mxlpy 0.24.0__py3-none-any.whl → 0.25.0__py3-none-any.whl

mxlpy/model.py

@@ -2271,6 +2271,24 @@ class Model:
                 dxdt[k] += n * dependent[flux]
         return tuple(dxdt[i] for i in cache.var_names)
 
+    def _get_right_hand_side(
+        self,
+        *,
+        args: dict[str, float],
+        var_names: list[str],
+        cache: ModelCache,
+    ) -> pd.Series:
+        dxdt = pd.Series(np.zeros(len(var_names), dtype=float), index=var_names)
+        for k, stoc in cache.stoich_by_cpds.items():
+            for flux, n in stoc.items():
+                dxdt[k] += n * args[flux]
+
+        for k, sd in cache.dyn_stoich_by_cpds.items():
+            for flux, dv in sd.items():
+                n = dv.fn(*(args[i] for i in dv.args))
+                dxdt[k] += n * args[flux]
+        return dxdt
+
     def get_right_hand_side(
         self,
         variables: dict[str, float] | None = None,
@@ -2307,16 +2325,22 @@ class Model:
             time=time,
             cache=cache,
         )
-        dxdt = pd.Series(np.zeros(len(var_names), dtype=float), index=var_names)
-        for k, stoc in cache.stoich_by_cpds.items():
-            for flux, n in stoc.items():
-                dxdt[k] += n * args[flux]
+        return self._get_right_hand_side(args=args, var_names=var_names, cache=cache)
 
-        for k, sd in cache.dyn_stoich_by_cpds.items():
-            for flux, dv in sd.items():
-                n = dv.fn(*(args[i] for i in dv.args))
-                dxdt[k] += n * args[flux]
-        return dxdt
+    def get_right_hand_side_time_course(self, args: pd.DataFrame) -> pd.DataFrame:
+        """Calculate the right-hand side of the differential equations for the model."""
+        if (cache := self._cache) is None:
+            cache = self._create_cache()
+        var_names = self.get_variable_names()
+
+        rhs_by_time = {}
+        for time, variables in args.iterrows():
+            rhs_by_time[time] = self._get_right_hand_side(
+                args=variables.to_dict(),
+                var_names=var_names,
+                cache=cache,
+            )
+        return pd.DataFrame(rhs_by_time).T
 
     ##########################################################################
     # Check units

mxlpy/types.py

@@ -798,6 +798,177 @@ class Result:
         """
         return pd.concat((self.variables, self.fluxes), axis=1)
 
+    @overload
+    def get_right_hand_side(  # type: ignore
+        self,
+        *,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[False],
+    ) -> list[pd.DataFrame]: ...
+
+    @overload
+    def get_right_hand_side(
+        self,
+        *,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[True],
+    ) -> pd.DataFrame: ...
+
+    @overload
+    def get_right_hand_side(
+        self,
+        *,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame: ...
+
+    def get_right_hand_side(
+        self,
+        *,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame | list[pd.DataFrame]:
+        """Get right hand side over time."""
+        args_by_simulation = self._compute_args()
+        return self._adjust_data(
+            [
+                self.model.update_parameters(p).get_right_hand_side_time_course(
+                    args=args
+                )
+                for args, p in zip(args_by_simulation, self.raw_parameters, strict=True)
+            ],
+            normalise=normalise,
+            concatenated=concatenated,
+        )
+
+    @overload
+    def get_producers(  # type: ignore
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[False],
+    ) -> list[pd.DataFrame]: ...
+
+    @overload
+    def get_producers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[True],
+    ) -> pd.DataFrame: ...
+
+    @overload
+    def get_producers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame: ...
+
+    def get_producers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame | list[pd.DataFrame]:
+        """Get fluxes of variable with positive stoichiometry."""
+        self.model.update_parameters(self.raw_parameters[0])
+        names = [
+            k
+            for k, v in self.model.get_stoichiometries_of_variable(variable).items()
+            if v > 0
+        ]
+
+        fluxes: list[pd.DataFrame] = [
+            i.loc[:, names]
+            for i in self.get_fluxes(normalise=normalise, concatenated=False)
+        ]
+
+        if scaled:
+            fluxes = [i.copy() for i in fluxes]
+            for v, p in zip(fluxes, self.raw_parameters, strict=True):
+                self.model.update_parameters(p)
+                stoichs = self.model.get_stoichiometries_of_variable(variable)
+                for k in names:
+                    v.loc[:, k] *= stoichs[k]
+
+        self.model.update_parameters(self.raw_parameters[-1])
+        if concatenated:
+            return pd.concat(fluxes, axis=0)
+        return fluxes
+
+    @overload
+    def get_consumers(  # type: ignore
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[False],
+    ) -> list[pd.DataFrame]: ...
+
+    @overload
+    def get_consumers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: Literal[True],
+    ) -> pd.DataFrame: ...
+
+    @overload
+    def get_consumers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame: ...
+
+    def get_consumers(
+        self,
+        variable: str,
+        *,
+        scaled: bool = False,
+        normalise: float | ArrayLike | None = None,
+        concatenated: bool = True,
+    ) -> pd.DataFrame | list[pd.DataFrame]:
+        """Get fluxes of variable with negative stoichiometry."""
+        self.model.update_parameters(self.raw_parameters[0])
+        names = [
+            k
+            for k, v in self.model.get_stoichiometries_of_variable(variable).items()
+            if v < 0
+        ]
+
+        fluxes: list[pd.DataFrame] = [
+            i.loc[:, names]
+            for i in self.get_fluxes(normalise=normalise, concatenated=False)
+        ]
+
+        if scaled:
+            fluxes = [i.copy() for i in fluxes]
+            for v, p in zip(fluxes, self.raw_parameters, strict=True):
+                self.model.update_parameters(p)
+                stoichs = self.model.get_stoichiometries_of_variable(variable)
+                for k in names:
+                    v.loc[:, k] *= -stoichs[k]
+
+        self.model.update_parameters(self.raw_parameters[-1])
+        if concatenated:
+            return pd.concat(fluxes, axis=0)
+        return fluxes
+
     def get_new_y0(self) -> dict[str, float]:
         """Get the new initial conditions after the simulation.
 

