pyreactlab-core 0.1.4__tar.gz → 0.1.6__tar.gz

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreactlab-core
-Version: 0.1.4
+Version: 0.1.6
 Summary: pyreactlab-core is the core foundation of the PyReactLab ecosystem, offering shared data structures and algorithms for chemical reaction representation, stoichiometry, and reaction analysis.
 Author-email: Sina Gilassi <sina.gilassi@gmail.com>
 License-Expression: Apache-2.0

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyproject.toml

@@ -1,74 +1,74 @@
-[build-system]
-requires = ["setuptools>=61.0", "wheel"]
-build-backend = "setuptools.build_meta"
-
-[project]
-name = "pyreactlab-core"
-version = "0.1.4"
-description = "pyreactlab-core is the core foundation of the PyReactLab ecosystem, offering shared data structures and algorithms for chemical reaction representation, stoichiometry, and reaction analysis."
-readme = "README.md"
-requires-python = ">=3.11"
-license = "Apache-2.0"
-license-files = ["LICENSE"]
-authors = [
-    {name = "Sina Gilassi", email = "sina.gilassi@gmail.com"}
-]
-keywords = [
-    "chemical-engineering",
-    "chemical-reactions",
-    "reaction-representation",
-    "reaction-stoichiometry",
-    "reaction-analysis",
-]
-classifiers = [
-    "Development Status :: 1 - Planning",
-    "Intended Audience :: Education",
-    "Programming Language :: Python :: 3.11",
-    "Operating System :: Unix",
-    "Operating System :: MacOS :: MacOS X",
-    "Operating System :: Microsoft :: Windows",
-]
-dependencies = [
-    "scipy>=1.17.1",
-    "numpy>=2.4.3",
-    "pydantic>=2.12.5",
-    "pydantic-settings>=2.12.0",
-    "rich>=14.2.0",
-    "pythermodb-settings",
-]
-
-[project.urls]
-Homepage = "https://github.com/sinagilassi/PyReactLab-Core"
-Documentation = "https://pyreactlab-core.readthedocs.io/en/latest/"
-Source = "https://github.com/sinagilassi/PyReactLab-Core"
-Tracker = "https://github.com/sinagilassi/PyReactLab-Core/issues"
-
-[tool.setuptools]
-include-package-data = true
-
-[tool.setuptools.packages.find]
-where = ["."]
-include = ["pyreactlab_core*"]
-exclude = [
-    "tests",
-    "tests.*",
-    "examples",
-    "examples.*",
-    "notebooks",
-    "notebooks.*",
-    "statics",
-    "statics.*",
-    "private",
-    "private.*",
-    "app",
-    "app.*"
-]
-
-[tool.setuptools.package-data]
-pyreactlab_core = [
-    "config/*.yml",
-    "data/*.csv",
-    "templates/*.html",
-    "static/*",
-    "static/**/*"
-]
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyreactlab-core"
+version = "0.1.6"
+description = "pyreactlab-core is the core foundation of the PyReactLab ecosystem, offering shared data structures and algorithms for chemical reaction representation, stoichiometry, and reaction analysis."
+readme = "README.md"
+requires-python = ">=3.11"
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+authors = [
+    {name = "Sina Gilassi", email = "sina.gilassi@gmail.com"}
+]
+keywords = [
+    "chemical-engineering",
+    "chemical-reactions",
+    "reaction-representation",
+    "reaction-stoichiometry",
+    "reaction-analysis",
+]
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Intended Audience :: Education",
+    "Programming Language :: Python :: 3.11",
+    "Operating System :: Unix",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: Microsoft :: Windows",
+]
+dependencies = [
+    "scipy>=1.17.1",
+    "numpy>=2.4.3",
+    "pydantic>=2.12.5",
+    "pydantic-settings>=2.12.0",
+    "rich>=14.2.0",
+    "pythermodb-settings",
+]
+
+[project.urls]
+Homepage = "https://github.com/sinagilassi/PyReactLab-Core"
+Documentation = "https://pyreactlab-core.readthedocs.io/en/latest/"
+Source = "https://github.com/sinagilassi/PyReactLab-Core"
+Tracker = "https://github.com/sinagilassi/PyReactLab-Core/issues"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["pyreactlab_core*"]
+exclude = [
+    "tests",
+    "tests.*",
+    "examples",
+    "examples.*",
+    "notebooks",
+    "notebooks.*",
+    "statics",
+    "statics.*",
+    "private",
+    "private.*",
+    "app",
+    "app.*"
+]
+
+[tool.setuptools.package-data]
+pyreactlab_core = [
+    "config/*.yml",
+    "data/*.csv",
+    "templates/*.html",
+    "static/*",
+    "static/**/*"
+]

