dynsight.utilities.read_xyz

dynsight.utilities.read_xyz(input_xyz, cols_order)[source]

Read an XYZ trajectory file into a pandas DataFrame.

The function parses a file in extended XYZ format where each frame begins with a line containing the number of atoms, followed by a comment/title line, and then one line per atom containing at least one of the columns specified in cols_order, following the correct order in the file.

Parameters:

  • input_xyz (Path | str) – Path to the XYZ file to read.

  • cols_order (Sequence[Literal['name', 'x', 'y', 'z', 'ID']]) – The expected column order for each atom line (e.g., [“name”, “x”, “y”, “z”, “ID”]).

Returns:

A DataFrame containing all parsed atomic entries. Each row corresponds to one atom in one frame, with columns given by cols_order plus the current frame indexing.

Return type:

DataFrame