modelbase2 0.1.78__py3-none-any.whl → 0.2.0__py3-none-any.whl

modelbase2/scan.py

@@ -0,0 +1,616 @@
+"""Parameter Scanning Module.
+
+This module provides functions and classes for performing parameter scans on metabolic models.
+It includes functionality for steady-state and time-course simulations, as well as protocol-based simulations.
+
+Classes:
+    TimePoint: Represents a single time point in a simulation.
+    TimeCourse: Represents a time course in a simulation.
+
+Functions:
+    parameter_scan_ss: Get steady-state results over supplied parameters.
+    parameter_scan_time_course: Get time course for each supplied parameter.
+    parameter_scan_protocol: Get protocol course for each supplied parameter.
+"""
+
+from __future__ import annotations
+
+__all__ = [
+    "ProtocolWorker",
+    "SteadyStateWorker",
+    "TimeCourse",
+    "TimeCourseWorker",
+    "TimePoint",
+    "steady_state",
+    "time_course",
+    "time_course_over_protocol",
+]
+
+from dataclasses import dataclass
+from functools import partial
+from typing import TYPE_CHECKING, Protocol, Self, cast
+
+import numpy as np
+import pandas as pd
+
+from modelbase2.parallel import Cache, parallelise
+from modelbase2.simulator import Simulator
+from modelbase2.types import ProtocolByPars, SteadyStates, TimeCourseByPars
+
+if TYPE_CHECKING:
+    from collections.abc import Callable
+
+    from modelbase2.model import Model
+    from modelbase2.types import Array
+
+
+def _update_parameters_and[T](
+    pars: pd.Series,
+    fn: Callable[[Model], T],
+    model: Model,
+) -> T:
+    """Update model parameters and execute a function.
+
+    Args:
+        pars: Series containing parameter values to update.
+        fn: Function to execute after updating parameters.
+        model: Model instance to update.
+
+    Returns:
+        Result of the function execution.
+
+    """
+    model.update_parameters(pars.to_dict())
+    return fn(model)
+
+
+def _empty_conc_series(model: Model) -> pd.Series:
+    """Create an empty concentration series for the model.
+
+    Args:
+        model: Model instance to generate the series for.
+
+    Returns:
+        pd.Series: Series with NaN values for each model variable.
+
+    """
+    return pd.Series(
+        data=np.full(shape=len(model.get_variable_names()), fill_value=np.nan),
+        index=model.get_variable_names(),
+    )
+
+
+def _empty_flux_series(model: Model) -> pd.Series:
+    """Create an empty flux series for the model.
+
+    Args:
+        model: Model instance to generate the series for.
+
+    Returns:
+        pd.Series: Series with NaN values for each model reaction.
+
+    """
+    return pd.Series(
+        data=np.full(shape=len(model.get_reaction_names()), fill_value=np.nan),
+        index=model.get_reaction_names(),
+    )
+
+
+def _empty_conc_df(model: Model, time_points: Array) -> pd.DataFrame:
+    """Create an empty concentration DataFrame for the model over given time points.
+
+    Args:
+        model: Model instance to generate the DataFrame for.
+        time_points: Array of time points.
+
+    Returns:
+        pd.DataFrame: DataFrame with NaN values for each model variable at each time point.
+
+    """
+    return pd.DataFrame(
+        data=np.full(
+            shape=(len(time_points), len(model.get_variable_names())),
+            fill_value=np.nan,
+        ),
+        index=time_points,
+        columns=model.get_variable_names(),
+    )
+
+
+def _empty_flux_df(model: Model, time_points: Array) -> pd.DataFrame:
+    """Create an empty concentration DataFrame for the model over given time points.
+
+    Args:
+        model: Model instance to generate the DataFrame for.
+        time_points: Array of time points.
+
+    Returns:
+        pd.DataFrame: DataFrame with NaN values for each model variable at each time point.
+
+    """
+    return pd.DataFrame(
+        data=np.full(
+            shape=(len(time_points), len(model.get_reaction_names())),
+            fill_value=np.nan,
+        ),
+        index=time_points,
+        columns=model.get_reaction_names(),
+    )
+
+
+###############################################################################
+# Single returns
+###############################################################################
+
+
+@dataclass(slots=True)
+class TimePoint:
+    """Represents a single time point in a simulation.
+
+    Attributes:
+        concs: Series of concentrations at the time point.
+        fluxes: Series of fluxes at the time point.
+
+    Args:
+        model: Model instance to generate the time point for.
+        concs: DataFrame of concentrations (default: None).
+        fluxes: DataFrame of fluxes (default: None).
