config

PyHDXConfig

PyHDX configuration class.

This object is a singleton, thus always the same instance is returned upon creation.

Attributes:

Name	Type	Description
conf	Optional[DictConfig]	OmegaConf DictConfig object.

Source code in pyhdx/config.py

class PyHDXConfig(metaclass=Singleton):
    """PyHDX configuration class.

    This object is a singleton, thus always the same instance is returned upon creation.

    Attributes:
        conf: OmegaConf DictConfig object.
    """

    __slots__ = ["conf"]

    def __init__(self) -> None:
        self.conf: Optional[DictConfig] = None

    def __getattr__(self, item: str) -> Any:
        return getattr(self.conf, item)

    def __setattr__(self, key: str, value: Any) -> None:
        if key in self.__slots__:
            super().__setattr__(key, value)
        elif key in self.conf.keys():
            setattr(self.conf, key, value)
        else:
            raise AttributeError(f"Config has no attribute {key}")

    def load_config(self, config_file: PathLike[str]) -> None:
        """Load a config file and merge with the current config.

        Args:
            config_file: Path to the config file to load.

        """
        conf_new = OmegaConf.create(Path(config_file).read_text())
        self.merge_config(conf_new)

    def merge_config(self, conf: Union[DictConfig, dict]) -> None:
        """Merge a new config with the current config.

        Args:
            conf: New config to merge with current config.

        """
        if isinstance(conf, dict):
            conf = OmegaConf.create(conf)
        conf = OmegaConf.merge(self.conf, conf)
        self.set_config(conf)

    def set_config(self, conf: DictConfig) -> None:
        self.conf = conf

    def get(self, key: DictKeyType, default_value: Any = None) -> Any:
        return self.conf.get(key, default_value)

    @property
    def assets_dir(self) -> Path:
        """PyHDX server assets directory"""
        spec_path = self.conf.server.assets_dir
        assets_dir = Path(spec_path.replace("~", str(Path().home())))

        return assets_dir

    @property
    def log_dir(self) -> Path:
        """PyHDX server log directory"""
        spec_path = self.conf.server.log_dir
        log_dir = Path(spec_path.replace("~", str(Path().home())))

        return log_dir

    @property
    def database_dir(self) -> Path:
        """HDXMS-datasets database directory"""
        spec_path = self.conf.server.database_dir
        database_dir = Path(spec_path.replace("~", str(Path().home())))

        return database_dir

    @property
    def TORCH_DTYPE(self) -> Union[torch.float64, torch.float32]:
        """PyTorch dtype used for ΔG calculations"""
        dtype = self.conf.fitting.dtype
        if dtype in ["float64", "double"]:
            return torch.float64
        elif dtype in ["float32", "float"]:
            return torch.float32
        else:
            raise ValueError(f"Unsupported data type: {dtype}")

    @property
    def TORCH_DEVICE(self) -> torch.device:
        """PyTorch device used for ΔG calculations"""
        device = self.conf.fitting.device
        return torch.device(device)

    @contextmanager
    def context(self, settings: dict) -> Generator[PyHDXConfig, None, None]:
        from pyhdx.support import rsetattr

        original_config = self.conf.copy()

        try:
            for attr, value in settings.items():
                rsetattr(cfg, attr, value)
            yield cfg
        finally:
            cfg.conf = original_config

TORCH_DEVICE property

PyTorch device used for ΔG calculations

TORCH_DTYPE property

PyTorch dtype used for ΔG calculations

assets_dir property

PyHDX server assets directory

database_dir property

HDXMS-datasets database directory

log_dir property

PyHDX server log directory

load_config(config_file)

Load a config file and merge with the current config.

Parameters:

Name	Type	Description	Default
config_file	PathLike[str]	Path to the config file to load.	required

Source code in pyhdx/config.py

def load_config(self, config_file: PathLike[str]) -> None:
    """Load a config file and merge with the current config.

    Args:
        config_file: Path to the config file to load.

    """
    conf_new = OmegaConf.create(Path(config_file).read_text())
    self.merge_config(conf_new)

merge_config(conf)

Merge a new config with the current config.

Parameters:

Name	Type	Description	Default
conf	Union[DictConfig, dict]	New config to merge with current config.	required

Source code in pyhdx/config.py

def merge_config(self, conf: Union[DictConfig, dict]) -> None:
    """Merge a new config with the current config.

    Args:
        conf: New config to merge with current config.

    """
    if isinstance(conf, dict):
        conf = OmegaConf.create(conf)
    conf = OmegaConf.merge(self.conf, conf)
    self.set_config(conf)

reset_config()

create a new config.yaml file in the ~home/.pyhdx folder

Source code in pyhdx/config.py

def reset_config() -> None:
    """create a new config.yaml file in the `~home/.pyhdx` folder"""

    with open(config_file_path, "w") as target:
        from pyhdx.__version__ import __version__

        version_string = f"# {PACKAGE_NAME} configuration file " + __version__ + "\n\n"
        target.write(version_string)

        with open(current_dir / "config.yaml") as source:
            for line in source:
                target.write(line)

valid_config()

Checks if the current config file in the user home directory is a valid config file for the current pyhdx version.

Source code in pyhdx/config.py

def valid_config() -> bool:
    """Checks if the current config file in the user home directory is a valid config
    file for the current pyhdx version.

    """
    if not config_file_path.exists():
        return False
    else:
        with open(config_file_path, "r") as f:
            version_string = f.readline().strip("; ").split(" ")[-1]

        from pyhdx.__version__ import __version__

        local_version = version.parse(__version__)
        cfg_version = version.parse(version_string)

        return local_version.public == cfg_version.public