Smeared radial distribution 3D descriptors
These distance-based molecular 3D descriptors are inspired by those of SchNet, with the additional summation over identical atom pairs. As such, these descriptors are invariant by global translation, rotation and inversion, as well as permutation of equivalent atoms (i.e. same atomic number).
More details can be found in the related paper: coming soon
usage: src/ddd.py [-h] -i INPUT [-o OUTPUT] [--min-cutoff MIN_CUTOFF] [--cutoff CUTOFF]
[--nb-basis-functions NB_BASIS_FUNCTIONS] [--centers CENTERS]
[--widths WIDTHS] [--basis-function BASIS_FUNCTION]
[--atomic-types ATOMIC_TYPES]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input file path (any format recognized by ASE) (default: None)
-o OUTPUT, --output OUTPUT
Output file path (prints to standard output if unspecified or empty) (default: None)
--min-cutoff MIN_CUTOFF
Minimum distance cutoff (Angstroms) (default: 0)
--cutoff CUTOFF Maximum distance cutoff (Angstroms). Default: 10 Bohr (default: 5.291772105638412)
--nb-basis-functions NB_BASIS_FUNCTIONS, --size NB_BASIS_FUNCTIONS
Number of basis functions for describing each atomic pair (default: 20)
--centers CENTERS Custom centers to use (JSON format, list of Angstroms) (default: None)
--widths WIDTHS Custom widths to use (JSON format, list of Angstroms) (default: None)
--basis-function BASIS_FUNCTION
Basis function ("gaussian_basic" or "gaussian_normalized") (default: gaussian_basic)
--atomic-types ATOMIC_TYPES
Atomic types to include in the descriptors (JSON format, list of atomic numbers). Default: the atomic types of the input (default: None)