pyreactlab-core 0.1.4__tar.gz → 0.1.5__tar.gz

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreactlab-core
-Version: 0.1.4
+Version: 0.1.5
 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-0.1.5}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pyreactlab-core"
-version = "0.1.4"
+version = "0.1.5"
 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"

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.5}/pyreactlab_core/configs/info.py

@@ -1,5 +1,5 @@
 # version
-__version__ = "0.1.4"
+__version__ = "0.1.5"
 # author
 __author__ = "Sina Gilassi"
 # email

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.5}/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__)
 
@@ -72,7 +75,8 @@ class ChemReact:
     def __init__(
         self,
         reaction_mode_symbol: ReactionMode,
-        components: Optional[List[Component]]
+        components: Optional[List[Component]],
+        component_key: ComponentKey
     ):
         """
         Initialize the ChemReactUtils class.
@@ -83,6 +87,8 @@ 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_key : ComponentKey
+            The key used to identify components in the reaction.
 
         Notes
         -----
@@ -98,6 +104,9 @@ class ChemReact:
         # NOTE: set components
         self.components = components
 
+        # NOTE: set component key
+        self.component_key = component_key
+
         # SECTION: Component id
         # NOTE: component ids
         if components is None:
@@ -396,6 +405,11 @@ class ChemReact:
                 products,
             )
 
+            # SECTION: reaction stoichiometry dict
+            reaction_stoichiometry_dict = self.reaction_stoichiometry_dict(
+                reaction_stoichiometry
+            )
+
             # res
             res = {
                 'name': name,
@@ -411,6 +425,7 @@ class ChemReact:
                 'reaction_coefficients': reaction_coefficients,
                 'reaction_stoichiometry': reaction_stoichiometry,
                 'reaction_stoichiometry_matrix': reaction_stoichiometry_matrix,
+                'reaction_stoichiometry_dict': reaction_stoichiometry_dict,
                 'carbon_count': carbon_count,
                 'reaction_state': reaction_state,
                 'reaction_phase': reaction_phase,
@@ -1017,3 +1032,42 @@ 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],
+    ) -> 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,
+                    self.component_key)  # type: ignore
+                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

{pyreactlab_core-0.1.4 → pyreactlab_core-0.1.5}/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 +82,10 @@ class Reaction(BaseModel):
         default_factory=dict,
         description="A dictionary containing the analysis results of the reaction."
     )
+    component_key: ComponentKey = Field(
+        default='Name-Formula',
+        description="The key used to identify components in the reaction analysis."
+    )
 
     @model_validator(mode="after")
     def _run_existing_analysis(self):
@@ -97,7 +104,8 @@ class Reaction(BaseModel):
         # NOTE: analyze reaction
         util = ChemReact(
             reaction_mode_symbol=self.reaction_mode_symbol,
-            components=self.components
+            components=self.components,
+            component_key=self.component_key
         )
 
         # NOTE: perform analysis
@@ -154,6 +162,11 @@ class Reaction(BaseModel):
     def reaction_stoichiometry_matrix(self) -> list[float]:
         return self.analysis.get("reaction_stoichiometry_matrix", [])
 
+    @computed_field
+    @property
+    def reaction_stoichiometry_dict(self) -> Dict[str, float]:
+        return self.analysis.get("reaction_stoichiometry_dict", {})
+
     @computed_field
     @property
     def carbon_count(self) -> int:

pyreactlab_core-0.1.5/pyreactlab_core/utils/component_tools.py

@@ -0,0 +1,36 @@
+# 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 = {}
+    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-0.1.5}/pyreactlab_core.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreactlab-core
-Version: 0.1.4
+Version: 0.1.5
 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-0.1.5}/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