+        idx: Index of the time point in the DataFrame (default: -1).
+
+    """
+
+    concs: pd.Series
+    fluxes: pd.Series
+
+    @classmethod
+    def from_scan(
+        cls,
+        model: Model,
+        concs: pd.DataFrame | None,
+        fluxes: pd.DataFrame | None,
+        idx: int = -1,
+    ) -> Self:
+        """Initialize the Scan object.
+
+        Args:
+            model (Model): The model object.
+            concs (pd.DataFrame | None): DataFrame containing concentration data. If None, an empty concentration series is created.
+            fluxes (pd.DataFrame | None): DataFrame containing flux data. If None, an empty flux series is created.
+            idx (int, optional): Index to select specific row from concs and fluxes DataFrames. Defaults to -1.
+
+        """
+        return cls(
+            concs=_empty_conc_series(model) if concs is None else concs.iloc[idx],
+            fluxes=_empty_flux_series(model) if fluxes is None else fluxes.iloc[idx],
+        )
+
+    @property
+    def results(self) -> pd.Series:
+        """Get the combined results of concentrations and fluxes.
+
+        Example:
+            >>> time_point.results
+            x1    1.0
+            x2    0.5
+            v1    0.1
+            v2    0.2
+
+        Returns:
+            pd.Series: Combined series of concentrations and fluxes.
+
+        """
+        return pd.concat((self.concs, self.fluxes), axis=0)
+
+
+@dataclass(slots=True)
+class TimeCourse:
+    """Represents a time course in a simulation.
+
+    Attributes:
+        concs: DataFrame of concentrations over time.
+        fluxes: DataFrame of fluxes over time.
+
+    Args:
+        model: Model instance to generate the time course for.
+        time_points: Array of time points.
+        concs: DataFrame of concentrations (default: None).
+        fluxes: DataFrame of fluxes (default: None).
+
+    """
+
+    concs: pd.DataFrame
+    fluxes: pd.DataFrame
+
+    @classmethod
+    def from_scan(
+        cls,
+        model: Model,
+        time_points: Array,
+        concs: pd.DataFrame | None,
+        fluxes: pd.DataFrame | None,
+    ) -> Self:
+        """Initialize the Scan object.
+
+        Args:
+            model (Model): The model object.
+            time_points (Array): Array of time points.
+            concs (pd.DataFrame | None): DataFrame containing concentration data. If None, an empty DataFrame is created.
+            fluxes (pd.DataFrame | None): DataFrame containing flux data. If None, an empty DataFrame is created.
+
+        """
+        return cls(
+            _empty_conc_df(model, time_points) if concs is None else concs,
+            _empty_flux_df(model, time_points) if fluxes is None else fluxes,
+        )
+
+    @property
+    def results(self) -> pd.DataFrame:
+        """Get the combined results of concentrations and fluxes over time.
+
+        Examples:
+            >>> time_course.results
+            Time   x1     x2     v1     v2
+            0.0   1.0   1.00   1.00   1.00
+            0.1   0.9   0.99   0.99   0.99
+            0.2   0.8   0.99   0.99   0.99
+
+        Returns:
+            pd.DataFrame: Combined DataFrame of concentrations and fluxes.
+
+        """
+        return pd.concat((self.concs, self.fluxes), axis=1)
+
+
+###############################################################################
+# Workers
+###############################################################################
+
+
+class SteadyStateWorker(Protocol):
+    """Worker function for steady-state simulations."""
+
+    def __call__(
+        self,
+        model: Model,
+        y0: dict[str, float] | None,
+        *,
+        rel_norm: bool,
+    ) -> TimePoint:
+        """Call the worker function."""
+        ...
+
+
+class TimeCourseWorker(Protocol):
+    """Worker function for time-course simulations."""
+
+    def __call__(
+        self,
+        model: Model,
+        y0: dict[str, float] | None,
+        time_points: Array,
+    ) -> TimeCourse:
+        """Call the worker function."""
+        ...
+
+
+class ProtocolWorker(Protocol):
+    """Worker function for protocol-based simulations."""
+
+    def __call__(
+        self,
+        model: Model,
+        y0: dict[str, float] | None,
+        protocol: pd.DataFrame,
+        time_points_per_step: int = 10,
+    ) -> TimeCourse:
+        """Call the worker function."""
+        ...
+
+
+def _steady_state_worker(
+    model: Model,
+    y0: dict[str, float] | None,
+    *,
+    rel_norm: bool,
+) -> TimePoint:
+    """Simulate the model to steady state and return concentrations and fluxes.
+
+    Args:
+        model: Model instance to simulate.
+        y0: Initial conditions as a dictionary {species: value}.
