scm_molsg.Input.read_3D_with_bonds¶

scm_molsg.Input.read_3D_with_bonds(symbols: List[str], xyz: List[List[float[3]]], indices: List[int], bonds: List[Tuple[int, int]]) → 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 strings
xyz (list(list)) – A list of lists of length 3 (see example) to represent the atomic coordinates of each atom
indices (list) – A list of integers representing the indices of each atom. This can be helpful to provide bond information relative to some existing index.
bonds (list) – A list of index pairs corresponding to every bond in the structure

Returns

An instance of a molecule

Return type

scm_molsg.Mol

Important

The atomic coordinates should be in units of Angstroms

Note

molsg will perform no sanity checks on the bonds provided and they will be used as is, so it’s advised to ensure the supplied connectivity is reasonable.

Example

We’ll input methane using its atomic symbols and 3D coordinates

mol = scm_molsg.Input.read_3D_with_bonds(
    ["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]],
    [0,1,2,3,4],
    [(0,1),(0,2),(0,3),(0,4)]
    )