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Mishima-syk / psikit

psi4+RDKit
BSD 3-Clause "New" or "Revised" License
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convert method is wrong #5

Closed kzfm closed 5 years ago

kzfm commented 5 years ago

RDKit stores atomic coordinates in Angstrom but Psi4 stores coordinates in Bohr, so when converting XYZ to RDKit mol, the coordinates become wrong.

kzfm commented 5 years ago

This is the DeepChem example.

    # RDKit stores atomic coordinates in Angstrom. Atomic unit of length is the
    # bohr (1 bohr = 0.529177 Angstrom). Converting units makes gradient calculation
    # consistent with most QM software packages.
    coords_in_bohr = [
        mol.GetConformer(0).GetAtomPosition(i).__idiv__(0.52917721092)
        for i in range(N)
    ]

    for atom in range(N):
      coords[atom, 0] = coords_in_bohr[atom].x
      coords[atom, 1] = coords_in_bohr[atom].y
      coords[atom, 2] = coords_in_bohr[atom].z

    coords = [coords]
    return coords