AutoREACTER 0.2b1__tar.gz → 0.2.3__tar.gz

autoreacter-0.2.3/AutoREACTER/__init__.py

@@ -0,0 +1,316 @@
+"""
+AutoREACTER
+
+AutoREACTER is a tool for automated reaction-based molecular system generation.
+"""
+__version__ = "0.2.3"
+
+__title__ = "AutoREACTER"
+__author__ = "Janitha Mahanthe, Jacob Gissinger"
+
+__package__ = "AutoREACTER"
+__release__ = __version__
+__license__ = "MIT"
+
+__authors__ = [
+    "Janitha Mahanthe",
+    "Jacob Gissinger",
+]
+
+__author__ = ", ".join(__authors__)
+
+# Import all public API symbols
+from importlib.metadata import version, PackageNotFoundError
+from pathlib import Path
+from typing import Optional
+from .session import Session
+
+
+
+
+"""
+Public API for the AutoREACTER (ARX) pipeline.
+
+This module exposes a **global-session** interface: call :func:`run` once to
+bootstrap a workflow from an input file, then use the remaining functions to
+inspect molecules, select reactions and non-reactants, and finally run the
+full simulation pipeline.  Each function delegates to the currently active
+:class:`ARXCLI` instance behind the scenes.
+
+Usage (e.g. in a Jupyter notebook)::
+
+    import AutoREACTER as arx
+
+    arx.run("input.json")
+    arx.show_molecules()
+    arx.show_functional_groups()
+    arx.show_reactions()
+    arx.select_reactions()
+    arx.show_non_reactants()
+    arx.select_non_reactants()
+    arx.process()
+
+All public symbols are listed in :data:`__all__`.
+
+:data:`__all__` includes:
+    - ``run``
+    - ``show_molecules``
+    - ``show_functional_groups``
+    - ``show_reactions``
+    - ``select_reactions``
+    - ``show_non_reactants``
+    - ``select_non_reactants``
+    - ``process``
+"""
+
+from .arx_cli import ARXCLI
+from PIL import Image
+
+# ---------------------------------------------------------------------------
+# Global session handle – holds the *single* active workflow instance.
+# The `run()` function is the only way to create (or replace) it.
+# ---------------------------------------------------------------------------
+_active_workflow = None  # type: ARXCLI | None
+
+
+def _ensure_workflow() -> ARXCLI:
+    """
+    Return the active :class:`ARXCLI` instance, raising if none exists.
+
+    This is the single choke-point used by every public function before
+    delegating.  It guarantees that the user called :func:`run` first.
+
+    Returns
+    -------
+    ARXCLI
+        The currently active workflow session.
+
+    Raises
+    ------
+    RuntimeError
+        If :func:`run` has not been called yet (i.e. no session is active).
+    """
+    if _active_workflow is None:
+        raise RuntimeError(
+            "No active session. Please run `arx.run('your_file.json')` first."
+        )
+    return _active_workflow
+
+
+# ===================================================================
+# UTILITY FUNCTIONS
+# ===================================================================
+
+def session() -> Session:
+    """
+    Get the active :class:`Session` object from the current workflow.
+    Returns
+    -------
+    Session
+        The active session object containing all workflow state and data.
+    """
+    return _ensure_workflow().session
+
+# ===================================================================
+# PUBLIC API
+# ===================================================================
+
+def run(input_file):
+    """
+    Create or replace the active AutoREACTER workflow session.
+
+    Parameters
+    ----------
+    input_file : str or pathlib.Path
+        Path to the AutoREACTER input JSON file.
+
+    Returns
+    -------
+    ARXCLI
+        Active AutoREACTER workflow object.
+    """
+    global _active_workflow
+
+    input_file = Path(input_file).expanduser().resolve()
+
+    if not input_file.exists():
+        raise FileNotFoundError(f"Input file not found: {input_file}")
+
+    _active_workflow = ARXCLI(input_file)
+    return _active_workflow
+
+
+def show_molecules() -> Image:
+    """
+    Display the 2D structures of all molecules in the current session.
