"""Common Molecular descriptors for (classical) machine learning.
Note they are defined only for one molecule not for batches.
"""
import numpy as np
from molreps.methods.geo_npy import coordinates_to_distancematrix, invert_distance, \
inversedistancematrix_to_coulombmatrix
from molreps.methods.props_py import element_list_to_value
[docs]def coulomb_matrix(atoms, coordinates):
"""
Calculate the Coulombmatrix representation of a molecule.
Args:
atoms (list): List of atoms as string, e.g. ["H","H","O"]
coordinates (np.array, list): List or numpy array of coordinates of shape (N,3)
Returns:
np.array: Coulombmatrix of shape (N,N).
"""
coordinates = np.array(coordinates)
protondict = {'H': 1, 'He': 2, 'Li': 3, 'Be': 4, 'b': 5, 'C': 6, 'N': 7, 'O': 8, 'F': 9, 'Ne': 10, 'Na': 11,
'Mg': 12, 'Al': 13, 'Si': 14, 'P': 15, 'S': 16, 'Cl': 17, 'Ar': 18, 'K': 19, 'Ca': 20, 'Sc': 21,
'Ti': 22, 'V': 23, 'Cr': 24, 'Mn': 25, 'Fe': 26, 'Co': 27, 'Ni': 28, 'Cu': 29, 'Zn': 30, 'Ga': 31,
'Ge': 32, 'As': 33, 'Se': 34, 'Br': 35, 'Kr': 36, 'Rb': 37, 'Sr': 38, 'Y': 39, 'Zr': 40, 'Nb': 41,
'Mo': 42, 'Tc': 43, 'Ru': 44, 'Rh': 45, 'Pd': 46, 'Ag': 47, 'Cd': 48, 'In': 49, 'Sn': 50, 'Sb': 51,
'Te': 52, 'I': 53, 'Xe': 54, 'Cs': 55, 'Ba': 56, 'La': 57, 'Ce': 58, 'Pr': 59, 'Nd': 60, 'Pm': 61,
'Sm': 62, 'Eu': 63, 'Gd': 64, 'Tb': 65, 'Dy': 66, 'Ho': 67, 'Er': 68, 'Tm': 69, 'Yb': 70, 'Lu': 71,
'Hf': 72, 'Ta': 73, 'W': 74, 'Re': 75, 'Os': 76, 'Ir': 77, 'Pt': 78, 'Au': 79, 'Hg': 80, 'Tl': 81,
'Pb': 82, 'Bi': 83, 'Po': 84, 'At': 85, 'Rn': 86, 'Fr': 87, 'Ra': 88, 'Ac': 89, 'Th': 90, 'Pa': 91,
'U': 92, 'Np': 93, 'Pu': 94, 'Am': 95, 'Cm': 96, 'Bk': 97, 'Cf': 98, 'Es': 99, 'Fm': 100, 'Md': 101,
'No': 102, 'Lr': 103, 'Rf': 104, 'Db': 105, 'Sg': 106, 'Bh': 107, 'Hs': 108, 'Mt': 109, 'Ds': 110,
'Rg': 111, 'Cn': 112, 'Nh': 113, 'Fl': 114, 'Mc': 115, 'Lv': 116, 'Ts': 117, 'Og': 118, 'Uue': 119}
d = coordinates_to_distancematrix(coordinates)
dinv = invert_distance(d)
nc = element_list_to_value(atoms, protondict) # Slow part here
nc = np.array(nc)
cm = inversedistancematrix_to_coulombmatrix(dinv, nc)
return cm
[docs]def bond_angles(atoms, coordinates, bond_table=None):
pass