molop.config

This page provides the API reference for the molop.config module.

Author: TMJ Date: 2025-01-15 23:01:22 LastEditors: TMJ LastEditTime: 2025-12-10 23:37:08 Description: 请填写简介

MolOPConfig

Bases: BaseModel

Configuration class for MolOP operations. Used to manage settings related to molecule processing, fingerprint generation, and logging.

源代码位于： src/molop/config/__init__.py

Python

class MolOPConfig(BaseModel):
    """
    Configuration class for MolOP operations.
    Used to manage settings related to molecule processing, fingerprint generation, and logging.
    """

    model_config = ConfigDict(arbitrary_types_allowed=True)

    # --- General Settings ---
    show_progress_bar: bool = Field(default=True, description="Whether to display the progress bar")
    max_jobs: int = Field(default=16, description="Maximum number of parallel jobs")

    # --- Fingerprint Generator Settings ---
    morgan_fpgen: FingerprintGenerator64 = Field(
        default=GetMorganGenerator(radius=3, fpSize=1024, includeChirality=True),
        description="Morgan fingerprint generator",
    )
    atompair_fpgen: FingerprintGenerator64 = Field(
        default=GetAtomPairGenerator(fpSize=1024, includeChirality=True),
        description="AtomPair fingerprint generator",
    )
    rdkit_fpgen: FingerprintGenerator64 = Field(
        default=GetRDKitFPGenerator(fpSize=1024),
        description="RDKit fingerprint generator",
    )
    topological_torsion_fpgen: FingerprintGenerator64 = Field(
        default=GetTopologicalTorsionGenerator(fpSize=1024),
        description="TopologicalTorsion fingerprint generator",
    )

    # --- Advanced Settings ---
    strict_structure_recovery: bool = Field(
        default=False, description="Whether to perform strict structure recovery"
    )
    max_structure_recovery_time: float = Field(
        default=10.0, description="Maximum structure recovery time (seconds)"
    )
    allow_spin_change: bool = Field(default=False, description="Whether to allow spin changes")
    force_unit_transform: bool = Field(
        default=False, description="Whether to force unit conversion"
    )
    parallel_max_size: int = Field(
        default=8 * 1024**2,
        description="Maximum data size for parallel processing (bytes)",
    )
    max_recursion_depth: int = Field(default=3000, description="Maximum recursion depth for Python")

    # --- Log File Control ---
    log_to_file: bool = Field(default=False, description="Whether to write log messages to a file")

    # --- DOF Effect Drawer Control ---
    use_dof_effect_drawer: bool = Field(
        default=True, description="Whether to use DOF effect drawer"
    )

    def __init__(self, **data):
        """
        Initializes the configuration object and configures the logger based on current settings.
        """
        super().__init__(**data)
        sys.setrecursionlimit(self.max_recursion_depth)
        # Set log state based on initial configuration values
        if self.show_progress_bar:
            self.verbose()
        else:
            self.quiet()

        if self.log_to_file:
            self.enable_file_logging()
        else:
            self.disable_file_logging()

        if self.use_dof_effect_drawer:
            self.set_dof_effect_drawer(enable=True)
        else:
            self.set_dof_effect_drawer(enable=False)

    def quiet(self):
        """
        Disables the progress bar and console log output.
        This allows the program to run silently in the background.
        """
        self.show_progress_bar = False
        if stream_handler in moloplogger.handlers:
            moloplogger.removeHandler(stream_handler)

    def verbose(self):
        """
        Enables the progress bar and console log output.
        """
        self.show_progress_bar = True
        if stream_handler not in moloplogger.handlers:
            moloplogger.addHandler(stream_handler)

    def enable_file_logging(self):
        """Enable logging to a file."""
        self.log_to_file = True
        if file_handler not in moloplogger.handlers:
            moloplogger.addHandler(file_handler)
        logging.info(
            f"File logging enabled. Logs will be written to: {getattr(file_handler, 'baseFilename', 'N/A')}"
        )

    def disable_file_logging(self):
        """Disable logging to a file."""
        self.log_to_file = False
        if file_handler in moloplogger.handlers:
            moloplogger.removeHandler(file_handler)

    def set_log_level(self, level: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]):
        """
        Sets the level for the molop logger.

        Args:
            level (str): The logging level, must be one of 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'.
        """
        try:
            moloplogger.setLevel(level)
            logging.info(f"Log level set to {level}")
        except ValueError as e:
            logging.error(f"Error setting log level: Invalid level '{level}'")
            raise ValueError(f"Invalid log level: {level}") from e

    def set_max_recursion_depth(self, depth: int):
        """
        Set the maximum recursion depth for Python.