+        rel_norm: Whether to use relative normalization.
+
+    Returns:
+        TimePoint: Object containing steady-state concentrations and fluxes.
+
+    """
+    try:
+        c, v = (
+            Simulator(model, y0=y0)
+            .simulate_to_steady_state(rel_norm=rel_norm)
+            .get_full_concs_and_fluxes()
+        )
+    except ZeroDivisionError:
+        c = None
+        v = None
+    return TimePoint.from_scan(model, c, v)
+
+
+def _time_course_worker(
+    model: Model,
+    y0: dict[str, float] | None,
+    time_points: Array,
+) -> TimeCourse:
+    """Simulate the model to steady state and return concentrations and fluxes.
+
+    Args:
+        model: Model instance to simulate.
+        y0: Initial conditions as a dictionary {species: value}.
+        time_points: Array of time points for the simulation.
+
+    Returns:
+        TimePoint: Object containing steady-state concentrations and fluxes.
+
+    """
+    try:
+        c, v = (
+            Simulator(model, y0=y0)
+            .simulate_time_course(time_points=time_points)
+            .get_full_concs_and_fluxes()
+        )
+    except ZeroDivisionError:
+        c = None
+        v = None
+    return TimeCourse.from_scan(model, time_points, c, v)
+
+
+def _protocol_worker(
+    model: Model,
+    y0: dict[str, float] | None,
+    protocol: pd.DataFrame,
+    time_points_per_step: int = 10,
+) -> TimeCourse:
+    """Simulate the model over a protocol and return concentrations and fluxes.
+
+    Args:
+        model: Model instance to simulate.
+        y0: Initial conditions as a dictionary {species: value}.
+        protocol: DataFrame containing the protocol steps.
+        time_points_per_step: Number of time points per protocol step (default: 10).
+
+    Returns:
+        TimeCourse: Object containing protocol series concentrations and fluxes.
+
+    """
+    c, v = (
+        Simulator(model, y0=y0)
+        .simulate_over_protocol(
+            protocol=protocol,
+            time_points_per_step=time_points_per_step,
+        )
+        .get_full_concs_and_fluxes()
+    )
+    time_points = np.linspace(
+        0,
+        protocol.index[-1].total_seconds(),
+        len(protocol) * time_points_per_step,
+    )
+    return TimeCourse.from_scan(model, time_points, c, v)
+
+
+def steady_state(
+    model: Model,
+    parameters: pd.DataFrame,
+    y0: dict[str, float] | None = None,
+    *,
+    parallel: bool = True,
+    rel_norm: bool = False,
+    cache: Cache | None = None,
+    worker: SteadyStateWorker = _steady_state_worker,
+) -> SteadyStates:
+    """Get steady-state results over supplied parameters.
+
+    Args:
+        model: Model instance to simulate.
+        parameters: DataFrame containing parameter values to scan.
+        y0: Initial conditions as a dictionary {variable: value}.
+        parallel: Whether to execute in parallel (default: True).
+        rel_norm: Whether to use relative normalization (default: False).
+        cache: Optional cache to store and retrieve results.
+        worker: Worker function to use for the simulation.
+
+    Returns:
+        SteadyStates: Steady-state results for each parameter set.
+
+    Examples:
+        >>> steady_state(
+        >>>     model,
+        >>>     parameters=pd.DataFrame({"k1": np.linspace(1, 2, 3)})
+        >>> ).concs
+        idx      x      y
+        1.0   0.50   1.00
+        1.5   0.75   1.50
+        2.0   1.00   2.00
+
+        >>> steady_state(
+        >>>     model,
+        >>>     parameters=cartesian_product({"k1": [1, 2], "k2": [3, 4]})
+        >>> ).concs
+
+        | idx    |    x |   y |
+        | (1, 3) | 0.33 |   1 |
+        | (1, 4) | 0.25 |   1 |
+        | (2, 3) | 0.66 |   2 |
+        | (2, 4) | 0.5  |   2 |
+
+    """
+    res = parallelise(
+        partial(
+            _update_parameters_and,
+            fn=partial(
+                worker,
+                y0=y0,
+                rel_norm=rel_norm,
+            ),
+            model=model,
+        ),
+        inputs=list(parameters.iterrows()),
+        cache=cache,
+        parallel=parallel,
+    )
+    concs = pd.DataFrame({k: v.concs.T for k, v in res.items()}).T
+    fluxes = pd.DataFrame({k: v.fluxes.T for k, v in res.items()}).T
+    idx = (
+        pd.Index(parameters.iloc[:, 0])
+        if parameters.shape[1] == 1
+        else pd.MultiIndex.from_frame(parameters)
+    )
+    concs.index = idx
+    fluxes.index = idx
+    return SteadyStates(concs, fluxes, parameters=parameters)
+
+
+def time_course(
+    model: Model,
+    parameters: pd.DataFrame,
+    time_points: Array,
+    y0: dict[str, float] | None = None,
+    *,
+    parallel: bool = True,
+    cache: Cache | None = None,
+    worker: TimeCourseWorker = _time_course_worker,
+) -> TimeCourseByPars:
+    """Get time course for each supplied parameter.
