Source code for ihm.analysis

"""Classes for handling the analysis of a modeling run.
"""


from ihm.util import _text_choice_property




class Step(object):
    """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(EmptyStep, self).__init__(
            feature='none', num_models_begin=None, num_models_end=None)





class Analysis(object):
    """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 = []