SPE calculation

Auto3D is mainly designed for generating low-energy 3D structures from the SMILES. It aslo provides a wrapper function calc_spe to do single point energy calculation for existing 3D structures, using ANI2x, AIMNET or ANI2xt as the engine.

Single point energy (SPE) calculation does not change the input geometry.

The source juputer notebook can be downloaded here

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import os, sys
root = os.path.dirname(os.path.dirname(os.path.abspath("__file__")))
sys.path.append(root)

import Auto3D
from Auto3D import Auto3DOptions, main, calc_spe

[2]:

#Always ensure that you have the latest version
print(Auto3D.__version__)

2.2.10

[4]:

path = os.path.join(root, "example/files/RDKIT_ANI2x_smiles/smiles_out.sdf")
spe = calc_spe(path, model_name="ANI2x")
print(spe)  #SPE are stored in the SDF file under the E_hartree entry

/home/jack/Auto3D_pkg/example/files/RDKIT_ANI2x_smiles/smiles_out_ANI2x_E.sdf

[5]:

help(calc_spe)

Help on function calc_spe in module Auto3D.SPE:

calc_spe(path: str, model_name: str, gpu_idx=0)
    Calculates single point energy.

    :param path: Input sdf file
    :type path: str
    :param model_name: AIMNET, ANI2x or ANI2xt
    :type model_name: str
    :param gpu_idx: GPU cuda index, defaults to 0
    :type gpu_idx: int, optional

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