+
+    Examples:
+        >>> time_course(
+        >>>     model,
+        >>>     parameters=pd.DataFrame({"k1": [1, 1.5, 2]}),
+        >>>     time_points=np.linspace(0, 1, 3)
+        >>> ).concs
+
+        | (n, time) |        x |       y |
+        |:----------|---------:|--------:|
+        | (0, 0.0)  | 1        | 1       |
+        | (0, 0.5)  | 0.68394  | 1.23865 |
+        | (0, 1.0)  | 0.567668 | 1.23254 |
+        | (1, 0.0)  | 1        | 1       |
+        | (1, 0.5)  | 0.84197  | 1.31606 |
+        | (1, 1.0)  | 0.783834 | 1.43233 |
+        | (2, 0.0)  | 1        | 1       |
+        | (2, 0.5)  | 1        | 1.39347 |
+        | (2, 1.0)  | 1        | 1.63212 |
+
+        >>> time_course(
+        >>>     model,
+        >>>     parameters=cartesian_product({"k1": [1, 2], "k2": [3, 4]}),
+        >>>     time_points=[0.0, 0.5, 1.0],
+        >>> ).concs
+
+        | (n, time) |        x |      y |
+        |:----------|---------:|-------:|
+        | (0, 0.0)  | 1        | 1      |
+        | (0, 0.5)  | 0.482087 | 1.3834 |
+        | (1, 0.0)  | 1        | 1      |
+        | (1, 0.5)  | 0.351501 | 1.4712 |
+        | (2, 0.0)  | 1        | 1      |
+
+    Args:
+        model: Model instance to simulate.
+        parameters: DataFrame containing parameter values to scan.
+        time_points: Array of time points for the simulation.
+        y0: Initial conditions as a dictionary {variable: value}.
+        cache: Optional cache to store and retrieve results.
+        parallel: Whether to execute in parallel (default: True).
+        worker: Worker function to use for the simulation.
+
+    Returns:
+        TimeCourseByPars: Time series results for each parameter set.
+
+
+    """
+    res = parallelise(
+        partial(
+            _update_parameters_and,
+            fn=partial(
+                worker,
+                time_points=time_points,
+                y0=y0,
+            ),
+            model=model,
+        ),
+        inputs=list(parameters.iterrows()),
+        cache=cache,
+        parallel=parallel,
+    )
+    concs = cast(dict, {k: v.concs for k, v in res.items()})
+    fluxes = cast(dict, {k: v.fluxes for k, v in res.items()})
+    return TimeCourseByPars(
+        parameters=parameters,
+        concs=pd.concat(concs, names=["n", "time"]),
+        fluxes=pd.concat(fluxes, names=["n", "time"]),
+    )
+
+
+def time_course_over_protocol(
+    model: Model,
+    parameters: pd.DataFrame,
+    protocol: pd.DataFrame,
+    time_points_per_step: int = 10,
+    y0: dict[str, float] | None = None,
+    *,
+    parallel: bool = True,
+    cache: Cache | None = None,
+    worker: ProtocolWorker = _protocol_worker,
+) -> ProtocolByPars:
+    """Get protocol series for each supplied parameter.
+
+    Examples:
+        >>> scan.time_course_over_protocol(
+        ...     model,
+        ...     parameters=pd.DataFrame({"k2": np.linspace(1, 2, 11)}),
+        ...     protocol=make_protocol(
+        ...         {
+        ...             1: {"k1": 1},
+        ...             2: {"k1": 2},
+        ...         }
+        ...     ),
+        ... )
+
+    Args:
+        model: Model instance to simulate.
+        parameters: DataFrame containing parameter values to scan.
+        protocol: Protocol to follow for the simulation.
+        time_points_per_step: Number of time points per protocol step (default: 10).
+        y0: Initial conditions as a dictionary {variable: value}.
+        parallel: Whether to execute in parallel (default: True).
+        cache: Optional cache to store and retrieve results.
+        worker: Worker function to use for the simulation.
+
+    Returns:
+        TimeCourseByPars: Protocol series results for each parameter set.