{mxlpy-0.24.0.dist-info → mxlpy-0.25.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mxlpy
-Version: 0.24.0
+Version: 0.25.0
 Summary: A package to build metabolic models
 Author-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
 Maintainer-email: Marvin van Aalst <marvin.vanaalst@gmail.com>
@@ -124,3 +124,10 @@ You have two choices here, using `uv` (pypi-only) or using `pixi` (conda-forge,
 ## LLMs
 
 We support the [llms.txt](https://llmstxt.org/) convention for making documentation available to large language models and the applications that make use of them. It is located at [docs/llms.txt](https://github.com/Computational-Biology-Aachen/MxlPy/tree/main/docs/llms.txt)
+
+## Tool family 🏠
+
+`MxlPy` is part of a larger family of tools that are designed with a similar set of abstractions. Check them out!
+
+- [MxlBricks](https://github.com/Computational-Biology-Aachen/mxl-bricks) is built on top of `MxlPy` to build mechanistic models composed of pre-defined reactions (bricks)
+- [MxlWeb](https://github.com/Computational-Biology-Aachen/mxl-web) brings simulation of mechanistic models to the browser!

{mxlpy-0.24.0.dist-info → mxlpy-0.25.0.dist-info}/RECORD

@@ -1,15 +1,14 @@
-mxlpy/__init__.py,sha256=MzR_lZLel95RyWISsF16mDLscGoaw79oD976MFo5_TI,4453
+mxlpy/__init__.py,sha256=coeuRJf1axEjUZEgMGLyM2CzroUutoHZfbb5fAO_1II,4544
 mxlpy/carousel.py,sha256=3M2rqi2bx87y8D-oqEKTKZ6Q_clDQHbdLNdVjLJeO7c,6013
 mxlpy/compare.py,sha256=rJPOXc-aX6I1EC3ERAAW5Jn04kMwrlqUqdBgbZa6LA4,8098
 mxlpy/distributions.py,sha256=ce6RTqn19YzMMec-u09fSIUA8A92M6rehCuHuXWcX7A,8734
-mxlpy/fit.py,sha256=UTNvbUcL9mg7NuH5qq3syqpXXqynT_lXmKQudxwWcsE,22880
 mxlpy/fns.py,sha256=NLxYwa3ylS7SkISBjw_TgQSKEm7WnkZF9wPigX_ZCAM,13915
-mxlpy/identify.py,sha256=G-Zyr_l-K2mDtIV1xGrQ52QJxoBYqRoNA5RW6GpbNjs,2213
+mxlpy/identify.py,sha256=4odLBh6Jq7_MttQBmrmyqZ6ASVMsVxHsaEqgJz9lTMY,2265
 mxlpy/label_map.py,sha256=PwYanfg07hC0ayyOOP72RFlCQNvhCTbpOhW6kZZ2GUU,17826
 mxlpy/linear_label_map.py,sha256=6Ye6IziWGKkYD_5z3FmTVwnJ2T9SvVGN3U4CfXjXseo,10320
 mxlpy/mc.py,sha256=uMHknTNHmK5b4REM3PtCpCjEr9LoSIBsGsCNU4_yHpg,18639
 mxlpy/mca.py,sha256=IoOHJbjPnAEDqKk64OjFjgRPX5K_aE9D4RrCJ1xFIkw,9457
-mxlpy/model.py,sha256=kjZTQo8yM62JX2GedwTCfxtTQpdprg8vJzgJvp_5XCI,79643
+mxlpy/model.py,sha256=ji5zM9CmNPGMYLMA2mh12DfB3-mSVbkVmZbemcUM6iE,80495
 mxlpy/parallel.py,sha256=yLQLw5O4vnPVp_Zmtw1UhPWtB3483foimxQB-TwFKPg,5016
