Module nlisim.molecule

Classes

class MoleculeGrid (*, grid: RectangularGrid, concentrations=NOTHING, sources=NOTHING, molecule_type: List[str] = NOTHING)

A class contains a list of grids for each molecule type.

Method generated by attrs for class MoleculeGrid.

Expand source code

class MoleculeGrid(object):
    """A class contains a list of grids for each molecule type."""

    grid: RectangularGrid = attr.ib()
    _concentrations = attr.ib()
    _sources = attr.ib()
    _diffusivity: Dict[str, int] = {}
    _molecule_type: List[str] = attr.ib(factory=list)

    @_concentrations.default
    def __set_default_concentrations(self):
        return np.empty(0)

    @_sources.default
    def __set_default_sources(self):
        return np.empty(0)

    def __attrs_post_init__(self):
        grid = self.grid
        # noinspection PyTypeChecker
        object.__setattr__(
            self,
            '_concentrations',
            grid.allocate_variable(
                dtype={
                    'names': [molecule.name for molecule in MoleculeTypes],
                    'formats': ['f4'] * len(MoleculeTypes),
                }
            ),
        )

        # noinspection PyTypeChecker
        object.__setattr__(
            self,
            '_sources',
            grid.allocate_variable(
                dtype={
                    'names': [molecule.name for molecule in MoleculeTypes],
                    'formats': ['f4'] * len(MoleculeTypes),
                }
            ),
        )

    @property
    def diffusivity(self):
        return self._diffusivity

    @property
    def concentrations(self):
        return self._concentrations[[name for name in self._molecule_type]].view(np.recarray)

    @property
    def sources(self):
        return self._sources[[name for name in self._molecule_type]].view(np.recarray)

    @property
    def types(self):
        return self._molecule_type

    def __getitem__(self, index: str) -> np.ndarray:
        if not isinstance(index, str):
            raise TypeError('Expected an str index representing the type of molecule')
        if index not in self._molecule_type:
            raise KeyError(f'Molecule {index} is not declared or is knocked out')
        return self._concentrations[index]

    def append_molecule_type(self, molecule: str):
        if molecule not in self._concentrations.dtype.names:
            raise KeyError(f'Molecule {molecule} is not declared')
        self._molecule_type.append(molecule)

    def set_diffusivity(self, molecule: str, diffusivity: int):
        self._diffusivity[molecule] = diffusivity

    def incr(self):
        concentrations = self._concentrations
        sources = self._sources
        for name in self._molecule_type:
            concentrations[name] += sources[name]

    def shape(self):
        return self._concentrations.shape

    def save(self, group: Group, name: str, metadata: dict) -> Group:
        """Save the molecule grid.

        Save the list of grid as a new composite data structure inside
        an HDF5 group.
        """
        concentrations = self._concentrations
        sources = self._sources

        composite_group = group.create_group(name)

        composite_group.attrs['type'] = 'MoleculeGrid'
        composite_group.attrs['class'] = get_class_path(self)
        composite_group.attrs['molecule_type'] = self.types
        composite_group.create_dataset(name='concentrations', data=concentrations)
        composite_group.create_dataset(name='sources', data=sources)

        return composite_group

    @classmethod
    def load(cls, global_state: State, group: Group, name: str, metadata: dict) -> 'MoleculeGrid':
        """Load a molecule grid object."""
        composite_dataset = group[name]

        # TODO: load back the molecule types

        concentrations = composite_dataset['concentrations'][:]
        sources = composite_dataset['sources'][:]
        molecule_type = composite_dataset.attrs['molecule_type']

        return cls(
            grid=global_state.grid,
            concentrations=concentrations,
            sources=sources,
            molecule_type=molecule_type,
        )

Class variables

var grid : RectangularGrid

Static methods

def load(global_state: State, group: h5py._hl.group.Group, name: str, metadata: dict) ‑> MoleculeGrid

Load a molecule grid object.

Expand source code

@classmethod
def load(cls, global_state: State, group: Group, name: str, metadata: dict) -> 'MoleculeGrid':
    """Load a molecule grid object."""
    composite_dataset = group[name]

    # TODO: load back the molecule types

    concentrations = composite_dataset['concentrations'][:]
    sources = composite_dataset['sources'][:]
    molecule_type = composite_dataset.attrs['molecule_type']

    return cls(
        grid=global_state.grid,
        concentrations=concentrations,
        sources=sources,
        molecule_type=molecule_type,
    )

Instance variables

var concentrations

Expand source code

@property
def concentrations(self):
    return self._concentrations[[name for name in self._molecule_type]].view(np.recarray)

var diffusivity

Expand source code

@property
def diffusivity(self):
    return self._diffusivity

var sources

Expand source code

@property
def sources(self):
    return self._sources[[name for name in self._molecule_type]].view(np.recarray)

var types

Expand source code

@property
def types(self):
    return self._molecule_type

Methods

def append_molecule_type(self, molecule: str)

Expand source code

def append_molecule_type(self, molecule: str):
    if molecule not in self._concentrations.dtype.names:
        raise KeyError(f'Molecule {molecule} is not declared')
    self._molecule_type.append(molecule)

def incr(self)

Expand source code

def incr(self):
    concentrations = self._concentrations
    sources = self._sources
    for name in self._molecule_type:
        concentrations[name] += sources[name]

def save(self, group: h5py._hl.group.Group, name: str, metadata: dict) ‑> h5py._hl.group.Group

Save the molecule grid.

Save the list of grid as a new composite data structure inside an HDF5 group.

Expand source code

def save(self, group: Group, name: str, metadata: dict) -> Group:
    """Save the molecule grid.

    Save the list of grid as a new composite data structure inside
    an HDF5 group.
    """
    concentrations = self._concentrations
    sources = self._sources

    composite_group = group.create_group(name)

    composite_group.attrs['type'] = 'MoleculeGrid'
    composite_group.attrs['class'] = get_class_path(self)
    composite_group.attrs['molecule_type'] = self.types
    composite_group.create_dataset(name='concentrations', data=concentrations)
    composite_group.create_dataset(name='sources', data=sources)

    return composite_group

def set_diffusivity(self, molecule: str, diffusivity: int)

Expand source code

def set_diffusivity(self, molecule: str, diffusivity: int):
    self._diffusivity[molecule] = diffusivity

def shape(self)

Expand source code

def shape(self):
    return self._concentrations.shape

class MoleculeTypes (value, names=None, *, module=None, qualname=None, type=None, start=1)

a enum class for the molecule type.

Expand source code

class MoleculeTypes(Enum):
    """a enum class for the molecule type."""

    iron = 0
    tf = 1
    tfbi = 2
    tafc = 3
    tafcbi = 4
    ros = 5
    lactoferrin = 6
    lactoferrinbi = 7
    il6 = 8
    tnfa = 9
    il8 = 10
    il10 = 11
    hepcidin = 12
    tgfb = 13
    mcp1 = 14
    mip2 = 15
    mip1b = 16
    m_cyto = 17
    n_cyto = 18

Ancestors

• enum.Enum

Class variables

var hepcidin

var il10

var il6

var il8

var iron

var lactoferrin

var lactoferrinbi

var m_cyto

var mcp1

var mip1b

var mip2

var n_cyto

var ros

var tafc

var tafcbi

var tf

var tfbi

var tgfb

var tnfa