scm_molsg.Input.read_3D¶
-
scm_molsg.Input.
read_3D
(symbols: List[str], xyz: List[List[float[3]]]) → scm_molsg_internal.Mol¶ Initializes a Mol from a list of atomic symbols and a nested list of atomic coordinates
- Parameters
symbols (
list
) – A list of atomic symbols as stringsxyz (
list(list)
) – A list of lists of length 3 (see example) to represent the atomic coordinates of each atom
- Returns
An instance of a molecule
- Return type
Important
The atomic coordinates should be in units of Angstroms
Note
molsg requires connectivity information to generate hashes. For this reason, bonds for molecules input with this function will be estimated by an internal molsg function.
Example
We’ll input methane using its atomic symbols and 3D coordinates
mol = scm_molsg.Input.read_3D( ["C","H","H","H","H"], [[-0.677, 0.491, -0.147], [ 0.274, 0.980, -0.298], [-1.389, 0.859, -0.871], [-0.557, -0.575, -0.270], [-1.036, 0.701, 0.849]] )