+
+    This triggers molecule visualisation (RDKit images) and is safe to call
+    multiple times – the underlying detection runs only once.
+
+    Returns
+    -------
+    Image
+        Visualisation of all molecules, saved to the session's output directory.
+    """
+    return _ensure_workflow().show_molecules()
+
+
+def show_functional_groups() -> Image:
+    """
+    Display the detected functional groups for each molecule.
+
+    Functional-group detection must have completed; if it hasn't, this method
+    triggers it automatically (idempotent).  The visualisation highlights the
+    matched SMARTS patterns on each molecule.
+
+    Returns
+    -------
+    Image
+        Visualisation of functional groups, saved to the session's output directory.
+    """
+    return _ensure_workflow().show_functional_groups()
+
+
+def show_reactions() -> Image:
+    """
+    Display the chemical reactions identified by the pipeline.
+
+    If reaction detection has not run yet, it is triggered first.  The output
+    includes reaction templates and their mappings onto the input molecules.
+
+    Returns
+    -------
+    Image
+        Visualisation of reactions, saved to the session's output directory.
+    """
+    return _ensure_workflow().show_reactions()
+
+
+def select_reactions() -> None:
+    """
+    Interactively select which reaction(s) to proceed with.
+
+    If multiple candidate reactions were identified, the user is prompted to
+    choose.  When only one reaction is found it is auto-selected.  This step
+    must complete before non-reactants can be selected or :func:`process` can
+    be called.
+
+    Returns
+    -------
+    None
+        Updates the internal :class:`ErrorHandler` state machine.
+    """
+    _ensure_workflow().select_reactions()
+
+
+def show_non_reactants() -> Image:
+    """
+    Display the non-reactant species detected in the simulation box.
+
+    Non-reactant detection depends on reaction selection having already
+    occurred; if it hasn't, an error will be raised.
+
+    Returns
+    -------
+    Image
+        Visualisation of non-reactant species, saved to the session's output directory.
+    """
+    return _ensure_workflow().show_non_reactants()
+
+
+def select_non_reactants() -> None:
+    """
+    Interactively select which non-reactant species to include.
+
+    This may prompt the user to pick from a list of detected species.  Must
+    be called after :func:`select_reactions` and before :func:`process`.
+
+    Returns
+    -------
+    None
+        Updates the internal :class:`ErrorHandler` state machine.
+    """
+    _ensure_workflow().select_non_reactants()
+
+def prepare_reactions() -> None:
+    """
+    Prepare the reaction templates for simulation.
+
+    This is an intermediate step that performs reaction-template preparation
+    without running the full pipeline.  It is not intended for end-users but
+    may be useful for debugging or development.
+
+    Returns
+    -------
+    None
+        Writes prepared reaction templates to the session's output directory.
+        Updates the internal :class:`ErrorHandler` state machine.
+    """
+    _ensure_workflow().prepare_reactions()
+
+
+def show_reaction_templates(highlight_type: Optional[str] = "template") -> Image:
+    """
+    Visualise the prepared reaction templates.
+
+    This is an intermediate step that visualises the reaction templates after
+    preparation.  It is not intended for end-users but may be useful for
+    debugging or development.
+
+    Returns
+    -------
+    Image
+        Visualisation of prepared reaction templates, saved to the session's output directory.
+    """
+    highlight_type = highlight_type.lower() if highlight_type else "template"
+    highlight_types = [
+        "template",    # Highlight the reaction template itself (i.e. the changed bonds).
+        "edge",        # Highlight the edge atoms (dihedral distance away from the reaction center).
+        "initiators",  # Highlight the initiator atoms/bonds that trigger the reaction.
+        "delete"       # Highlight the atoms/bonds that are deleted in the reaction.