        Args:
            depth (int): The maximum recursion depth.
        """
        sys.setrecursionlimit(depth)
        self.max_recursion_depth = depth
        logging.info(f"Maximum recursion depth set to {depth}")

    def set_n_jobs(self, n_jobs: int):
        return (
            min(n_jobs, multiprocessing.cpu_count())
            if n_jobs > 0
            else min(multiprocessing.cpu_count(), self.max_jobs)
        )

    def set_dof_effect_drawer(self, enable: bool):
        """
        Set whether to use the DOF effect drawer.

        Args:
            enable (bool): Whether to use the DOF effect drawer.
        """
        dofconfig.enable_ipython_integration(enable)

__init__(**data)

Initializes the configuration object and configures the logger based on current settings.

源代码位于： src/molop/config/__init__.py

Python

def __init__(self, **data):
    """
    Initializes the configuration object and configures the logger based on current settings.
    """
    super().__init__(**data)
    sys.setrecursionlimit(self.max_recursion_depth)
    # Set log state based on initial configuration values
    if self.show_progress_bar:
        self.verbose()
    else:
        self.quiet()

    if self.log_to_file:
        self.enable_file_logging()
    else:
        self.disable_file_logging()

    if self.use_dof_effect_drawer:
        self.set_dof_effect_drawer(enable=True)
    else:
        self.set_dof_effect_drawer(enable=False)

disable_file_logging()

Disable logging to a file.

源代码位于： src/molop/config/__init__.py

Python

def disable_file_logging(self):
    """Disable logging to a file."""
    self.log_to_file = False
    if file_handler in moloplogger.handlers:
        moloplogger.removeHandler(file_handler)

enable_file_logging()

Enable logging to a file.

源代码位于： src/molop/config/__init__.py

Python

def enable_file_logging(self):
    """Enable logging to a file."""
    self.log_to_file = True
    if file_handler not in moloplogger.handlers:
        moloplogger.addHandler(file_handler)
    logging.info(
        f"File logging enabled. Logs will be written to: {getattr(file_handler, 'baseFilename', 'N/A')}"
    )

quiet()

Disables the progress bar and console log output. This allows the program to run silently in the background.

源代码位于： src/molop/config/__init__.py

Python

def quiet(self):
    """
    Disables the progress bar and console log output.
    This allows the program to run silently in the background.
    """
    self.show_progress_bar = False
    if stream_handler in moloplogger.handlers:
        moloplogger.removeHandler(stream_handler)

set_dof_effect_drawer(enable)

Set whether to use the DOF effect drawer.

参数：

名称	类型	描述	默认
enable	bool	Whether to use the DOF effect drawer.	必需

源代码位于： src/molop/config/__init__.py

Python

def set_dof_effect_drawer(self, enable: bool):
    """
    Set whether to use the DOF effect drawer.

    Args:
        enable (bool): Whether to use the DOF effect drawer.
    """
    dofconfig.enable_ipython_integration(enable)

set_log_level(level)

Sets the level for the molop logger.

参数：

名称	类型	描述	默认
level	str	The logging level, must be one of ‘DEBUG’, ‘INFO’, ‘WARNING’, ‘ERROR’, ‘CRITICAL’.	必需

源代码位于： src/molop/config/__init__.py

Python

def set_log_level(self, level: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"]):
    """
    Sets the level for the molop logger.

    Args:
        level (str): The logging level, must be one of 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'.
    """
    try:
        moloplogger.setLevel(level)
        logging.info(f"Log level set to {level}")
    except ValueError as e:
        logging.error(f"Error setting log level: Invalid level '{level}'")
        raise ValueError(f"Invalid log level: {level}") from e

set_max_recursion_depth(depth)

Set the maximum recursion depth for Python.

参数：

名称	类型	描述	默认
depth	int	The maximum recursion depth.	必需

源代码位于： src/molop/config/__init__.py

Python

def set_max_recursion_depth(self, depth: int):
    """
    Set the maximum recursion depth for Python.

    Args:
        depth (int): The maximum recursion depth.
    """
    sys.setrecursionlimit(depth)
    self.max_recursion_depth = depth
    logging.info(f"Maximum recursion depth set to {depth}")

verbose()

Enables the progress bar and console log output.

源代码位于： src/molop/config/__init__.py

Python

def verbose(self):
    """
    Enables the progress bar and console log output.
    """
    self.show_progress_bar = True
    if stream_handler not in moloplogger.handlers:
        moloplogger.addHandler(stream_handler)