 mxlpy/parameterise.py,sha256=IgbvfEnkmaqVq_5GgFjHqApGUN9CJrsVD3Fr7pg9iFA,758
 mxlpy/paths.py,sha256=TK2wO4N9lG-UV1JGfeB64q48JVDbwqIUj63rl55MKuQ,1022
@@ -18,10 +17,14 @@ mxlpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mxlpy/report.py,sha256=v597yzKecgtoNmlNZ_nVhBCa3czNw0tksOK5mLtAQvE,10631
 mxlpy/scan.py,sha256=KXFdeWwgUBqJBCiOGDdMAGU5nS3PRVn7Cg0ISpzzK1U,17160
 mxlpy/simulator.py,sha256=-jsSP1fEnJnHj1hcj37cAPUyyP57mP_ow2cL-xd9iw8,16699
-mxlpy/types.py,sha256=Vg3ekCkhbH8HjqdDTA7vaAdFp9Diney3ARZZfbq0MoA,33475
+mxlpy/types.py,sha256=zcbC9XyBd2Vp4UxOr4rI7hznlJPe_iA1XvxFGWNO1y8,38456
 mxlpy/units.py,sha256=4bKXkCYsONUVWRdzV7aVcWFQSA6sxilebgXXFUEKw_c,2091
 mxlpy/experimental/__init__.py,sha256=kZTE-92OErpHzNRqmgSQYH4CGXrogGJ5EL35XGZQ81M,206
 mxlpy/experimental/diff.py,sha256=fmsM53lH86TD2iglQILK-XeZnIAtwHAcGC3Afs8V-tc,9457
+mxlpy/fit/__init__.py,sha256=rvIlXrWzuHfz5xYKpSeZpf7wACvweyBlvl9iE7SZJ3w,121
+mxlpy/fit/common.py,sha256=CQyg39oePkYACwwYxOhG3M8Yw4byf6yvG58i5Tg12XM,7600
+mxlpy/fit/global_.py,sha256=kIKyn1uQKA2Sc_0zLYuDuyo0zjGya6Yg1lPXDMxoZ30,15139
+mxlpy/fit/local_.py,sha256=-KtnIhCh1ytU9zORRKmkJ3bgrSsEceM-JYs5H7CJ_sU,16689
 mxlpy/integrators/__init__.py,sha256=TKo2dkJqdW3_n7YrmF6k3kEjr8_kr3-7MDaLu-zFWRg,533
 mxlpy/integrators/int_assimulo.py,sha256=1cvR8cOBdrl_DQs9v0o7wItSG5iyYqwZVh7EO0fg3ro,5021
 mxlpy/integrators/int_diffrax.py,sha256=q_8NZgIZ6T-SRRcI8kSjEb6l-DbXqPv6rjj9KApkQac,3326
@@ -51,7 +54,7 @@ mxlpy/surrogates/_torch.py,sha256=gU0secuRBYgewhNqZmSo6_Xf804dSzwWwIYmdKA7y60,63
 mxlpy/symbolic/__init__.py,sha256=_vM5YM5I6OH0QDbFt9uGYKO8Z5Vly0wbGuvUScVrPRU,258
 mxlpy/symbolic/strikepy.py,sha256=tzo3uvPpXLDex09hWTuitVzuTNwbgl7jWGjD8g6a8iI,20033
 mxlpy/symbolic/symbolic_model.py,sha256=cKfWoktvFmXjuo8egE7gXKrKBq2iBUiy_BcIKIvvz8A,3026
-mxlpy-0.24.0.dist-info/METADATA,sha256=Hqld-ntG-lfZey_b-aHgJo-T8KYylrC-iSf9CxMs-XA,4980
-mxlpy-0.24.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-mxlpy-0.24.0.dist-info/licenses/LICENSE,sha256=lHX9Eu70g3Iv1aOxXTWNHa3vq9vaVYSPQx4jOLYmDpw,1096
-mxlpy-0.24.0.dist-info/RECORD,,
+mxlpy-0.25.0.dist-info/METADATA,sha256=ENFh6nylpjiupCmhYEhozQCuP1FuyO0vGMegm3VPyvU,5413
+mxlpy-0.25.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+mxlpy-0.25.0.dist-info/licenses/LICENSE,sha256=lHX9Eu70g3Iv1aOxXTWNHa3vq9vaVYSPQx4jOLYmDpw,1096
+mxlpy-0.25.0.dist-info/RECORD,,