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Utility Functions

Sierra provides a simple and convenient set of functions to store and load any of its models.

sierra.dump

dump((Any) obj, (Union[str, Path, io.IOBase]) file, (str) encoding) -> None:

The dump() function writes the given obj into a file.

Arguments

obj

The object to be dumped into a file. This can be any model type supported by Sierra, e.g. be a ConformersInput, a HessianResult or a Molecule.

  • Type: Any
file

The file (or filename) into which the data will be written.

  • Type: One of: [str, Path, io.IOBase]
encoding

The format in which the file will be written.

  • Type: str
  • Default: "msgpack-entos"

Returns

None

sierra.dumps

dumps((Any) obj, (str) encoding) -> Union[str, bytes]:

The dumps() function creates a str or bytes representation of a model.

Arguments

obj

The object to be dumped into a file. This can be any model type supported by Sierra, e.g. be a ConformersInput, a HessianResult or a Molecule.

  • Type: Any
encoding

The format in which the string will be written.

  • Type: str
  • Default: "msgpack-entos"

Returns

Depending on the encoding, a str or bytes representation of the model.

sierra.load

load((Union[str, Path, io.IOBase]) file, (str) encoding, (bool) object_hooks) -> Any:

The load() function loads data which has been written using the dump() function and converts it into a Sierra model.

Arguments

file

The file (or filename) from which the data is read.

  • Type: One of: [str, Path, io.IOBase]
encoding

The format of the data in the file.

  • Type: str
  • Default: "msgpack-entos"
object_hooks

A flag that can be set to False to avoid conversion of the raw data into known Sierra models.

  • Type: bool
  • Default: True

Returns

A Sierra model containing the data present in the file.

sierra.loads

loads((Union[str, bytes]) blob, (str) encoding, (bool) object_hooks) -> Any:

The loads() function decodes data given in a str or bytes representation and converts it into a Sierra model.

Arguments

blob

The data that will be decoded.

  • Type: One of: [str, bytes]
encoding

The format of the data in the blob.

  • Type: str
  • Default: "msgpack-entos"
object_hooks

A flag that can be set to False to avoid conversion of the raw data into known Sierra models.

  • Type: bool
  • Default: True

Returns

A Sierra model containing the data present in the blob of data.

sierra.build_concatenated_xyzplus

build_concatenated_xyzplus((List[Molecule]) molecules, (Optional[Union[str, Path]]) filename) -> Optional[str]:

This function builds, and optionally writes to 'filename', the geometry of the 'molecules' in concatenated XYZ+ format.

A newline is added to the end of the text as per the POSIX file standards.

Arguments

molecules

The list of molecules to write.

  • Type: List[Molecule]
filename

If specified, the molecule is written to this file. If no filename is provided, the result is returned as a str.

  • Type: Optional[Union[str, Path]]
  • Default: None

Returns

None if a filename has been specified, and otherwise a str with the same content.