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyreactlab_core/__init__.py

@@ -8,7 +8,12 @@ from .configs.info import (
     __license__,
 )
 
-from .app import rxn, rxn_stoichiometry, rxns_stoichiometry
+from .app import (
+    rxn,
+    rxn_stoichiometry_matrix,
+    rxns_stoichiometry,
+    build_rxns_stoichiometry
+)
 
 __all__ = [
     # config
@@ -20,6 +25,7 @@ __all__ = [
     "__license__",
     # app
     "rxn",
-    "rxn_stoichiometry",
+    "rxn_stoichiometry_matrix",
     "rxns_stoichiometry",
+    "build_rxns_stoichiometry",
 ]

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyreactlab_core/app.py

@@ -1,9 +1,10 @@
 # import libs
 import logging
-from typing import List, Optional, Dict
+from typing import List, Optional, Dict, Tuple
+from pythermodb_settings.models import Component, ComponentKey
 # locals
 from .models.reaction import Reaction
-from .docs.chem_utils import build_stoichiometry_matrix
+from .docs.chem_utils import build_stoichiometry_matrix, build_rxn_stoichiometry_source
 
 # NOTE: configure logger
 logger = logging.getLogger(__name__)
@@ -11,7 +12,7 @@ logger = logging.getLogger(__name__)
 
 def rxn(
         reaction_str: str,
-        name: Optional[str] = None
+        name: Optional[str] = None,
 ) -> Optional[Reaction]:
     """
     Create and analyze a chemical reaction.
@@ -50,7 +51,7 @@ def rxn(
         return None
 
 
-def rxn_stoichiometry(
+def rxn_stoichiometry_matrix(
         reaction: Reaction,
 ) -> Optional[List[float]]:
     """
@@ -85,6 +86,8 @@ def rxn_stoichiometry(
 
 def rxns_stoichiometry(
         reactions: List[Reaction],
+        components: Optional[List[Component]] = None,
+        component_key: ComponentKey = "Name-Formula"
 ) -> Optional[Dict]:
     """
     Get the reaction stoichiometry matrices for a list of chemical reactions.
@@ -109,11 +112,16 @@ def rxns_stoichiometry(
             return None
 
         # SECTION: retrieve stoichiometry matrices
-        result = build_stoichiometry_matrix(reactions=reactions)
+        result = build_stoichiometry_matrix(
+            reactions=reactions,
+            components=components,
+            component_key=component_key
+        )
 
