filter'
class ClusterStep(Step):
"""A single clustering step in an :class:`Analysis`.
See :class:`Step` for a description of the parameters.
"""
type = 'cluster'
class RescoreStep(Step):
"""A single rescoring step in an :class:`Analysis`.
See :class:`Step` for a description of the parameters.
"""
type = 'rescore'
class ValidationStep(Step):
"""A single validation step in an :class:`Analysis`.
See :class:`Step` for a description of the parameters.
"""
type = 'validation'
class EmptyStep(Step):
"""A 'do nothing' step in an :class:`Analysis`.
This can be used if modeling outputs were used directly without
any kind of analysis.
"""
type = 'none'
def __init__(self):
super().__init__(
feature='none', num_models_begin=None, num_models_end=None)
class Analysis:
"""Analysis of a modeling run.
Each analysis consists of a number of steps (e.g. filtering,
rescoring, clustering). A modeling run may be followed by any number
of separate analyses.
See :attr:`ihm.protocol.Protocol.analyses`.
"""
def __init__(self):
#: All analysis steps (:class:`Step` objects)
self.steps = []
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