+        ]
+    if highlight_type not in highlight_types:
+        raise ValueError(f"Invalid highlight_type: {highlight_type}. Must be one of {highlight_types}.")
+    return _ensure_workflow().show_reaction_templates(highlight_type=highlight_type)
+
+
+def process() -> None:
+    """
+    Execute the full simulation setup pipeline.
+
+    This is the final step.  It performs, in order:
+
+    1. 3D geometry generation
+    2. Force-field assignment (via :class:`FFWrapper`)
+    3. REACTER file creation
+    4. LAMMPS input generation
+
+    All preceding steps (reaction selection, non-reactant selection) must have
+    completed first; otherwise a :class:`RuntimeError` is raised.
+
+    Returns
+    -------
+    None
+        Writes all simulation artifacts to the session's output directory.
+    """
+    _ensure_workflow().process()
+
+
+# Expose only these commands to the user
+__all__ = [
+    "__title__",
+    "__version__",
+    "__release__",
+    "__authors__",
+    "__license__",
+    "run",
+    "show_molecules",
+    "show_functional_groups",
+    "show_reactions",
+    "select_reactions",
+    "show_non_reactants",
+    "select_non_reactants",
+    "prepare_reactions",
+    "show_reaction_templates",
+    "process",
+]

autoreacter-0.2.3/AutoREACTER/_compat.py

@@ -0,0 +1,60 @@
+import sys
+import collections
+import collections.abc
+import numpy as np
+
+def apply_legacy_patches():
+    """
+    Injects removed aliases back into numpy and collections at runtime, 
+    and bridges the OpenMM simtk namespace for older versions of Foyer/mBuild.
+    """
+    # 1. Restore removed Collections aliases
+    _missing_classes = [
+        "MutableSet", "MutableMapping", "Mapping", "MutableSequence",
+        "Sequence", "Set", "Iterable", "Iterator", "Callable",
+        "Container", "Hashable", "ItemsView", "KeysView", "ValuesView"
+    ]
+    for _name in _missing_classes:
+        if not hasattr(collections, _name) and hasattr(collections.abc, _name):
+            setattr(collections, _name, getattr(collections.abc, _name))
+
+    # 2. Restore removed NumPy aliases
+    if not hasattr(np, "float"): np.float = float
+    if not hasattr(np, "int"): np.int = int
+    if not hasattr(np, "complex"): np.complex = complex
+    if not hasattr(np, "bool"): np.bool = np.bool_
+    if not hasattr(np, "object"): np.object = np.object_
+    if not hasattr(np, "str"): np.str = np.str_
+
+    # 3. Robust OpenMM 'simtk' shim for Python 3.12+
+    try:
+        import sys
+        import types
+        import openmm
+        import openmm.app
+        import openmm.app.element
+        import openmm.unit
+
+        # Create pure, fake modules to bypass strict filesystem import checks
+        simtk = types.ModuleType("simtk")
+        simtk_openmm = types.ModuleType("simtk.openmm")
+        simtk_openmm_app = types.ModuleType("simtk.openmm.app")
+
+        # Copy the contents of the real modules into our fake ones
+        simtk_openmm.__dict__.update(openmm.__dict__)
+        simtk_openmm_app.__dict__.update(openmm.app.__dict__)
+        
+        # Manually wire the internal tree together
+        simtk.openmm = simtk_openmm
+        simtk.unit = openmm.unit
+        simtk_openmm.app = simtk_openmm_app
+        simtk_openmm_app.element = openmm.app.element
+
+        # Register them in sys.modules so the 'import' statements find them instantly
+        sys.modules["simtk"] = simtk
+        sys.modules["simtk.openmm"] = simtk_openmm
+        sys.modules["simtk.openmm.app"] = simtk_openmm_app
+        sys.modules["simtk.openmm.app.element"] = openmm.app.element
+        sys.modules["simtk.unit"] = openmm.unit
+    except ImportError:
+        pass