         # NOTE: res
         return {
-            "components": result["component_list"],
+            "components": result["components"],
+            "component_list": result["component_list"],
             "component_ids": result["component_dict"],
             "stoichiometry_matrices_list": result["comp_coeff"],
             "stoichiometry_matrices_dict": result["comp_list"],
@@ -121,3 +129,71 @@ def rxns_stoichiometry(
     except Exception as e:
         logger.error(f"Error retrieving reaction stoichiometry matrices: {e}")
         return None
+
+# SECTION: Build stoichiometry for reactions
+
+
+def build_rxns_stoichiometry(
+    reactions: List[Reaction],
+    components: List[Component],
+    component_key: ComponentKey
+) -> Optional[
+    Dict[str, List[Dict[str, float]] | List[List[float]]]
+]:
+    """
+    Build the reaction stoichiometry matrices for a list of chemical reactions.
+
+    Parameters
+    ----------
+    reactions : List[Reaction]
+        List of Reaction instances.
+    components : List[Component]
+        List of all components involved in the reactions.
+    component_key : ComponentKey
+        The key to use for mapping components (e.g., "Name-Formula").
+
+    Returns
+    -------
+    Optional[Dict[str, List[Dict[str, float]] | List[List[float]]]]
+        A dictionary containing the stoichiometry source and matrices if successful, None otherwise. The dictionary has the following structure:
+        - "source": List[Dict[str, float]] - A list of dictionaries representing the stoichiometry source for each reaction.
+        - "matrix": List[List[float]] - A list of stoichiometry matrices corresponding to each reaction.
+    """
+    try:
+        # SECTION: validate inputs
+        if (
+            not isinstance(reactions, list) or
+            not all(isinstance(rxn, Reaction) for rxn in reactions)
+        ):
+            logger.error("Invalid reactions list provided.")
+            return None
+
+        if (
+            not isinstance(components, list) or
+            not all(isinstance(comp, Component) for comp in components)
+        ):
+            logger.error("Invalid components list provided.")
+            return None
+
+        # SECTION: build stoichiometry source
+        stoichiometry_source = build_rxn_stoichiometry_source(
+            reactions=reactions,
+            components=components,
+            component_key=component_key
+        )
+
+        # >> check
+        if not stoichiometry_source:
+            logger.error("Failed to build reaction stoichiometry source.")
+            return None
+
+        # result
+        res = {
+            "source": stoichiometry_source[0],
+            "matrix": stoichiometry_source[1]
+        }
+
+        return res
+    except Exception as e:
+        logger.error(f"Error building reaction stoichiometry: {e}")
+        return None

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyreactlab_core/configs/info.py

@@ -1,5 +1,5 @@
 # version
-__version__ = "0.1.4"
+__version__ = "0.1.6"
 # author
 __author__ = "Sina Gilassi"
 # email

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyreactlab_core/core/chem_react.py

@@ -2,13 +2,16 @@
 import logging
 import re
 from typing import Dict, Any, List, Optional, Literal, TypedDict
-from pythermodb_settings.models import Component
+from pythermodb_settings.models import Component, ComponentKey
+from pythermodb_settings.utils import set_component_id
+# locals
 from ..configs.constants import (
     R_CONST_J__molK,
     PRESSURE_REF_Pa,
     TEMPERATURE_REF_K,
 )
 
+
 # NOTE: logger
 logger = logging.getLogger(__name__)
 
@@ -69,10 +72,14 @@ class ChemReact:
     # NOTE: component checker
     _component_checker: bool = False
 
+    # NOTE: stoichiometry source
+    _stoichiometry_source: dict[str, Any] = {}
+
     def __init__(
         self,
         reaction_mode_symbol: ReactionMode,
-        components: Optional[List[Component]]
+        components: Optional[List[Component]],
+        component_keys: Optional[List[ComponentKey]] = None
     ):
         """
         Initialize the ChemReactUtils class.
@@ -83,6 +90,8 @@ class ChemReact:
             The symbol used to separate reactants and products in a reaction equation.
         components : Optional[List[Component]]
             A list of Component objects involved in the reaction.
+        component_keys : List[ComponentKey], optional
+            The key used to identify components in the reaction.
 
