Source code for PyOpenWorm.channelworm

from yarom.utils import slice_dict

import six
from .experiment import Experiment
from .dataObject import DataObject, DatatypeProperty, ObjectProperty
from .channel_common import CHANNEL_RDF_TYPE
from . import SCI_BIO_CTX


class PatchClampExperiment(Experiment):
    """
    Store experimental conditions for a patch clamp experiment.
    """

    class_context = SCI_BIO_CTX.identifier

    Ca_concentration = DatatypeProperty()
    '''Calcium concentration'''

    Cl_concentration = DatatypeProperty()
    '''Chlorine concentration'''

    blockers = DatatypeProperty()
    '''Channel blockers used for this experiment'''

    cell = DatatypeProperty()
    '''The cell this experiment was performed on'''

    cell_age = DatatypeProperty()
    '''Age of the cell'''

    delta_t = DatatypeProperty()

    duration = DatatypeProperty()

    end_time = DatatypeProperty()

    extra_solution = DatatypeProperty()

    initial_voltage = DatatypeProperty()
    '''Starting voltage of the patch clamp'''

    ion_channel = DatatypeProperty()
    '''The ion channel being clamped'''

    membrane_capacitance = DatatypeProperty()
    '''Initial membrane capacitance'''

    mutants = DatatypeProperty()
    '''Type(s) of mutants being used in this experiment'''

    patch_type = DatatypeProperty()
    '''Type of patch clamp being used ('voltage' or 'current')'''

    pipette_solution = DatatypeProperty()
    '''Type of solution in the pipette'''

    protocol_end = DatatypeProperty()

    protocol_start = DatatypeProperty()

    protocol_step = DatatypeProperty()

    start_time = DatatypeProperty()

    temperature = DatatypeProperty()

    type = DatatypeProperty()


class ChannelModelType:
    patchClamp = "Patch clamp experiment"
    homologyEstimate = "Estimation based on homology"


class ChannelModel(DataObject):
    """
    A model for an ion channel.

    There may be multiple models for a single channel.

    Example usage::

        # Create a ChannelModel
        >>> cm = P.ChannelModel()
        # Create Evidence object
        >>> ev = P.Evidence(author='White et al.', date='1986')
        # Assert
        >>> ev.asserts(cm)
        >>> ev.save()
    """
    class_context = SCI_BIO_CTX.identifier

    modelType = DatatypeProperty()
    ''' The type of model employed to describe a channel '''

    ion = DatatypeProperty(multiple=True)
    ''' The type of ion this channel selects for '''

    gating = DatatypeProperty(multiple=True)
    ''' The gating mechanism for this channel ("voltage" or name of ligand(s) ) '''

    conductance = DatatypeProperty()
    ''' The conductance of this ion channel. This is the initial value, and should be entered as a Quantity object. '''

    def __init__(self, modelType=None, *args, **kwargs):
        super(ChannelModel, self).__init__(*args, **kwargs)

        #Change modelType value to something from ChannelModelType class on init
        if isinstance(modelType, six.string_types):
            modelType = modelType.lower()
            if modelType in ('homology', ChannelModelType.homologyEstimate):
                self.modelType(ChannelModelType.homologyEstimate)
            elif modelType in ('patch-clamp', ChannelModelType.patchClamp):
                self.modelType(ChannelModelType.patchClamp)


class PatchClampChannelModel(ChannelModel):
    modeled_from = ObjectProperty(value_type=PatchClampExperiment)

    def __init__(self, **kwargs):
        super(PatchClampChannelModel, self).__init__(modelType='patch-clamp',
                                                     **kwargs)


class HomologyChannelModel(ChannelModel):
    homolog = ObjectProperty(value_rdf_type=CHANNEL_RDF_TYPE)

    def __init__(self, **kwargs):
        super(HomologyChannelModel, self).__init__(modelType='homology',
                                                   **kwargs)


__yarom_mapped_classes__ = (ChannelModel, HomologyChannelModel, PatchClampChannelModel, PatchClampExperiment)