Improve Monomer Input Schema

[janitha-mahanthe]

This pull request introduces significant improvements and new functionality to the polymerization reaction detection system. The main changes include the addition of a new detector for identifying non-reacting monomers, extensive documentation and refactoring for clarity, and enhanced error handling. These updates improve the usability, maintainability, and robustness of the codebase.

Addressed issue #32 to aligns with the new replicas-based system configuration.

Key changes

• Monomer definitions are separated from system composition.
• Monomer quantities are now defined inside replicas.systems using monomer_counts or monomer_ratios.
• Monomer name is now required and acts as the unique identifier used to reference monomers throughout the input file.

This removes ambiguity in monomer referencing and enables reliable JSON Schema validation for user inputs.

Example

"monomer_counts": {
  "tmc": 220,
  "mpd": 220,
  "CCO": 110
}

New Functionality

• Added NonReactantsDetector class in non_monomer_detector.py to identify monomers that do not participate in any detected reactions, visualize them, and provide user interaction for retaining or discarding these monomers.

Documentation and Refactoring

• Added comprehensive docstrings and comments to classes and methods in reaction_detector.py, clarifying the purpose and attributes of FunctionalGroupInfo, MonomerRole, ReactionTemplate, ReactionInstance, and ReactionDetector. [1] [2] [3] [4]
• Refactored the _matching_fgs method in ReactionDetector to use list comprehensions and type annotations for improved readability and correctness.

Error Handling Improvements

• Introduced new custom exceptions: SMARTSerror for developer-defined SMARTS pattern errors, and EmptyReactionListError for handling cases where no reactions are detected but user selection is attempted.

Deprecation Notice

• Added a deprecation warning to detector.py to inform users that the script and CLI will be removed in future versions, and to recommend using the Jupyter notebook interface.

Dependency and Import Updates

• Updated import statements in reaction_detector.py for consistency and added missing imports for new functionality.

These changes collectively enhance the detection workflow, improve user interaction, and make the codebase easier to maintain and extend.

[Copilot]

Pull request overview

This PR updates AutoREACTER’s input format to a replicas-based schema (moving monomer quantities into replicas.systems) and extends the detection workflow with a new non-reactant monomer detector, alongside refactors/documentation improvements in the reaction detector.

Changes:

• Refactors input parsing to support replicas.systems.{monomer_counts|monomer_ratios} and updates examples accordingly.
• Adds NonReactantsDetector and wires it into the example notebook workflow.
• Refactors/documentation updates in reaction_detector.py, plus a deprecation warning in the legacy CLI detector script.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 18 comments.

Show a summary per file

File	Description
examples/example_1_inputs_stoichiometry_mode.json	Removes old stoichiometry-mode example.
examples/example_1_inputs_ratio_mode.json	Adds new replicas-based ratio-mode example.
examples/example_1_inputs_count_mode_with_non_monomers.json	Adds new replicas-based counts-mode example (intended to demonstrate non-reactants).
examples/example_1_inputs_count_mode_FF.json	Updates force-field counts example to replicas schema.
examples/example_1_inputs_count_mode.json	Updates counts-mode example to replicas schema.
examples/example_1_inputs.json	Removes legacy v0.1-style example input.
examples/example_1.ipynb	Updates notebook to import/use NonReactantsDetector and new flow.
AutoREACTER/reaction_template_builder/run_reaction_template_pipeline.py	Removes large stale TODO/comment blocks.
AutoREACTER/input_parser.py	Implements replicas-based parsing + validation changes.
AutoREACTER/detectors/reaction_detector.py	Adds docstrings, refactors matching logic, adds new exceptions.
AutoREACTER/detectors/non_monomer_detector.py	Adds new detector for identifying/visualizing/selecting non-reactant monomers.
AutoREACTER/detectors/detector.py	Adds module-level deprecation warning for the legacy script/CLI.

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[Copilot]

This module imports FunctionalGroupInfo / MonomerRole from functional_groups_detector, but then redefines classes with the same names below, overriding the imports. That redundancy is confusing and can lead to subtle type mismatches across modules. Consider deleting the import and using the local definitions, or (preferably) deleting the local redefinitions and re-exporting/using the shared types from functional_groups_detector.

[janitha-mahanthe]

@copilot open a new pull request to apply changes based on this feedback

[Copilot]

@janitha-mahanthe I've opened a new pull request, #43, to work on those changes. Once the pull request is ready, I'll request review from you.

[Copilot]

@janitha-mahanthe I've opened a new pull request, #44, to work on those changes. Once the pull request is ready, I'll request review from you.

[janitha-mahanthe]

@copilot open a new pull request to apply changes based on the comments in this thread

[Copilot]

@janitha-mahanthe I've opened a new pull request, #45, to work on those changes. Once the pull request is ready, I'll request review from you.