         Notes
         -----
@@ -98,6 +107,12 @@ class ChemReact:
         # NOTE: set components
         self.components = components
 
+        # NOTE: set component key
+        if component_keys is not None:
+            self.component_keys = component_keys
+        else:
+            self.component_keys = []
+
         # SECTION: Component id
         # NOTE: component ids
         if components is None:
@@ -115,6 +130,12 @@ class ChemReact:
             raise ValueError("System inputs are not set.")
         return self._system_inputs
 
+    @property
+    def stoichiometry_source(self) -> Dict[str, Any]:
+        """Get the stoichiometry source."""
+        # res
+        return self._stoichiometry_source
+
     def count_carbon(self, molecule: str, coefficient: float) -> float:
         """
         Count the number of carbon atoms in a molecule.
@@ -396,6 +417,11 @@ class ChemReact:
                 products,
             )
 
+            # SECTION: build stoichiometry source
+            stoichiometry_source = self.build_stoichiometry_source(
+                reaction_stoichiometry=reaction_stoichiometry
+            )
+
             # res
             res = {
                 'name': name,
@@ -411,6 +437,7 @@ class ChemReact:
                 'reaction_coefficients': reaction_coefficients,
                 'reaction_stoichiometry': reaction_stoichiometry,
                 'reaction_stoichiometry_matrix': reaction_stoichiometry_matrix,
+                'reaction_stoichiometry_source': stoichiometry_source,
                 'carbon_count': carbon_count,
                 'reaction_state': reaction_state,
                 'reaction_phase': reaction_phase,
@@ -1017,3 +1044,79 @@ class ChemReact:
             return component_map
         except Exception as e:
             raise Exception(f"Error mapping components: {e}")
+
+    def reaction_stoichiometry_dict(
+        self,
+        reaction_stoichiometry: Dict[str, float],
+        component_key: ComponentKey = "Name-Formula"
+    ) -> Dict[str, float]:
+        '''
+        Generate the reaction stoichiometry matrix.
+
+        Parameters
+        ----------
+        reaction_stoichiometry: dict
+            A dictionary containing the stoichiometry of the reaction, where keys are component IDs and values are their coefficients.
+
+        Returns
+        -------
+        dict
+            A dictionary representing the reaction stoichiometry, where keys are component IDs and values are their coefficients.
+        '''
+        # >> check
+        if self.components is None:
+            return {}
+
+        # NOTE: component ids
+        component_ids = list(reaction_stoichiometry.keys())
+
+        id_to_component = {}
+        for comp in self.components:
+            comp_id = set_component_id(comp, 'Formula-State')  # type: ignore
+            if comp_id in component_ids:
+                # create component id
+                comp_id_new = set_component_id(
+                    comp,
+                    component_key
+                )
+                id_to_component[comp_id_new] = reaction_stoichiometry[comp_id]
+            else:
+                logging.warning(
+                    f"Component '{comp_id}' not found in reaction stoichiometry.")
+
+        return id_to_component
+
+    def build_stoichiometry_source(
+            self,
+            reaction_stoichiometry: Dict[str, float],
+    ) -> Dict[str, Any]:
+        """
+        Build the stoichiometry source for the reaction according to the component keys.
+
+        Parameters
+        ----------
+        reaction_stoichiometry : Dict[str, float]
+            A dictionary containing the stoichiometry of the reaction, where keys are component IDs and values are their coefficients.
+        """
+        # >> check
+        if self.components is None:
+            return {}
+
+        # NOTE: component ids
+        component_ids = list(reaction_stoichiometry.keys())
+
+        # NOTE: build stoichiometry source
+        stoichiometry_source = {}
+
+        for key in self.component_keys:
+            id_to_component = self.reaction_stoichiometry_dict(
+                reaction_stoichiometry,
+                component_key=key
+            )
+
+            # set
+            stoichiometry_source[key] = id_to_component
+
+        # set stoichiometry source
+        self._stoichiometry_source = stoichiometry_source
+        return stoichiometry_source

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyreactlab_core/docs/chem_utils.py

@@ -1,14 +1,21 @@
 # import libs
 import logging
-from typing import List, Optional
+from typing import List, Optional, Tuple, Dict
+from pythermodb_settings.models import Component, ComponentKey
+from pythermodb_settings.utils import set_component_id
 # locals
 from ..models.reaction import Reaction
+from ..utils.component_tools import map_component_ids
 
 # NOTE: configure logger
 logger = logging.getLogger(__name__)
 
 
-def build_stoichiometry_matrix(reactions: List[Reaction]):
+def build_stoichiometry_matrix(
+        reactions: List[Reaction],
+        components: Optional[List[Component]],
+        component_key: ComponentKey = "Name-Formula"
+):
     '''
     Build stoichiometry matrix for reactions
 
@@ -16,6 +23,10 @@ def build_stoichiometry_matrix(reactions: List[Reaction]):
     ----------
     reactions : List[Reaction]
         List of Reaction instances
+    components : Optional[List[Component]]
+        List of Component instances
+    component_key : ComponentKey
+        The key used to identify components in the reaction.
 
