pyreactlab-core 0.1.0__py3-none-any.whl

pyreactlab_core/__init__.py

@@ -0,0 +1,25 @@
+# config
+from .configs.info import (
+    __version__,
+    __author__,
+    __package_name__,
+    __description__,
+    __email__,
+    __license__,
+)
+
+from .app import rxn, rxn_stoichiometry, rxns_stoichiometry
+
+__all__ = [
+    # config
+    "__version__",
+    "__author__",
+    "__package_name__",
+    "__description__",
+    "__email__",
+    "__license__",
+    # app
+    "rxn",
+    "rxn_stoichiometry",
+    "rxns_stoichiometry",
+]

pyreactlab_core/app.py

@@ -0,0 +1,123 @@
+# import libs
+import logging
+from typing import List, Optional, Dict
+# locals
+from .models.reaction import Reaction
+from .docs.chem_utils import build_stoichiometry_matrix
+
+# NOTE: configure logger
+logger = logging.getLogger(__name__)
+
+
+def rxn(
+        reaction_str: str,
+        name: Optional[str] = None
+) -> Optional[Reaction]:
+    """
+    Create and analyze a chemical reaction.
+
+    Parameters
+    ----------
+    reaction_str : str
+        reaction expression string such as "A + B => C + D"
+    name : Optional[str]
+        Name of the reaction
+
+    Returns
+    -------
+    Reaction
+        An instance of the Reaction class containing analysis results.
+    """
+    try:
+        # SECTION: validate inputs
+        if not isinstance(reaction_str, str) or not reaction_str.strip():
+            logger.error("Invalid reaction string provided.")
+            return None
+
+        # check name format
+        if name is not None and not isinstance(name, str):
+            logger.error("Invalid name format provided.")
+            return None
+
+        # SECTION: create Reaction instance
+        reaction = Reaction(
+            name=name if name else "Unnamed Reaction",
+            reaction=reaction_str
+        )
+        return reaction
+    except Exception as e:
+        logger.error(f"Error creating Reaction instance: {e}")
+        return None
+
+
+def rxn_stoichiometry(
+        reaction: Reaction,
+) -> Optional[List[float]]:
+    """
+    Get the reaction stoichiometry matrix for a given chemical reaction.
+
+    Parameters
+    ----------
+    reaction : Reaction
+        An instance of the Reaction class.
+
+    Returns
+    -------
+    Optional[List[float]]
+        The reaction stoichiometry matrix if successful, None otherwise.
+    """
+    try:
+        # SECTION: validate inputs
+        if not isinstance(reaction, Reaction):
+            logger.error("Invalid Reaction instance provided.")
+            return None
+
+        # SECTION: retrieve stoichiometry matrix
+        if reaction:
+            return reaction.reaction_stoichiometry_matrix
+        else:
+            logger.error("Failed to create Reaction instance.")
+            return None
+    except Exception as e:
+        logger.error(f"Error retrieving reaction stoichiometry matrix: {e}")
+        return None
+
+
+def rxns_stoichiometry(
+        reactions: List[Reaction],
+) -> Optional[Dict]:
+    """
+    Get the reaction stoichiometry matrices for a list of chemical reactions.
+
+    Parameters
+    ----------
+    reactions : List[Reaction]
+        List of Reaction instances.
+
+    Returns
+    -------
+    Optional[List[List[float]]]
+        List of reaction stoichiometry matrices if successful, None otherwise.
+    """
+    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
+
+        # SECTION: retrieve stoichiometry matrices
+        result = build_stoichiometry_matrix(reactions=reactions)
+
+        # NOTE: res
+        return {
+            "components": result["component_list"],
+            "component_ids": result["component_dict"],
+            "stoichiometry_matrices_list": result["comp_coeff"],
+            "stoichiometry_matrices_dict": result["comp_list"],
+        }
+    except Exception as e:
+        logger.error(f"Error retrieving reaction stoichiometry matrices: {e}")
+        return None

pyreactlab_core/configs/constants.py

@@ -0,0 +1,40 @@
+# import libs
+
+# SECTION: PyThermoDBLink/PyThermoDB
+import math
+DATASOURCE = "datasource"
+EQUATIONSOURCE = "equationsource"
+
+# NOTE: universal gas constant [J/mol.K]
+R_CONST_J__molK = 8.314472
+
+# NOTE: pi
+PI_CONST = math.pi
+
+# NOTE: STP condition
+# pressure [Pa]
+PRESSURE_STP_Pa = 101325
+# temperature [K]
+TEMPERATURE_STP_K = 273.15
+# reference pressure [Pa]
+PRESSURE_REF_Pa = 101325
+# reference temperature [K]
+TEMPERATURE_REF_K = 298.15
+
+# SECTION: Periodic Table Elements
+PERIODIC_TABLE_ELEMENTS = [
+    "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne",
+    "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar",
+    "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni",
+    "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr",
+    "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd",
+    "Ag", "Cd", "In", "Sn", "Sb", "Te", "I", "Xe",
+    "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd",
+    "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu",
+    "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt",
+    "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn",
+    "Fr", "Ra", "Ac", "Th", "Pa", "U", "Np", "Pu",
+    "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr",
+    "Rf", "Db", "Sg", "Bh", "Hs", "Mt", "Ds", "Rg", "Cn",
+    "Nh", "Fl", "Mc", "Lv", "Ts", "Og",
+]

pyreactlab_core/configs/info.py

@@ -0,0 +1,12 @@
+# version
+__version__ = "0.1.0"
+# author
+__author__ = "Sina Gilassi"
+# email
+__email__ = "sina.gilassi@gmail.com"
+# license
+__license__ = "Apache-2.0"
+# package name
+__package_name__ = "PyReactLab-Core"
+# package description
+__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."

pyreactlab_core/core/__init__.py

@@ -0,0 +1 @@
+