torchani.io

Convenience functions for reading and writing molecules in “.xyz” format

Functions

write_xyz	Write an xyz file with possibly many coordinates and species.
read_xyz	Read an xyz file with possibly many molecules.

torchani.io.write_xyz(species, coordinates, dest, cell=None, pad=False, pad_coord_value=0.0, pad_species_value=100)

Write an xyz file with possibly many coordinates and species.

The shapes of the input tensors should be (C, A) and (C, A, 3) respectively, where C is the number of conformations, and A the maximum number of atoms. Output is compatible with ASE’s ‘extxyz’. If a cell is passed it is written in the comment line of all conformations.

If pad=True, output species are padded with atomic number pad_species_value (100 by default) and with coordinates pad_coord_value (0.0 by default), otherwise atoms with species number -1 are not written to the file. Note that many programs (e.g. vmd) require that all conformations in multi-conformation *.xyz files have the same number of atoms, so padding may be useful for visualization in some cases.

torchani.io.read_xyz(path, dtype=None, device=None, detect_padding=True, pad_species_value=100, dividing_char='>', return_comments=False)

Read an xyz file with possibly many molecules. Return them in tensor form

Returns a (species, coordinates) tuple of tensors. The shapes of the tensors are (C, A) and (C, A, 3) respectively, where C is the number of conformations, A the maximum number of atoms (conformations with less atoms are padded with species=-1 and coords = 0.0).

If detect_padding is True, species with atomic number pad_species_value (100 by default) are considered “padding atoms” and are changed to -1. All their coordinates are set to 0.0, no matter their value.

Cell is read from the first conformation.