     Returns
     -------
@@ -102,8 +113,18 @@ def build_stoichiometry_matrix(reactions: List[Reaction]):
             [comp_list[j][item] for item in component_dict.keys()] for j in range(reaction_num)
         ]
 
+        # NOTE: map component ids to components
+        components_ext = {}
+        if components is not None:
+            components_ext = map_component_ids(
+                component_ids=component_list,
+                component=components,
+                component_key=component_key
+            )
+
         # res
         return {
+            "components": components_ext,
             "component_list": component_list,
             "component_dict": component_dict,
             "component_state_list": component_state_list,
@@ -112,3 +133,72 @@ def build_stoichiometry_matrix(reactions: List[Reaction]):
         }
     except Exception as e:
         raise Exception(f"Error defining component ID: {e}")
+
+
+# SECTION: build stoichiometry matrix for reactions
+def build_rxn_stoichiometry_source(
+        reactions: List[Reaction],
+        components: List[Component],
+        component_key: ComponentKey
+) -> Optional[
+    Tuple[
+        List[Dict[str, float]],
+        List[List[float]]
+    ]
+]:
+    try:
+        # NOTE: stoichiometry source
+        stoichiometry_source = []
+
+    #    iterate over reactions
+        for reaction in reactions:
+            # stoichiometry
+            stoichiometry_ = reaction.reaction_stoichiometry_source.get(
+                component_key, {})
+            # >> check
+            if not stoichiometry_:
+                logger.warning(
+                    f"Stoichiometry source not found for reaction: {reaction.name}")
+                return None
+
+            # store
+            stoichiometry_source.append(stoichiometry_)
+
+        # NOTE: map component ids to components
+        components_source = [
+            set_component_id(
+                component=item,
+                component_key=component_key
+            ) for item in components
+        ]
+
+        # NOTE: stoichiometry
+        stoichiometry_result: List[Dict[str, float]] = []
+
+        # iterate over stoichiometry source
+        for i in range(len(reactions)):
+            sto_ = {}
+            for item in components_source:
+                # raw data
+                sto_[item] = 0.0
+
+            # update
+            stoichiometry_result.append(sto_)
+
+        # update stoichiometry result
+        for i, item in enumerate(stoichiometry_result):
+            for key, value in stoichiometry_source[i].items():
+                item[key] = value
+
+        # NOTE: create a matrix of stoichiometry
+        stoichiometry_result_matrix: List[List[float]] = []
+        for item in stoichiometry_result:
+            row = []
+            for key in components_source:
+                row.append(float(item[key]))
+            stoichiometry_result_matrix.append(row)
+
+        return stoichiometry_result, stoichiometry_result_matrix
+    except Exception as e:
+        logger.error(f"Error building reaction stoichiometry source: {e}")
+        return None

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyreactlab_core/models/reaction.py

@@ -1,9 +1,9 @@
 # import libs
 from __future__ import annotations
-
+import logging
 from typing import Any, Dict, Optional, List
 from pydantic import BaseModel, Field, computed_field, model_validator
-from pythermodb_settings.models import Component
+from pythermodb_settings.models import Component, ComponentKey
 # local imports
 from ..core.chem_react import (
     ChemReact,
@@ -11,6 +11,9 @@ from ..core.chem_react import (
     PhaseRule
 )
 
