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exceptions

AutoPoly's exception hierarchy. Library code raises these instead of calling sys.exit().

AutoPoly.core.exceptions

Custom exception classes for AutoPoly.

This module defines the exception hierarchy used throughout AutoPoly for proper error handling and testing.

Exceptions are used instead of sys.exit() to enable: - Proper unit testing with pytest.raises() - Graceful cleanup and error recovery - Full stack traces for debugging - Programmatic error handling by library users

Classes:

Name Description
AutoPolyError

Base exception for all AutoPoly errors.
ValidationError

Raised when input validation fails.
GenerationError

Raised when monomer or polymer generation fails.
WorkflowError

Raised when workflow execution fails.

AutoPolyError

Bases: Exception

Base exception for all AutoPoly errors.

All AutoPoly-specific exceptions inherit from this class, allowing users to catch all AutoPoly errors with a single except clause.

Example

try: poly = Polymer(...) except AutoPolyError as e: print(f"AutoPoly error: {e}")

Source code in AutoPoly/core/exceptions.py 
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class AutoPolyError(Exception):
    """Base exception for all AutoPoly errors.

    All AutoPoly-specific exceptions inherit from this class, allowing
    users to catch all AutoPoly errors with a single except clause.

    Example:
        try:
            poly = Polymer(...)
        except AutoPolyError as e:
            print(f"AutoPoly error: {e}")
    """
    pass

ValidationError

Bases: AutoPolyError

Raised when input validation fails.

This exception is raised when user-provided input does not meet validation requirements, such as: - Invalid parameter values (e.g., ChainNum=0) - Invalid sequence length - Missing required fields - Invalid SMILES strings

Example

from AutoPoly.core.exceptions import ValidationError try: ... Polymer(ChainNum=0, Sequence=["[]CC[]"]) ... except ValidationError as e: ... print(f"Validation failed: {e}")

Source code in AutoPoly/core/exceptions.py 
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class ValidationError(AutoPolyError):
    """Raised when input validation fails.

    This exception is raised when user-provided input does not meet
    validation requirements, such as:
    - Invalid parameter values (e.g., ChainNum=0)
    - Invalid sequence length
    - Missing required fields
    - Invalid SMILES strings

    Example:
        >>> from AutoPoly.core.exceptions import ValidationError
        >>> try:
        ...     Polymer(ChainNum=0, Sequence=["[*]CC[*]"])
        ... except ValidationError as e:
        ...     print(f"Validation failed: {e}")
    """

    pass

GenerationError

Bases: AutoPolyError

Raised when monomer or polymer generation fails.

This exception is raised when the generation process encounters an error, such as: - RDKit monomer generation failures - SMILES parsing errors - Force field application failures - Moltemplate file generation errors

Example

from AutoPoly.core.exceptions import GenerationError try: ... generate_monomer_from_smiles("invalid_smiles") ... except GenerationError as e: ... print(f"Generation failed: {e}")

Source code in AutoPoly/core/exceptions.py 
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class GenerationError(AutoPolyError):
    """Raised when monomer or polymer generation fails.

    This exception is raised when the generation process encounters
    an error, such as:
    - RDKit monomer generation failures
    - SMILES parsing errors
    - Force field application failures
    - Moltemplate file generation errors

    Example:
        >>> from AutoPoly.core.exceptions import GenerationError
        >>> try:
        ...     generate_monomer_from_smiles("invalid_smiles")
        ... except GenerationError as e:
        ...     print(f"Generation failed: {e}")
    """

    pass

WorkflowError

Bases: AutoPolyError

Raised when workflow execution fails.

This exception is raised when the overall workflow process fails, such as: - Moltemplate execution failures - LAMMPS data file generation errors - File system operation failures - External tool integration errors

Example

from AutoPoly.core.exceptions import WorkflowError try: ... generate(system, name, models, force_field="oplsaa") ... except WorkflowError as e: ... print(f"Workflow failed: {e}")

Source code in AutoPoly/core/exceptions.py 
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class WorkflowError(AutoPolyError):
    """Raised when workflow execution fails.

    This exception is raised when the overall workflow process fails,
    such as:
    - Moltemplate execution failures
    - LAMMPS data file generation errors
    - File system operation failures
    - External tool integration errors

    Example:
        >>> from AutoPoly.core.exceptions import WorkflowError
        >>> try:
        ...     generate(system, name, models, force_field="oplsaa")
        ... except WorkflowError as e:
        ...     print(f"Workflow failed: {e}")
    """

    pass