# for multiple molecules.
feat = CoulombMatrix()
HCN = (HCN_ELES, HCN_COORDS)
feat.fit([H2, HCN])
print("Transformed H2")
print(feat.transform([H2]))
print("H2 and HCN transformed")
print(feat.transform([H2, HCN]))
print()
# Example of generating the Coulomb matrix with elements, coords, and
# connections.
feat = CoulombMatrix()
H2_conn = (H2_ELES, H2_COORDS, H2_CONNS)
HCN_conn = (HCN_ELES, HCN_COORDS, HCN_CONNS)
print(feat.fit_transform([H2_conn, HCN_conn]))
print()
# Example of generating the Coulomb matrix using a specified input_type
print("User specified input_type")
feat = CoulombMatrix(input_type=("coords", "numbers"))
H2_spec = (H2_COORDS, H2_NUMS)
HCN_spec = (HCN_COORDS, HCN_NUMS)
print(feat.fit_transform([H2_spec, HCN_spec]))
print()
# Example of generating the Local Coulomb matrix (atom-wise
# representation)
print("Atom feature")
feat = LocalCoulombMatrix()
print(feat.fit_transform([H2, HCN]))
from molml.features import CoulombMatrix
feat = CoulombMatrix(input_type='list',
n_jobs=1,
sort=False,
eigen=False,
drop_values=False,
only_lower_triangle=False)
H2 = (['H', 'H'], [
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
])
HCN = (['H', 'C', 'N'], [
[-1.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
[1.0, 0.0, 0.0],
])
feat.fit([H2, HCN])
print(feat.transform([H2]))
print(feat.transform([H2, HCN]))
feat2 = CoulombMatrix(input_type='filename')
paths = ['data/qm7/qm-%04d.out' % i for i in range(2)]
print(feat2.fit_transform(paths))