+# NOTE: set up logger
+logger = logging.getLogger(__name__)
+
 
 class Reaction(BaseModel):
     """
@@ -79,6 +82,14 @@ class Reaction(BaseModel):
         default_factory=dict,
         description="A dictionary containing the analysis results of the reaction."
     )
+    component_keys: List[ComponentKey] = Field(
+        default_factory=lambda: [
+            "Formula-State",
+            "Name-State",
+            "Name-Formula",
+        ],
+        description="The key used to identify components in the reaction analysis."
+    )
 
     @model_validator(mode="after")
     def _run_existing_analysis(self):
@@ -97,7 +108,8 @@ class Reaction(BaseModel):
         # NOTE: analyze reaction
         util = ChemReact(
             reaction_mode_symbol=self.reaction_mode_symbol,
-            components=self.components
+            components=self.components,
+            component_keys=self.component_keys
         )
 
         # NOTE: perform analysis
@@ -141,8 +153,8 @@ class Reaction(BaseModel):
 
     @computed_field
     @property
-    def reaction_coefficients(self) -> Dict[str, float]:
-        return self.analysis.get("reaction_coefficients", {})
+    def reaction_coefficients(self) -> float:
+        return self.analysis.get("reaction_coefficients", 0.0)
 
     @computed_field
     @property
@@ -156,8 +168,13 @@ class Reaction(BaseModel):
 
     @computed_field
     @property
-    def carbon_count(self) -> int:
-        return self.analysis.get("carbon_count", 0)
+    def reaction_stoichiometry_source(self) -> Dict[str, Dict[str, float]]:
+        return self.analysis.get("reaction_stoichiometry_source", {})
+
+    @computed_field
+    @property
+    def carbon_count(self) -> Dict[str, float]:
+        return self.analysis.get("carbon_count", {})
 
     @computed_field
     @property
@@ -166,7 +183,7 @@ class Reaction(BaseModel):
 
     @computed_field
     @property
-    def reaction_phase(self) -> Optional[PhaseRule]:
+    def reaction_phase(self) -> Optional[str]:
         return self.analysis.get("reaction_phase", None)
 
     @computed_field

pyreactlab_core-0.1.6/pyreactlab_core/utils/component_tools.py

@@ -0,0 +1,38 @@
+# import libs
+import logging
+from typing import Dict, Any, List, Optional, Literal
+from pythermodb_settings.models import Component, ComponentKey
+from pythermodb_settings.utils import set_component_id
+
+
+def map_component_ids(
+        component_ids: list[str],
+        component: List[Component],
+        component_key: ComponentKey
+):
+    """
+    Map component IDs to their corresponding components.
+
+    Parameters
+    ----------
+    component_ids : list[str]
+        A list of component IDs to be mapped.
+    component : List[Component]
+        A list of Component objects to be mapped against.
+    component_key : ComponentKey
+        The key used to identify components in the reaction.
+
+    Returns
+    -------
+    Dict[str, Component]
+        A dictionary mapping component IDs to their corresponding Component objects.
+    """
+    id_to_component = {}
+
+    # iterate over components and map ids
+    for comp in component:
+        comp_id = set_component_id(comp, component_key)
+        if comp_id in component_ids:
+            id_to_component[comp_id] = comp
+
+    return id_to_component

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyreactlab_core.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreactlab-core
-Version: 0.1.4
+Version: 0.1.6
 Summary: pyreactlab-core is the core foundation of the PyReactLab ecosystem, offering shared data structures and algorithms for chemical reaction representation, stoichiometry, and reaction analysis.
 Author-email: Sina Gilassi <sina.gilassi@gmail.com>
 License-Expression: Apache-2.0

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.6}/pyreactlab_core.egg-info/SOURCES.txt

@@ -19,4 +19,5 @@ pyreactlab_core/docs/chem_utils.py
 pyreactlab_core/models/__init__.py
 pyreactlab_core/models/reaction.py
 pyreactlab_core/utils/__init__.py
+pyreactlab_core/utils/component_tools.py
 pyreactlab_core/utils/tools.py