+
+    """
+    res = parallelise(
+        partial(
+            _update_parameters_and,
+            fn=partial(
+                worker,
+                protocol=protocol,
+                y0=y0,
+                time_points_per_step=time_points_per_step,
+            ),
+            model=model,
+        ),
+        inputs=list(parameters.iterrows()),
+        cache=cache,
+        parallel=parallel,
+    )
+    concs = cast(dict, {k: v.concs for k, v in res.items()})
+    fluxes = cast(dict, {k: v.fluxes for k, v in res.items()})
+    return ProtocolByPars(
+        parameters=parameters,
+        protocol=protocol,
+        concs=pd.concat(concs, names=["n", "time"]),
+        fluxes=pd.concat(fluxes, names=["n", "time"]),
+    )

modelbase2/scope.py

@@ -0,0 +1,96 @@
+"""Label Scope Module.
+
+This module provides functions for creating and managing label scopes in metabolic models.
+It includes functionality for initializing label scopes and retrieving reachable label positions.
+
+Functions:
+    get_label_scope: Return all label positions that can be reached step by step.
+"""
+
+from __future__ import annotations
+
+# def _create_label_scope_seed(
+#     self, *, initial_labels: dict[str, int] | dict[str, list[int]]
+# ) -> dict[str, int]:
+#     """Create initial label scope seed."""
+#     # initialise all compounds with 0 (no label)
+#     labelled_compounds = {compound: 0 for compound in self.get_compounds()}
+#     # Set all unlabelled compounds to 1
+#     for name, compound in self.label_compounds.items():
+#         num_labels = compound["num_labels"]
+#         labelled_compounds[f"{name}__{'0' * num_labels}"] = 1
+#     # Also set all non-label compounds to 1
+#     for name in self.nonlabel_compounds:
+#         labelled_compounds[name] = 1
+#     # Set initial label
+#     for i in [
+#         self.get_compound_isotopomer_with_label_position(
+#             base_compound=base_compound, label_position=label_position
+#         )
+#         for base_compound, label_position in initial_labels.items()
+#     ]:
+#         labelled_compounds[i] = 1
+#     return labelled_compounds
+
+
+# def get_label_scope(
+#     self,
+#     initial_labels: dict[str, int] | dict[str, list[int]],
+# ) -> dict[int, set[str]]:
+#     """Return all label positions that can be reached step by step.
+
+#     Parameters:
+#     initial_labels : dict(str: num)
+
+#     Returns:
+#     label_scope : dict{step : set of new positions}
+
+#     Examples:
+#     >>> l.get_label_scope({"x": 0})
+#     >>> l.get_label_scope({"x": [0, 1], "y": 0})
+
+#     """
+#     labelled_compounds = self._create_label_scope_seed(initial_labels=initial_labels)
+#     new_labels = set("non empty entry to not fulfill while condition")
+#     # Loop until no new labels are inserted
+#     loop_count = 0
+#     result = {}
+#     while new_labels != set():
+#         new_cpds = labelled_compounds.copy()
+#         for rec, cpd_dict in self.get_stoichiometries().items():
+#             # Isolate substrates
+#             cpds = [i for i, j in cpd_dict.items() if j < 0]
+#             # Count how many of the substrates are 1
+#             i = 0
+#             for j in cpds:
+#                 i += labelled_compounds[j]
+#             # If all substrates are 1, set all products to 1
+#             if i == len(cpds):
+#                 for cpd in self.get_stoichiometries()[rec]:
+#                     new_cpds[cpd] = 1
+#             if self.rates[rec]["reversible"]:
+#                 # Isolate substrates
+#                 cpds = [i for i, j in cpd_dict.items() if j > 0]
+#                 # Count how many of the substrates are 1
+#                 i = 0
+#                 for j in cpds:
+#                     i += labelled_compounds[j]
+#                 # If all substrates are 1, set all products to 1
+#                 if i == len(cpds):
+#                     for cpd in self.get_stoichiometries()[rec]:
+#                         new_cpds[cpd] = 1
+#         # Isolate "old" labels
+#         s1 = pd.Series(labelled_compounds)
+#         s1 = cast(pd.Series, s1[s1 == 1])
+#         # Isolate new labels
+#         s2 = pd.Series(new_cpds)
+#         s2 = cast(pd.Series, s2[s2 == 1])
+#         # Find new labels
+#         new_labels = cast(set[str], set(s2.index).difference(set(s1.index)))
+#         # Break the loop once no new labels can be found
+#         if new_labels == set():
+#             break
+#         labelled_compounds = new_cpds
+#         result[loop_count] = new_labels
+#         loop_count += 1
+#     return result