Loading Files

To read a file, use something like this:

from iodata import load_one

mol = load_one("water.xyz")  # XYZ files contain atomic coordinates in Angstrom
print(mol.atcoords)  # print coordinates in Bohr.

Note that IOData will automatically convert units from the file format’s official specification to atomic units (which is the format used throughout HORTON3).

The file format is inferred from the extension, but one can override the detection mechanism by manually specifying the format:

from iodata import load_one

mol = load_one("water.foo", "xyz")  # XYZ file with unusual extension
print(mol.atcoords)

IOData also has basic support for loading databases of molecules. For example, the following will iterate over all frames in an XYZ file:

from iodata import load_many

# print the title line from each frame in the trajectory.
for mol in load_many("trajectory.xyz"):
    print(mol.title)
    print(mol.atcoords)

More details can be found in the API documentation of iodata.api.load_one() and iodata.api.load_many().