iodata.formats.extxyz module

Extended XYZ file format.

The extended XYZ file format is defined in the ASE documentation.

Usually, the different frames in a trajectory describe different geometries of the same molecule, with atoms in the same order. The load_many function below can also handle an XYZ with different molecules, e.g. a molecular database.

load_many(lit)

Load multiple frames from a EXTXYZ file.

Parameters:

lit (LineIterator) – The line iterator to read the data from.

Yields:

result (dict) – A dictionary with IOData attributes. The following attribtues are guaranteed to be loaded: title. The following may be loaded if present in the file: atcoords, atgradient, atmasses, atnums, cellvecs, charge, energy, extra.

Return type:

Iterator[dict]

Notes

load_one(lit)

Load a single frame from a EXTXYZ file.

Parameters:

lit (LineIterator) – The line iterator to read the data from.

Return type:

dict

Returns:

result (dict) – A dictionary with IOData attributes. The following attributes are guaranteed to be loaded: title. The following may be loaded if present in the file: atcoords, atgradient, atmasses, atnums, cellvecs, charge, energy, extra.

Notes